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Kordzadeh A, Sa AR. Investigating the mechanisms of ethanol-induced disruption of COVID-19 lipid bilayers through molecular dynamics simulations. J Mol Model 2025; 31:117. [PMID: 40095111 DOI: 10.1007/s00894-025-06332-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 02/21/2025] [Indexed: 03/19/2025]
Abstract
CONTEXT The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, began in December 2019 in Wuhan, China. To mitigate the spread of COVID-19, public health officials strongly recommended preventive measures such as disinfectants, alcohol-based hand sanitizers, and face masks. The effect of ethanol on virus structure and inactivation remains unclear, and its molecular mechanism needs to be elucidated. This study elucidates how ethanol solutions interact with the lipid bilayer of the COVID-19 virus utilizing molecular dynamics (MD) simulations. Its findings indicated that ethanol can deactivate the virus through two primary mechanisms. First, when ethanol penetrates the viral membrane, it disrupts the structural integrity of the lipid bilayer, leading to membrane disruption. This alteration in morphology is critical as it compromises the virus's ability to maintain its structure and function. METHODS For the simulation, a lipid bilayer containing the spike protein of SARS-CoV-2 was constructed. The interaction between the viral membrane and ethanol solution was then simulated using GROMACS 5.1.4 for molecular dynamics (MD) analysis. Also, visual molecular dynamics (VMD1.9.3) was used for visualization. The study calculated the Lennard-Jones (LJ) and electrostatic interactions between ethanol and the lipid bilayer, and it analyzed the conformational changes in the spike protein following ethanol adsorption. Additionally, the effects of ethanol penetration on the morphology of the lipid bilayer were evaluated.
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Affiliation(s)
- Azadeh Kordzadeh
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Ahmad Ramazani Sa
- Chemical and Petroleum Engineering Department, Sharif University of Technology, Tehran, Iran.
- Center for Bioscience & Technology, Institute for Convergence Science & Technology, Sharif University of Technology, Tehran, Iran.
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2
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Aruna AS, Remesh Babu KR, Deepthi K. Autoencoder-based drug-virus association prediction with reliable negative sample selection: A case study with COVID-19. Biophys Chem 2025; 322:107434. [PMID: 40096790 DOI: 10.1016/j.bpc.2025.107434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 03/07/2025] [Accepted: 03/09/2025] [Indexed: 03/19/2025]
Abstract
Emergence of viruses cause unprecedented challenges and thus leading to wide-ranging consequences today. The world has faced massive disruptions like COVID-19 and continues to suffer in terms of public health and world economy. Fighting with this emergence of viruses and its reemergence plays a critical role in the health care industry. Identification of novel virus-drug associations is a vital step in drug discovery. Prediction and prioritization of novel virus-drug associations through computational approaches is an alternative and best choice considering the cost and risk of biological experiments. This study proposes a method, KR-AEVDA that relies on k-nearest neighbor based reliable negative sample selection and autoencoder based feature extraction to explore promising virus-drug associations for further experimental validation. The method analyzes complex relationships among drugs and viruses by investigating similarity and association data between drugs and viruses. It generates feature vectors from the similarity data, and reliable negative samples are extracted through an effective distance-based algorithm from the unlabeled samples in the dataset. Then high level features are extracted via an autoencoder and is fed to an ensemble classifier for inferring novel associations. Experimental results on three different datasets showed that KR-AEVDA reliably attained better performance than other state-of-the-art methods. Molecular docking is carried out between the top-predicted drugs and the crystal structure of the SARS-CoV-2's main protease to further validate the predictions. Case studies for SARS-CoV-2 illustrate the effectiveness of KR-AEVDA in identifying potential virus-drug associations.
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Affiliation(s)
- A S Aruna
- Dept. of Information Technology, Government Engineering College Palakkad, Palakkad-678633, APJ Abdul Kalam Technological University, Kerala, India; Department of Computer Science, College of Engineering Vadakara, Kozhikode 673105, Kerala, India.
| | - K R Remesh Babu
- Dept. of Information Technology, Government Engineering College Palakkad, Palakkad-678633, APJ Abdul Kalam Technological University, Kerala, India.
| | - K Deepthi
- Department of Computer Science, Central University of Kerala (Govt. of India), Kasaragod 671320, Kerala, India.
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3
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Kumar M, Baig MS, Bhardwaj K. Advancements in the development of antivirals against SARS-Coronavirus. Front Cell Infect Microbiol 2025; 15:1520811. [PMID: 39917633 PMCID: PMC11798951 DOI: 10.3389/fcimb.2025.1520811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Accepted: 01/02/2025] [Indexed: 02/09/2025] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) caused an outbreak in 2002-2003, spreading to 29 countries with a mortality rate of about 10%. Strict quarantine and infection control methods quickly stopped the spread of the disease. Later research showed that SARS-CoV came from animals (zoonosis) and stressed the possibility of a similar spread from host to human, which was clearly shown by the COVID-19 outbreak. The COVID-19 pandemic, instigated by SARS-CoV-2, has affected 776 million confirmed cases and more than seven million deaths globally as of Sept 15, 2024. The existence of animal reservoirs of coronaviruses continues to pose a risk of re-emergence with improved fitness and virulence. Given the high death rate (up to 70 percent) and the high rate of severe sickness (up to 68.7 percent in long-COVID patients), it is even more critical to identify new therapies as soon as possible. This study combines research on antivirals that target SARS coronaviruses that have been conducted over the course of more than twenty years. It is a beneficial resource that might be useful in directing future studies.
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Affiliation(s)
- Mrityunjay Kumar
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, India
| | - Mirza Sarwar Baig
- Centre for Virology, School of Interdisciplinary Science and Technology, Jamia Hamdard, New Delhi, India
| | - Kanchan Bhardwaj
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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4
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Adha SA, Afifah NN, Latarissa IR, Iftinan GN, Kusuma ASW, Febriyanti RM, Barliana MI, Lestari K. Herbal Medicines as Complementary Therapy for Managing Complications in COVID-19 Patients with Diabetes Mellitus. Diabetes Metab Syndr Obes 2025; 18:135-146. [PMID: 39840393 PMCID: PMC11746946 DOI: 10.2147/dmso.s498774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 12/26/2024] [Indexed: 01/23/2025] Open
Abstract
Diabetes mellitus (DM) is recognized and classified as a group of conditions marked by persistent high blood glucose levels. It is also an inflammatory condition that may influence concurrent disease states, including Coronavirus Disease 2019 (COVID-19). Currently, no effective drug has been found to treat COVID-19, especially in DM patients. Many herbal medicines, such as the well-known Andrographis paniculata, have been explored as drugs and complementary therapies due to their antidiabetic, antibacterial, antiviral, anti-inflammatory, and immunomodulatory effects. This study aimed to examine the potential of herbal medicines as complementary therapy in DM patients with COVID-19 complications, drawing from in-vitro and in-vivo investigations. This study analyzed articles published within the last 15 years using keywords including "herbal medicines", "COVID-19", "Diabetes Mellitus", "antidiabetics", "antiviral", and "anti-inflammatory". The results showed that several herbal medicines could serve as complementary therapy for DM patients with COVID-19 complications. These include Andrographis paniculata, Ageratum conyzoides, Artocarpus altilis, Centella asiatica, Momordica charantia, Persea gratissima, Phyllanthus urinaria, Physalis angulata, Tinospora cordifolia, and Zingiber zerumbet. Herbal medicines may serve as a complementary therapy for DM patients with COVID-19, but these claims need experimental validation in infection models and among affected patients.
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Affiliation(s)
- Syah Akbarul Adha
- Department of Biological Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Nadiya Nurul Afifah
- Department of Biological Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang, Indonesia
| | - Irma Rahayu Latarissa
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Medication Therapy Adherence Clinic (MTAC), Universitas Padjadjaran, Sumedang, Indonesia
| | - Ghina Nadhifah Iftinan
- Medication Therapy Adherence Clinic (MTAC), Universitas Padjadjaran, Sumedang, Indonesia
| | - Arif Satria Wira Kusuma
- Department of Biological Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang, Indonesia
| | - Raden Maya Febriyanti
- Department of Biological Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Melisa Intan Barliana
- Department of Biological Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang, Indonesia
| | - Keri Lestari
- Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Sumedang, Indonesia
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Medication Therapy Adherence Clinic (MTAC), Universitas Padjadjaran, Sumedang, Indonesia
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HAMDAN M, KULABAŞ N, KÜÇÜKGÜZEL İ. In silico Evaluation of H1-Antihistamine as Potential Inhibitors of SARS-CoV-2 RNA-dependent RNA Polymerase: Repurposing Study of COVID-19 Therapy. Turk J Pharm Sci 2025; 21:566-576. [PMID: 39801109 PMCID: PMC11730003 DOI: 10.4274/tjps.galenos.2024.49768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/23/2024] [Indexed: 01/16/2025]
Abstract
Introduction Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), from the family Coronaviridae, is the seventh known coronavirus to infect humans and cause acute respiratory syndrome. Although vaccination efforts have been conducted against this virus, which emerged in Wuhan, China, in December 2019 and has spread rapidly around the world, the lack of an Food and Drug Administration-approved antiviral agent has made drug repurposing an important approach for emergency response during the COVID-19 pandemic. The aim of this study was to investigate the potential of H1-antihistamines as antiviral agents against SARS-CoV-2 RNA-dependent RNA polymerase enzyme. Materials and Methods Using molecular docking techniques, we explored the interactions between H1-antihistamines and RNA-dependent RNA polymerase (RdRp), a key enzyme involved in viral replication. The three-dimensional structure of 37 H1-antihistamine molecules was drawn and their energies were minimized using Spartan 0.4. Subsequently, we conducted a docking study with Autodock Vina to assess the binding affinity of these molecules to the target site. The docking scores and conformations were then visualized using Discovery Studio. Results The results examined showed that the docking scores of the H1-antihistamines were between 5.0 and 8.3 kcal/mol. These findings suggested that among all the analyzed drugs, bilastine, fexofenadine, montelukast, zafirlukast, mizolastine, and rupatadine might bind with the best binding energy (< -7.0 kcal/mol) and inhibit RdRp, potentially halting the replication of the virus. Conclusion This study highlights the potential of H1-antihistamines in combating COVID-19 and underscores the value of computational approaches in rapid drug discovery and repurposing efforts. Finally, experimental studies are required to measure the potency of H1-antihistamines before their clinical use against COVID-19 as RdRp inhibitors.
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Affiliation(s)
- Mazin HAMDAN
- Marmara University Institute of Health Sciences, Department of Pharmaceutical Chemistry, İstanbul, Türkiye
| | - Necla KULABAŞ
- Marmara University Faculty of Pharmacy, Department of Pharmaceutical Chemistry, İstanbul, Türkiye
| | - İlkay KÜÇÜKGÜZEL
- Fenerbahçe University Faculty of Pharmacy, Department of Pharmaceutical Chemistry, İstanbul, Türkiye
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Bhatia T, Sharma S. Drug Repurposing: Insights into Current Advances and Future Applications. Curr Med Chem 2025; 32:468-510. [PMID: 37946344 DOI: 10.2174/0109298673266470231023110841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 11/12/2023]
Abstract
Drug development is a complex and expensive process that involves extensive research and testing before a new drug can be approved for use. This has led to a limited availability of potential therapeutics for many diseases. Despite significant advances in biomedical science, the process of drug development remains a bottleneck, as all hypotheses must be tested through experiments and observations, which can be timeconsuming and costly. To address this challenge, drug repurposing has emerged as an innovative strategy for finding new uses for existing medications that go beyond their original intended use. This approach has the potential to speed up the drug development process and reduce costs, making it an attractive option for pharmaceutical companies and researchers alike. It involves the identification of existing drugs or compounds that have the potential to be used for the treatment of a different disease or condition. This can be done through a variety of approaches, including screening existing drugs against new disease targets, investigating the biological mechanisms of existing drugs, and analyzing data from clinical trials and electronic health records. Additionally, repurposing drugs can lead to the identification of new therapeutic targets and mechanisms of action, which can enhance our understanding of disease biology and lead to the development of more effective treatments. Overall, drug repurposing is an exciting and promising area of research that has the potential to revolutionize the drug development process and improve the lives of millions of people around the world. The present review provides insights on types of interaction, approaches, availability of databases, applications and limitations of drug repurposing.
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Affiliation(s)
- Trisha Bhatia
- School of Pharmacy, National Forensic Sciences University, Gandhinagar, Gujarat, 382007, India
| | - Shweta Sharma
- School of Pharmacy, National Forensic Sciences University, Gandhinagar, Gujarat, 382007, India
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Jami SA, Helwan A, Tarin T, Aysha M, Mobarak SA. Factors affecting poor prognosis of COVID-19 in people living with human immunodeficiency virus: A systematic review and meta-analysis of co-infection. Int J Health Sci (Qassim) 2025; 19:49-55. [PMID: 39760054 PMCID: PMC11699234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2025] Open
Abstract
Objectives This study aims to assess the correlation between clinical features and mortality in human immunodeficiency virus (HIV)-infected individuals with COVID-19. Methods A systematic literature search was conducted for cohort, cross-sectional, and case series that reported co-infection with HIV and COVID-19 published from January to September 2020. Clinical features such as age, comorbidities, CD4+T lymphocyte counts, HIV RNA levels, and antiretroviral regimens were evaluated using meta-analyses and systematic reviews. Meta-analysis was performed using Stata 15.0 software. Results A total of 24 articles with 939 cases of HIV/COVID-19 co-infection were included in this study. The overall mortality rate was 10.3% (97/939). Older age and comorbidities including hypertension, diabetes, renal insufficiency, chronic obstructive pulmonary disease/asthma, and tumors were significantly associated with increased mortality (95% confidence interval 0.005-0.050, 0.042-2.294, 0.390-2.754, 0.513-2.848, 0.348-3.743, and 1.943-7.101, respectively, P = 0.021, 0.043, 0.012, 0.008, 0.022, and 0.005). There was no significant correlation between mortality and CD4+T lymphocyte count <200/μL or >500/μL, HIV RNA level below the detection limit, or antiretroviral drugs (including tenofovir) (all P > 0.05). Improved HIV treatment, complex immune interactions, study population variability, and lack of direct SARS-CoV-2 targeting by ART likely obscure the correlation between CD4+ counts or ART and COVID-19 mortality in HIV patients. Conclusion HIV-infected individuals with COVID-19 have a similar prognosis to the general population. However, older age, comorbidities (hypertension and diabetesetc.), and lower CD4+ T-cell counts are associated with increased mortality. Mainstream anti-HIV drugs do not offer significant protection against COVID-19.
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Affiliation(s)
- Sayed Abdulla Jami
- Department of Spine Orthopaedic Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China
| | | | - Tamima Tarin
- Department of Medicine, Ibn Sina Medical College Hospital, Dhaka, Bangladesh
| | - Mosammad Aysha
- Department of Medicine, Ibn Sina Medical College Hospital, Dhaka, Bangladesh
| | - Siam Al Mobarak
- Department of Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
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8
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Kota S, Nelapati AK, Govada VR. Plant resources for immunonutrients and immunomodulators to combat infectious respiratory viral diseases: a review. 3 Biotech 2024; 14:302. [PMID: 39554986 PMCID: PMC11568085 DOI: 10.1007/s13205-024-04143-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 10/26/2024] [Indexed: 11/19/2024] Open
Abstract
Boosting the immune system has become a crucial aspect in the global battle against the COVID-19 pandemic and other similar infections to protect oneself against symptoms, especially in the prevention of viral infections of the lower respiratory tract. The importance of conducting more studies to create successful herbal formulations as infection prevention measures is emphasized in this review, which looks at the function of immune-boosting nutrients, medicinal plants, and herbal treatments. We reviewed and analyzed 207 studies published from 1946 to the present using reputable databases like Google Scholar, PubMed, and NCBI. The review examined 115 plant species in total and identified 12 key nutrients, including vitamins A, D, C, omega-3 fatty acids, iron, and zinc, while noting that four plant families, Rosaceae, Asteraceae, Amaryllidaceae, and Acanthaceae, show potential against respiratory infections like influenza, RSV, and SARS-CoV. To lower the risk of infection, it is recommended to consume nutritious meals that have immune-modulating qualities. Information on the bioactive components of medicinal herbs, spices, and plants that have been effective in treating respiratory viral infections and related conditions is compiled in this review, which highlights phytoactive substances with antibacterial and antiviral activity as effective modulators to lower the risk of infections. Furthermore, it is highlighted that ancient knowledge systems, like Ayurveda and Naturopathy, should be integrated to help develop new herbal formulations. To improve immunity and lessen vulnerability to serious respiratory infections, the results highlight the need for including immune-modulating foods and plant-based medicines into everyday routines.
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Affiliation(s)
- Sobha Kota
- Department of Chemical Engineering, RVR & JC College of Engineering, Guntur, Andhra Pradesh 522 019 India
| | - Anand Kumar Nelapati
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research, Vadlamudi, Guntur, Andhra Pradesh 522 213 India
| | - Vayunandana Rao Govada
- Department of Chemical Engineering, RVR & JC College of Engineering, Guntur, Andhra Pradesh 522 019 India
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Das S, Nath S, Shahjahan, Dey SK. Plausible mechanism of drug resistance and side-effects of COVID-19 therapeutics: a bottleneck for its eradication. Daru 2024; 32:801-823. [PMID: 39026019 PMCID: PMC11554973 DOI: 10.1007/s40199-024-00524-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 06/11/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND COVID-19 pandemic has turned our world upside down by meddling with our normal lives. While there is no definitive drug against SARS-CoV-2, antiviral drugs that are already in the market, are being repurposed against it, could now complete long-term as well as all age-specific investigations, and they are successful in saving millions of lives. Nevertheless, side-effects are emergingly seen in the patients undergoing treatment, and ineffectiveness is increasingly found due to the emerging notorious variants of the virus. Many of them are also facing serious co-infections including black fungus, Zika, and H1N1 virus to name a few. OBJECTIVES Therefore, this review highlights both drug resistance, their side-effects, and the significance for proper and long-term clinical trials of all age groups including children. METHODS We have explored and proposed the mechanisms of drug resistance that may arise due to the misuse or overuse of drugs based on available experimental reports. RESULTS The review provides solutions to the aforesaid issues of drug-resistance and side-effects by providing combination therapies, ancillary treatments, and other preventive strategies that can be useful in preventing drawbacks thereby curbing COVID-19 or similar future infections to maintain our normal lives. CONCLUSION COVID-19 and its long-term effects, if any, can be eradicated with strategic and mindful use of related therapeutics in a controlled manner.
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Affiliation(s)
- Swarnali Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 208016, India
| | - Sreyashi Nath
- Imaging Cell Signaling and Therapeutics Lab, Advanced Centre for Training Research and Education in Cancer, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Shahjahan
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
| | - Sanjay Kumar Dey
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
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Hamed A, Abdel-Razek AS, Abdelwahab AB, El Taweel A, GabAllah M, Sewald N, Shaaban M. Diverse bioactive secondary metabolites from Aspergillus terreus: antimicrobial, anticancer, and anti-SARS-CoV-2 activity studies. Z NATURFORSCH C 2024; 79:361-369. [PMID: 38916050 DOI: 10.1515/znc-2024-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/09/2024] [Indexed: 06/26/2024]
Abstract
Owing to its high interest as prolific source of diverse bioactive compounds referred in our previous research work, we have scaled-up the fermentation of the marine Aspergillus terreus LGO13 on a liquid culture medium to isolate and identify the very minor/further promising bioactive secondary metabolites and to study their antibacterial, cytotoxic, and antiviral properties. Twenty-three known bioactive metabolites, including the recently discovered microbial natural product N-benzoyl-tryptophan (1), were obtained herein. Their structures were determined using HR-ESI-MS 1D/2D NMR spectroscopy and data from the literature. The biological properties of the microbial extract and the resulting compounds were examined using a set of microorganisms, cervix carcinoma KB-3-1, nonsmall cell lung cancer (NSCLC) A549, and coronavirus (SARS-CoV-2), respectively. Molecular docking (MD) simulations were used to investigate the potential targets of the separated metabolites as anti-SARS-CoV-2 drugs. According to the current study, a viral protein that may be the target of anticovid drugs is a papain-like protease (PLpro), and chaetominine (2) appears to be a viable choice against this protein. We evaluated the antiviral efficacy of chaetominine (2), fumitremorgin C (6), and azaspirofuran A (9) against SARS-CoV-2 based on MD data. Chaetominine (2) and azaspirofuran A (9) displayed intermediate selectivity indices (SI = 6.6 and 3.2, respectively), while fumitremorgin C (6) displayed a high selectivity index (SI = 19.77). These findings show that fumitremorgin C has promising antiviral action against SARS-CoV-2.
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Affiliation(s)
- Abdelaaty Hamed
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed S Abdel-Razek
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
| | - Ahmed B Abdelwahab
- Temisis Therapeutics, 19 avenue de la Forêt de Haye, 54500 Vandœuvre-lès-Nancy, France
| | - Ahmed El Taweel
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt
| | - Mohamed GabAllah
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
| | - Mohamed Shaaban
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
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Barghash RF, Gemmati D, Awad AM, Elbakry MMM, Tisato V, Awad K, Singh AV. Navigating the COVID-19 Therapeutic Landscape: Unveiling Novel Perspectives on FDA-Approved Medications, Vaccination Targets, and Emerging Novel Strategies. Molecules 2024; 29:5564. [PMID: 39683724 PMCID: PMC11643501 DOI: 10.3390/molecules29235564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/21/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024] Open
Abstract
Amidst the ongoing global challenge of the SARS-CoV-2 pandemic, the quest for effective antiviral medications remains paramount. This comprehensive review delves into the dynamic landscape of FDA-approved medications repurposed for COVID-19, categorized as antiviral and non-antiviral agents. Our focus extends beyond conventional narratives, encompassing vaccination targets, repurposing efficacy, clinical studies, innovative treatment modalities, and future outlooks. Unveiling the genomic intricacies of SARS-CoV-2 variants, including the WHO-designated Omicron variant, we explore diverse antiviral categories such as fusion inhibitors, protease inhibitors, transcription inhibitors, neuraminidase inhibitors, nucleoside reverse transcriptase, and non-antiviral interventions like importin α/β1-mediated nuclear import inhibitors, neutralizing antibodies, and convalescent plasma. Notably, Molnupiravir emerges as a pivotal player, now licensed in the UK. This review offers a fresh perspective on the historical evolution of COVID-19 therapeutics, from repurposing endeavors to the latest developments in oral anti-SARS-CoV-2 treatments, ushering in a new era of hope in the battle against the pandemic.
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Affiliation(s)
- Reham F. Barghash
- Institute of Chemical Industries Research, National Research Centre, Dokki, Cairo 12622, Egypt
- Faculty of Biotechnology, October University for Modern Sciences and Arts (MSA), Cairo 12451, Egypt
| | - Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Ahmed M. Awad
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Mustafa M. M. Elbakry
- Faculty of Biotechnology, October University for Modern Sciences and Arts (MSA), Cairo 12451, Egypt
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Veronica Tisato
- Centre Hemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Kareem Awad
- Institute of Pharmaceutical and Drug Industries Research, National Research Center, Dokki, Cairo 12622, Egypt;
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
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Jia N, Shi Y, Qi J, Yang W, Bu Q, Zhao R, Yang L, Tang J. Effects of dissolved organic matter from different sources on ritonavir photolysis. CHEMOSPHERE 2024; 367:143685. [PMID: 39505073 DOI: 10.1016/j.chemosphere.2024.143685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 09/24/2024] [Accepted: 11/04/2024] [Indexed: 11/08/2024]
Abstract
With the misuse of antiviral drugs, the residual levels of ritonavir (RTV) in aquatic environments continue to increase, potentially posing threats to ecosystems and human health. However, the current understanding of the photochemical behavior of RTV in water, especially the mechanism by which dissolved organic matter (DOM) from different sources affects the indirect photolysis of RTV, remains limited. This study systematically investigated the effects of DOM from different sources (including sludge, algae, dustfall, and soil, namely SL-DOM, AL-DOM, DF-DOM, and SO-DOM, respectively) on the photodegradation of RTV for the first time. DOM exhibited a dual role in RTV degradation, with SL-DOM and AL-DOM accelerating the degradation process, while DF-DOM and SO-DOM inhibited it. Direct photolysis accounted for 40-53% of the overall photodegradation, underscoring its significant contribution to the degradation process. Quenching and competitive kinetics experiments revealed that 3DOM⁎ is the dominant contributor to the indirect photolysis of RTV. Exogenous DOM (DF-DOM, SO-DOM) exhibited higher generation rate and steady-state concentraiton of 3DOM⁎, while endogenous DOM (SL-DOM, AL-DOM) exhibited higher quantum yields of 3DOM⁎ and reactivity, leading to distinct mechanisms for the indirect photodegradation of RTV. This study explored the effects of DOM from different sources on the photodegradation of RTV, providing important insights into how DOM affects the photochemical behavior and ecological risk of RTV. It also provides a reference for exploring the photochemical behavior of other drugs.
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Affiliation(s)
- Nan Jia
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Yue Shi
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Jinyuan Qi
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Weiwei Yang
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Qingwei Bu
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Ruiqing Zhao
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing, 100083, PR China.
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, PR China.
| | - Jianfeng Tang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China.
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13
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Mawazi SM, Fathima N, Mahmood S, Al-Mahmood SMA. Antiviral therapy for COVID-19 virus: A narrative review and bibliometric analysis. Am J Emerg Med 2024; 85:98-107. [PMID: 39244809 DOI: 10.1016/j.ajem.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/28/2024] [Accepted: 09/01/2024] [Indexed: 09/10/2024] Open
Abstract
The COVID-19 epidemic has become a major international health emergency. Millions of people have died as a result of this phenomenon since it began. Has there been any successful pharmacological treatment for COVID-19 since the initial report on the virus? How many searches are undertaken to address the impact of the infection? What is the number of drugs that have undergone investigation? What are the mechanisms of action and adverse effects associated with the investigated pharmaceuticals used to treat COVID-19? Has the Food and Drug Administration (FDA) approved any medication to treat COVID-19? To date, our understanding is based on a restricted corpus of published investigations into the treatment of COVID-19. It is important to note that no single study comprehensively encompasses all pharmacological interventions for COVID-19. This paper provides an introductory summary of a bibliometric analysis conducted on the data about COVID-19, sourced explicitly from two platforms, namely PubMed and ScienceDirect. The analysis encompasses the period spanning from 2019 to 2022. Furthermore, this study examines the published literature about the pharmacological interventions for the novel coronavirus disease 2019 (COVID-19), explicitly focusing on the safety and effectiveness of different medications such as Remdesivir (marketed as Veklury®), Lopinavir/Ritonavir (commercially known as Kaletra® or Aluvia®), Ribavirin, Favipiravir (marketed as Avigan®), Ivermectin, Casirivimab and Imdevimab (branded as Ronapreve®), Sotrovimab (marketed as Xevudy®), Anakinra, Molnupiravir, Nirmatrelvir/Ritonavir (marketed as Paxlovid®), and Galidesivir. Findings indicate that while Remdesivir and Nirmatrelvir/Ritonavir show significant efficacy in reducing hospitalization and severe outcomes, drugs like Lopinavir/Ritonavir and Ivermectin have inconsistent results. Our insights suggest a multifaceted approach incorporating these therapies can significantly improve patient outcomes. Repurposing drugs has been critical in rapidly responding to COVID-19, allowing existing medications to be used in new ways to combat the virus. Combination therapies and further research are essential to optimize treatment strategies.
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Affiliation(s)
- Saeid Mezail Mawazi
- School of Pharmacy, Management & Science University (MSU), Section 13, 40100 Shah Alam, Selangor, Malaysia.
| | - Nousheen Fathima
- Department of Pharmacology, Global College of Pharmacy, Jawaharlal Technology University, Hyderabad (Jntuh) 501504, India
| | - Syed Mahmood
- Faculty of Pharmacy, University of Malaya, 50603 Kuala Lumpur, Malaysia
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14
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Sharma A, Jakhar RK, Kakkar V, Singal G. Persistent ENT Manifestations in Individuals who Recovered from COVID-19: A Systematic Review. Int Arch Otorhinolaryngol 2024; 28:e697-e701. [PMID: 39464351 PMCID: PMC11511282 DOI: 10.1055/s-0043-1777805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/12/2023] [Indexed: 10/29/2024] Open
Abstract
Introduction Long coronavirus disease (COVID) refers to the persistence of symptoms long after the recovery from the acute phase of the illness, and it is due to the interplay of various inflammatory mechanisms. This has led to emergence of new deficits, including otorhinolaryngological symptoms, in patients wo have recovered from COVID. The plethora of otorhinolaryngological symptoms associated with long COVID are tinnitus, sensorineural hearing loss (SNHL), vertigo, nasal congestion, sinonasal discomfort, hyposmia/anosmia, dysgeusia, sore throat, dry cough, dyspnea, dysphagia, and hoarseness of voice. Objective To evaluate the possible ENT symptoms in patients wo have recovered from COVID and to combine those findings with our experience. Data Synthesis We conducted a search on the PubMed, ENT Cochrane, Web of Science, and Google Scholar databases, and a total of 44 studies were selected for the present review. Conclusion Otorhinolaryngological complications such as tinnitus, SNHL, vertigo, nasal congestion, sinonasal discomfort, hyposmia/anosmia, dysgeusia, sore throat, dry cough, dyspnea, dysphagia, and hoarseness of voice have been widely reported among in long-COVID patients.
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Affiliation(s)
- Akriti Sharma
- Department of Ear, Nose, and Throat, SGT Medical College, Hospital, and Research Institute, Gurgaon, Haryana, India
| | - Rohit Kumar Jakhar
- Department of Ear, Nose, and Throat, SGT Medical College, Hospital, and Research Institute, Gurgaon, Haryana, India
| | - Vikas Kakkar
- Department of Ear, Nose, and Throat, SGT Medical College, Hospital, and Research Institute, Gurgaon, Haryana, India
| | - Garima Singal
- Department of Ear, Nose, and Throat, SGT Medical College, Hospital, and Research Institute, Gurgaon, Haryana, India
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15
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Umar AK, Roy D, Abdalla M, Modafer Y, Al-Hoshani N, Yu H, Zothantluanga JH. In-silico screening of Acacia pennata and Bridelia retusa reveals pinocembrin-7-O-β-D-glucopyranoside as a promising β-lactamase inhibitor to combat antibiotic resistance. J Biomol Struct Dyn 2024; 42:8800-8812. [PMID: 37587843 DOI: 10.1080/07391102.2023.2248272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
The β-lactamase of Pseudomonas aeruginosa is known to degrade β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems. With the discovery of an extended-spectrum β-lactamase in a clinical isolate of P. aeruginosa, the bacterium has become multi-drug resistant. In this study, we aim to identify new β-lactamase inhibitors by virtually screening a total of 43 phytocompounds from two Indian medicinal plants. In the molecular docking studies, pinocembrin-7-O-β-D-glucopyranoside (P7G) (-9.6 kcal/mol) from Acacia pennata and ellagic acid (EA) (-9.2 kcal/mol) from Bridelia retusa had lower binding energy than moxalactam (-8.4 kcal/mol). P7G and EA formed 5 (Ser62, Asn125, Asn163, Thr209, and Ser230) and 4 (Lys65, Ser123, Asn125, and Glu159) conventional hydrogens bonds with the active site residues. 100 ns MD simulations revealed that moxalactam and P7G (but not EA) were able to form a stable complex. The binding free energy calculations further revealed that P7G (-59.6526 kcal/mol) formed the most stable complex with β-lactamase when compared to moxalactam (-46.5669 kcal/mol) and EA (-28.4505 kcal/mol). The HOMO-LUMO and other DFT parameters support the stability and chemical reactivity of P7G at the active site of β-lactamase. P7G passed all the toxicity tests and bioavailability tests indicating that it possesses drug-likeness. Among the studied compounds, we identified P7G of A. pennata as the most promising phytocompound to combat antibiotic resistance by potentially inhibiting the β-lactamase of P. aeruginosa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Dhritiman Roy
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yosra Modafer
- Department of Biology, Faculty of Science, Jazan University, Jazan, Saudi Arabia
| | - Nawal Al-Hoshani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Han Yu
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
- Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
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16
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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17
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Amanah A, Ariyanto IA, Bela B, Primanagara R, Sudarmono P. Evaluation of the Effect of mRNA and Inactivated SARS-CoV-2 Vaccines on the Levels of Cytokines IL-2, IFN-γ, and Anti-RBD Spike SARS-CoV-2 Antibodies in People Living with HIV (PLHIV). Biomedicines 2024; 12:2115. [PMID: 39335628 PMCID: PMC11429386 DOI: 10.3390/biomedicines12092115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 09/07/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The safety of the mRNA and inactivated SARS-CoV-2 vaccine has been demonstrated for people living with HIV (PLHIV). However, vaccine studies in PLHIV are limited, and there is a gap in which vaccine type provides the best response in PLHIV. Thus, PLHIV may benefit from mRNA vaccine types compared to inactivated vaccines. This study aims to assess the immune responses to vaccination by measuring specific antibodies (IgG) targeting the receptor binding sites (RBDs) of the SARS-CoV-2 virus and the levels of IL-2 and IFN-γ in plasma. A total of 41 PLHIV who regularly take antiretroviral therapy (ART) over a period of six months, along with 31 individuals in a healthy control group (HC), were administered either two mRNA or inactivated vaccines. Data regarding demographics and clinical information were gathered from the medical records. An analysis was conducted on the neutralisation antibody IgG specific to RBD using the chemiluminescence microparticle assay (CMIA). The levels of IL-2 and IFN-γ were quantified using the Luminex assay method from plasma samples. Data were collected in the laboratory 28 days after each vaccination. After the first vaccination, the level of anti-SARS-CoV-2 RBD IgG was higher in PLHIV who received the mRNA vaccines than those who received inactivated vaccines (p = 0.006). The levels of mRNA in the PLHIV group showed a significant correlation with IL-2 and IFN-γ after the second vaccination (r = 0.51, p = 0.0035; r = 0.68, p = 0.002). The group of PLHIV who received the inactivated vaccine showed increased IL-2 and IFN-γ after the initial vaccination, compared to PLHIV who received the mRNA vaccine (p = 0.04; p = 0.08). Administering a two-dose vaccination is essential to increase the levels of neutralising antibodies significantly (p = 0.013) in PLHIV who have received inactivated vaccines; further study is needed to make this a recommendation. The responses observed after vaccination in PLHIV were not affected by their CD4 cell counts. PLHIV showed higher levels of SARS-CoV-2 IgG and increased IL-2 and IFN-γ levels. Our study encourages SARS-CoV-2 vaccination in PLHIV regardless of its CD4 cell counts. Furthermore, the mRNA vaccine may give robust high antibody responses in PLHIV.
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Affiliation(s)
- Amanah Amanah
- Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Department of Immunology, Faculty of Medicine, Swadaya Gunung Jati University, Cirebon 45132, Indonesia
| | - Ibnu Agus Ariyanto
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Budiman Bela
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Virology and Cancer Pathobiology Research Center, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Risnandya Primanagara
- Department of Bioinformatics, Faculty of Medicine, Swadaya Gunung Jati University, Cirebon 45132, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
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18
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Cardoza S, Singh A, Sur S, Singh M, Dubey KD, Samanta SK, Mandal A, Tandon V. Computational investigation of novel synthetic analogs of C-1'β substituted remdesivir against RNA-dependent RNA-polymerase of SARS-CoV-2. Heliyon 2024; 10:e36786. [PMID: 39286185 PMCID: PMC11402944 DOI: 10.1016/j.heliyon.2024.e36786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
Remdesivir, a C-nucleotide prodrug binds to the viral RNA-dependent-RNA polymerase (RdRp) and inhibits the viral replication by terminating RNA transcription prematurely. It is reported in literature that interaction between the C-1'β-CN moiety of Remdesivir (RDV) and the Ser861 residue in RdRp enzyme, causes a delayed chain termination during the RNA replication process and is one of the important aspect of its mechanism of action. In the pursuance of increasing the biological activity of RDV and enhancing the SAR studies, against RNA viruses, we have designed its fourteen C1'β substituted analogs, 10 -23 bearing 4/5-membered heterocyclic rings. The docking and 100 ns molecular dynamics (MD) simulations of 10-23 to the RdRp protein (PDB ID: 7L1F) revealed important interactions between 2',3'-diol, oxo group of phosphoramidate, nitrogen residues of heterocyclic rings of synthetic molecules with Arg555, Arg553, Ser759, Cys622, Asn691, Asp623 amino acid residues of protein. The docking score of 2-ethylbutyl ((S)-(((2R,3S,4R,5R)-5-(4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl)-3,4-dihydroxy-5-(1H-1,2,3-triazol-4-yl)tetrahydrofuran-2-yl)methoxy)(phenoxy)phosphoryl)-L-alaninate, 11 was found to be the higher than RDV among 14 new compounds i.e. -5.20 kcal/mol. Out of 3 compounds, 10, 12 and 13 submitted for MD simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis, trifluoro-oxadiazole derivative, 13 showed higher binding energy as compared to Remdesivir. The predicted ADMET properties of 14 compounds showed their potential for being drug candidates. The present study suggests that substitution at the C1'β position by 4/5-membered rings plays an important role in the interactions between nucleoside/tide and target protein.
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Affiliation(s)
- Savio Cardoza
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211012, Uttar Pradesh, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Moradabad, Uttar Pradesh, 240001, India
| | - Mintu Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kshatresh D Dubey
- Department of Chemistry, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211012, Uttar Pradesh, India
| | - Ajay Mandal
- Symbol Discovery Ltd, ASPIRE-TBI, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
- CSIR- Indian Institute of Chemical Biology (IICB), 4, Raja S C Mullick Road, Jadavpur, Kolkata, 700032, India
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19
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Jena NR, Shukla PK. Hydroxyl radical-induced C1'-H abstraction reaction of different artificial nucleotides. J Mol Model 2024; 30:330. [PMID: 39269493 DOI: 10.1007/s00894-024-06126-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]
Abstract
CONTEXT Recently, a few antiviral drugs viz Molnupiravir (EIDD-1931), Favipiravir, Ribavirin, Sofosbuvir, Galidesivir, and Remdesivir are shown to be beneficial against COVID-19 disease. These drugs bind to the viral RNA single strand to inhibit the virus genome replication. Similarly, recently, some artificial nucleotides, such as P, J, B, X, Z, V, S, and K were proposed to behave as potent antiviral candidates. However, their activity in the presence of the most reactive hydroxyl (OH) radical is not yet known. Here, the possibility of RNA strand break due to the OH radical-induced C1'-hydrogen (H) abstraction reaction of the above molecules (except Remdesivir) is studied in detail by considering their nucleotide conformation. The results are compared with those of the natural RNA nucleotides (G, C, A, and U). Due to low Gibbs barrier-free energy and high exothermicity, all these nucleotides (except Remdesivir) are prone to OH radical-induced C1'-H abstraction reaction. As Remdesivir contains a C1'-CN bond, the OH radical substitution reactions at the CN and C1' sites would likely liberate the catalytically important CN group, thereby downgrading its activity. METHOD Initially, the B3LYP-D3 dispersion-corrected density functional theory method and 6-31 + G* basis set were used to optimize all reactant, transition state, and product complexes in the implicit aqueous medium. Subsequently, the structures of these complexes were further optimized by using the ωB97X-D dispersion-corrected density functional theory method and cc-PVTZ basis set in the aqueous medium. The IEFPCM method was used to model the aqueous medium.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, 482005, India.
| | - P K Shukla
- Department of Physics, Assam University, Silcharm, 788011, India
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20
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Artigues Serra F, Pinecki Socias S, Fanjul FJ, Peñaranda M, Homar F, Sorni P, Serra J, Rey A, Ventayol L, Macia MD, Ribas MÀ, Riera M. Factors associated with SARS-CoV-2 infection among people living with HIV: Data from the Balearic cohort (EVHIA). PLoS One 2024; 19:e0308568. [PMID: 39110761 PMCID: PMC11305541 DOI: 10.1371/journal.pone.0308568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
INTRODUCTION The impact of SARS-CoV-2 infection among people living with HIV (PLWH) has been a matter of research. We evaluated the incidence and factors associated with SARS-CoV-2 diagnosis among PLWH. We also assessed factors related to vaccination coverage in the Balearic Islands. METHODS A retrospective analytical study was performed, including patients from the Balearic cohort (EVHIA) who were visited at least twice between 1st January 2020 and 31st March 2022. Chi-square test and Mann-Whitney U test were used to compare categorical and continuous variables respectively. Multivariable Cox proportional hazards regression models were estimated to identify risk factors. RESULTS A total of 3567 patients with HIV were included. The median age was 51 years (IQR 44-59). Most of them were male (77,3%), from Europe (82,1%) or South America (13,8%). During the study period 1036 patients were diagnosed with SARS-CoV-2 infection (29%). The incidence rate was 153,24 cases per 1000 person-year. After multivariable analysis, men who have sex with men (MSM) were associated with an increased risk of SARS-CoV-2 infection (adjusted hazard ratio 1,324, 95% CI 1,138-1,540), whereas African origin, tobacco use and complete or booster vaccination coverage were negatively related. Overall, complete vaccination or booster coverage was recorded in 2845 (79,75%) patients. When analysing vaccination uptake, older patients (adjusted hazard ratio 5,122, 95% CI 3,170-8,288) and those with a modified comorbidity index of 2-3 points (adjusted hazard ratio 1,492, 95% CI 1,056-2,107) had received more vaccine doses. CONCLUSIONS In our study no HIV related factor was associated with an increased risk of SARS-CoV-2 infection, except for differences in the transmission route. Possible confounding variables such as mask wearing or social interactions could not be measured. Vaccines were of utmost importance to prevent SARS-CoV-2 infection. Efforts should be made to encourage vaccination in those groups of PLWH with less coverage.
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Affiliation(s)
- Francisca Artigues Serra
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Sophia Pinecki Socias
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Francisco Javier Fanjul
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Maria Peñaranda
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Francisco Homar
- Department of Internal Medicine, Son Llatzer University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Patricia Sorni
- Department of Internal Medicine, Son Llatzer University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Julia Serra
- Department of Internal Medicine, Inca Regional Hospital, Inca, Balearic Islands, Spain
| | - Adelaida Rey
- Department of Internal Medicine, Inca Regional Hospital, Inca, Balearic Islands, Spain
| | - Lola Ventayol
- Department of Internal Medicine, Manacor Regional Hospital, Manacor, Balearic Islands, Spain
| | - Maria Dolores Macia
- Department of Microbiology, Son Espases University Hospital-IDISBA CIBERINFEC, Palma, Balearic Islands, Spain
| | - Maria Àngels Ribas
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA, Palma, Balearic Islands, Spain
| | - Melchor Riera
- Department of Internal Medicine, Section of Infectious Diseases, Son Espases University Hospital-IDISBA CIBERINFEC, Palma, Balearic Islands, Spain
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21
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Lanrewaju AA, Enitan-Folami AM, Nyaga MM, Sabiu S, Swalaha FM. Metabolites profiling and cheminformatics bioprospection of selected medicinal plants against the main protease and RNA-dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2024; 42:6740-6760. [PMID: 37464870 DOI: 10.1080/07391102.2023.2236718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Despite the existence of some vaccines, SARS-CoV-2 (S-2) infections persist for various reasons relating to vaccine reluctance, rapid mutation rate, and an absence of specific treatments targeted to the infection. Due to their availability, low cost and low toxicity, research into potentially repurposing phytometabolites as therapeutic alternatives has gained attention. Therefore, this study explored the antiviral potential of metabolites of some medicinal plants [Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum (Sesame plant)] identified using liquid chromatography-mass spectrometry (LCMS) as possible inhibitory agents against the S-2 main protease (S-2 MP) and RNA-dependent RNA polymerase (RP) using computational approaches. Molecular docking was used to identify the compounds with the best affinities for the selected therapeutics targets. Afterwards, compounds with poor physicochemical characteristics, pharmacokinetics, and drug-likeness were screened out. The top-ranked compounds were further subjected to a 120-ns molecular dynamics (MD) simulation. Only quercetin 3-O-rhamnoside (-48.77 kcal/mol) had higher binding free energy than the reference standard (zafirlukast) (-44.99 kcal/mol) against S-2 MP. Conversely, all the top-ranked compounds (ellagic acid hexoside, spiraeoside, apigenin-4'-glucoside and chrysoeriol 7-glucuronide) except gnetin L (-24.24 kcal/mol) had higher binding free energy (-55.19 kcal/mol, -52.75 kcal/mol, -47.22 kcal/mol and -43.35 kcal/mol) respectively, against S-2 RP relative to the reference standard (-34.79 kcal/mol). The MD simulations study further revealed that the investigated inhibitors are thermodynamically stable and form structurally compatible complexes that impede the regular operation of the respective S-2 therapeutic targets. Although, these S-2 therapeutic candidates are promising, further in vitro and in vivo evaluation is required and highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | | | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
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22
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Deng H, Cao H, Wang Y, Li J, Dai J, Li LF, Qiu HJ, Li S. Viral replication organelles: the highly complex and programmed replication machinery. Front Microbiol 2024; 15:1450060. [PMID: 39144209 PMCID: PMC11322364 DOI: 10.3389/fmicb.2024.1450060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Viral infections usually induce the rearrangement of cellular cytoskeletal proteins and organelle membrane structures, thus creating independent compartments [termed replication organelles (ROs)] to facilitate viral genome replication. Within the ROs, viral replicases, including polymerases, helicases, and ligases, play functional roles during viral replication. These viral replicases are pivotal in the virus life cycle, and numerous studies have demonstrated that the viral replicases could be the potential targets for drugs development. Here, we summarize primarily the key replicases within viral ROs and emphasize the advancements of antiviral drugs targeting crucial viral replicases, providing novel insights into the future development of antiviral strategies.
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Affiliation(s)
| | | | | | | | | | | | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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23
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Li Y, Lu SM, Wang JL, Yao HP, Liang LG. Progress in SARS-CoV-2, diagnostic and clinical treatment of COVID-19. Heliyon 2024; 10:e33179. [PMID: 39021908 PMCID: PMC11253070 DOI: 10.1016/j.heliyon.2024.e33179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/20/2024] Open
Abstract
Background Corona Virus Disease 2019(COVID-19)is a global pandemic novel coronavirus infection disease caused by Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Although rapid, large-scale testing plays an important role in patient management and slowing the spread of the disease. However, there has been no good and widely used drug treatment for infection and transmission of SARS-CoV-2. Key findings Therefore, this review updates the body of knowledge on viral structure, infection routes, detection methods, and clinical treatment, with the aim of responding to the large-section caused by SARS-CoV-2. This paper focuses on the structure of SARS-CoV-2 viral protease, RNA polymerase, serine protease and main proteinase-like protease as well as targeted antiviral drugs. Conclusion In vitro or clinical trials have been carried out to provide deeper thinking for the pathogenesis, clinical diagnosis, vaccine development and treatment of SARS-CoV-2.
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Affiliation(s)
- Yang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Si-Ming Lu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Key Laboratory of Clinical in Vitro Diagnostic Techniques, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Jia-Long Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Guo Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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24
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Abbas EE, Fayed AS, Hegazy MA, Salama NN, Mohamed MA. Toward an Improved Electrocatalytic Determination of Immunomodulator COVID Medication Baricitinib Using Multiwalled Carbon Nanotube Nickel Hybrid. ACS APPLIED BIO MATERIALS 2024; 7:3865-3876. [PMID: 38780243 DOI: 10.1021/acsabm.4c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The study presents a first electrochemical method for the determination of the immunomodulator drug Baricitinib (BARI), crucial in managing COVID-19 patients requiring oxygen support. A unique electrode was developed by modifying graphite carbon nickel nanoparticles (NiNPs) with functionalized multiwalled carbon nanotubes (f.MWCNTs), resulting in nanohybrids tailored for highly sensitive BARI detection. Comparative analysis revealed the superior electrocatalytic performance of the nanohybrid-modified electrode over unmodified counterparts and other modifications, attributed to synergistic interactions between f.MWCNTs and nickel nanoparticles. Under optimized conditions, the sensors exhibited linear detection within a concentration range from 4.00 × 10-8 to 5.56 × 10-5 M, with a remarkably low detection limit of 9.65 × 10-9 M. Notably, the modified electrode displayed minimal interference from common substances and demonstrated high precision in detecting BARI in plasma and medicinal formulations, underscoring its clinical relevance and potential impact on COVID-19 treatment strategies.
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Affiliation(s)
- Enas E Abbas
- Pharmaceutical Chemistry Department, Egyptian Drug Authority, Giza 12512, Egypt
| | - Ahmed S Fayed
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elaini St., P.O. Box 11562 Cairo, Egypt
| | - Maha A Hegazy
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elaini St., P.O. Box 11562 Cairo, Egypt
| | - Nahla N Salama
- Pharmaceutical Chemistry Department, Egyptian Drug Authority, Giza 12512, Egypt
| | - Mona A Mohamed
- Pharmaceutical Chemistry Department, Egyptian Drug Authority, Giza 12512, Egypt
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25
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Yengoyan A, Gomktsyan T, Pivazyan V, Ghazaryan E, Shainova R, Karapetyan A, Avetyan D, Aslanyan L, Baroyan K, Tuzikov A, Sargsyan M, Baghdasaryan B, Bayramyan N, Hakobyan S, Poghosyan A, Avetisyan A, Avagyan H, Hakobyan L, Zaven K. Study of different heterocycles showing significant anti-severe acute respiratory syndrome 2 activity in vitro and in vivo. Vet World 2024; 17:1281-1290. [PMID: 39077461 PMCID: PMC11283614 DOI: 10.14202/vetworld.2024.1281-1290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/13/2024] [Indexed: 07/31/2024] Open
Abstract
Background and Aim With the emergence of severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), antiviral drug development has gained increased significance due to the high incidence and potentially severe complications of the resulting coronavirus infection. Heterocycle compounds, acting as antimetabolites of DNA and RNA monomers, rank among the most effective antiviral drugs. These compounds' antiviral effects on various SARS-CoV-2 isolates, as found in existing data collections, form the basis for further research. The aim of this study was to examine the possible antiviral effect of some originally synthesized heterocyclic compounds. Materials and Methods The main methods were cell culturing, cytotoxicity assay, qRT-PCR assay, tissue and blood cells analysis, and micro-computed tomography (micro-CT) imaging. Results In both in vitro and in vivo conditions, the elimination of SARS-Cov-2 occurred significantly earlier after administration of the compounds compared to the control group. In hamsters, the primary symptoms of coronavirus disease disappeared following administration of heterocycle compounds. Conclusion Using delta and omicron strains of the SARS-CoV-2 virus, newly created heterocycle compound analogs dramatically reduced SARS-CoV-2 multiplication, resulting in a drop in viral RNA load in the supernatant under in vitro conditions. Improvements in pathological manifestations in the blood, bone marrow, and internal organs of hamsters demonstrated that heterocycle compounds inhibited SARS-CoV-2 replication both in vitro and in vivo.
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Affiliation(s)
- Aleksandr Yengoyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
- Department of Chemistry Laboratory of Structural Bioinformatics, Russian-Armenian University, H. Emin, 123, Yerevan, 0051, Armenia
| | - Tiruhi Gomktsyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Vergush Pivazyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Emma Ghazaryan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Roza Shainova
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Armen Karapetyan
- Department of Pesticides Synthesis and Expertise National Agrarian University of Armenia, Teryan 74, Yerevan, 0009, Armenia
| | - Diana Avetyan
- Laboratory of Human Genomics and Immunomics, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Levon Aslanyan
- Department of Mathematics, Institute for Informatics and Automation Problems of NAS RA, Yerevan, Armenia
| | - Karine Baroyan
- Department of Anatomy, Yerevan State Medical University after M. Heratsi, Armenia Yerevan, Armenia
| | - Alexander Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Belarus
| | - Mariam Sargsyan
- Department of Epidemiology and Parasitology, Armenian National Agrarian University, Yerevan, Armenia
| | - Bagrat Baghdasaryan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Nane Bayramyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Sona Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Arpine Poghosyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Aida Avetisyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Hranush Avagyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Lina Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
| | - Karalyan Zaven
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology, National Academy of Sciences RA, Yerevan, 0014, Armenia
- Department of Human Anatomy, Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
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26
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Li S, Li H, Lian R, Xie J, Feng R. New perspective of small-molecule antiviral drugs development for RNA viruses. Virology 2024; 594:110042. [PMID: 38492519 DOI: 10.1016/j.virol.2024.110042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
High variability and adaptability of RNA viruses allows them to spread between humans and animals, causing large-scale infectious diseases which seriously threat human and animal health and social development. At present, AIDS, viral hepatitis and other viral diseases with high incidence and low cure rate are still spreading around the world. The outbreaks of Ebola, Zika, dengue and in particular of the global pandemic of COVID-19 have presented serious challenges to the global public health system. The development of highly effective and broad-spectrum antiviral drugs is a substantial and urgent research subject to deal with the current RNA virus infection and the possible new viral infections in the future. In recent years, with the rapid development of modern disciplines such as artificial intelligence technology, bioinformatics, molecular biology, and structural biology, some new strategies and targets for antivirals development have emerged. Here we review the main strategies and new targets for developing small-molecule antiviral drugs against RNA viruses through the analysis of the new drug development progress against several highly pathogenic RNA viruses, to provide clues for development of future antivirals.
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Affiliation(s)
- Shasha Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Huixia Li
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Ruiya Lian
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Jingying Xie
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Ruofei Feng
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China.
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Kim J, Jeong Y, An H, Suh J, Sohn J, Yoon Y. Clinical Outcomes of Coronavirus Disease 2019 in People Living With Human Immunodeficiency Virus in South Korea: A Nationwide Population-Based Cohort Study. Influenza Other Respir Viruses 2024; 18:e13337. [PMID: 38857604 PMCID: PMC11164560 DOI: 10.1111/irv.13337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND We aimed to compare the epidemiological and clinical characteristics of coronavirus disease 2019 (COVID-19) in people living with human immunodeficiency virus (HIV) (PLWH) with those in people living without HIV (PLWoH). METHODS This nationwide descriptive epidemiological study was conducted in South Korea between January 2020 and February 2022. The National Health Insurance claim data, comprising the data of the entire Korean population, were collected through the Health Insurance Review and Assessment Service. RESULTS Among 3,653,808 individuals who were diagnosed with COVID-19, 1311 (0.04%) were PLWH. All PLWH received antiretroviral therapy, and 26.47% had more than one underlying disease other than HIV infection. The overall in-hospital mortality rates of PLWH and PLWoH were 0.76% and 0.25%, respectively (P = 0.002). According to the Cox proportional hazard model, no significant difference was observed in the in-hospital mortality rate (hazard ratio [HR]: 1.80, 95% confidence interval [CI]: 0.70-4.67) between the PLWH and PLWoH. However, progression to severe or critical COVID-19 was more common in PLWH (HR: 2.70, 95% CI: 1.37-5.33). In PLWH diagnosed with COVID-19, a multivariable Cox regression analysis found old age (≥ 60 years) (HR: 6.9, 95% CI: 2.57-18.56) and diabetes mellitus (HR: 5.13, 95% CI: 2.02-13.00) as the independent risk factors for severe or critical COVID-19. CONCLUSIONS PLWH had a significantly higher risk of developing severe or critical COVID-19 compared with PLWoH. Our findings suggest the need for implementing tailored strategies to decrease the impact of COVID-19 on PLWH.
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Affiliation(s)
- Jeong Yeon Kim
- Division of Infectious Diseases, Department of Internal MedicineKorea University College of MedicineSeoulRepublic of Korea
| | - Yujin Jeong
- Department of BiostatisticsKorea University College of MedicineSeoulRepublic of Korea
| | - Hyonggin An
- Department of BiostatisticsKorea University College of MedicineSeoulRepublic of Korea
| | - Jin Woong Suh
- Division of Infectious Diseases, Department of Internal MedicineKorea University College of MedicineSeoulRepublic of Korea
| | - Jang Wook Sohn
- Division of Infectious Diseases, Department of Internal MedicineKorea University College of MedicineSeoulRepublic of Korea
| | - Young Kyung Yoon
- Division of Infectious Diseases, Department of Internal MedicineKorea University College of MedicineSeoulRepublic of Korea
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28
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Oršolić N, Jazvinšćak Jembrek M. Royal Jelly: Biological Action and Health Benefits. Int J Mol Sci 2024; 25:6023. [PMID: 38892209 PMCID: PMC11172503 DOI: 10.3390/ijms25116023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/25/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Royal jelly (RJ) is a highly nutritious natural product with great potential for use in medicine, cosmetics, and as a health-promoting food. This bee product is a mixture of important compounds, such as proteins, vitamins, lipids, minerals, hormones, neurotransmitters, flavonoids, and polyphenols, that underlie the remarkable biological and therapeutic activities of RJ. Various bioactive molecules like 10-hydroxy-2-decenoic acid (10-HDA), antibacterial protein, apisin, the major royal jelly proteins, and specific peptides such as apisimin, royalisin, royalactin, apidaecin, defensin-1, and jelleins are characteristic ingredients of RJ. RJ shows numerous physiological and pharmacological properties, including vasodilatory, hypotensive, antihypercholesterolaemic, antidiabetic, immunomodulatory, anti-inflammatory, antioxidant, anti-aging, neuroprotective, antimicrobial, estrogenic, anti-allergic, anti-osteoporotic, and anti-tumor effects. Moreover, RJ may reduce menopause symptoms and improve the health of the reproductive system, liver, and kidneys, and promote wound healing. This article provides an overview of the molecular mechanisms underlying the beneficial effects of RJ in various diseases, aging, and aging-related complications, with special emphasis on the bioactive components of RJ and their health-promoting properties. The data presented should be an incentive for future clinical studies that hopefully will advance our knowledge about the therapeutic potential of RJ and facilitate the development of novel RJ-based therapeutic opportunities for improving human health and well-being.
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Affiliation(s)
- Nada Oršolić
- Division of Animal Physiology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia
| | - Maja Jazvinšćak Jembrek
- Division of Molecular Medicine, Laboratory for Protein Dynamics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia;
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
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29
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Bera S, Kabadwal LM, Banerjee D. Harnessing alcohols as sustainable reagents for late-stage functionalisation: synthesis of drugs and bio-inspired compounds. Chem Soc Rev 2024; 53:4607-4647. [PMID: 38525675 DOI: 10.1039/d3cs00942d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Alcohol is ubiquitous with unparalleled structural diversity and thus has wide applications as a native functional group in organic synthesis. It is highly prevalent among biomolecules and offers promising opportunities for the development of chemical libraries. Over the last decade, alcohol has been extensively used as an environmentally friendly chemical for numerous organic transformations. In this review, we collectively discuss the utilisation of alcohol from 2015 to 2023 in various organic transformations and their application toward intermediates of drugs, drug derivatives and natural product-like molecules. Notable features discussed are as follows: (i) sustainable approaches for C-X alkylation (X = C, N, or O) including O-phosphorylation of alcohols, (ii) newer strategies using methanol as a methylating reagent, (iii) allylation of alkenes and alkynes including allylic trifluoromethylations, (iv) alkenylation of N-heterocycles, ketones, sulfones, and ylides towards the synthesis of drug-like molecules, (v) cyclisation and annulation to pharmaceutically active molecules, and (vi) coupling of alcohols with aryl halides or triflates, aryl cyanide and olefins to access drug-like molecules. We summarise the synthesis of over 100 drugs via several approaches, where alcohol was used as one of the potential coupling partners. Additionally, a library of molecules consisting over 60 fatty acids or steroid motifs is documented for late-stage functionalisation including the challenges and opportunities for harnessing alcohols as renewable resources.
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Affiliation(s)
- Sourajit Bera
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Lalit Mohan Kabadwal
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Debasis Banerjee
- Department of Chemistry, Laboratory of Catalysis and Organic Synthesis, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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Guezane-Lakoud S, Ferrah M, Merabet-Khelassi M, Touil N, Toffano M, Aribi-Zouioueche L. 2-Hydroxymethyl-18-crown-6 as an efficient organocatalyst for α -aminophosphonates synthesized under eco-friendly conditions, DFT, molecular docking and ADME/T studies. J Biomol Struct Dyn 2024; 42:3332-3348. [PMID: 37184142 DOI: 10.1080/07391102.2023.2213336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
Eco-friendly and simple procedure has been developed for the synthesis of α-aminophosphonates that act as topoisomerase II α-inhibiting anticancer agent, using 2-hydroxymethyl-18-crown-6 as an unexpected homogeneous organocatalyst in multicomponents reaction of aromatic aldehyde, aniline and diethylphosphite in one pot via Kabachnik-Fields reaction. This efficient method proceeds with catalytic amount, transition metal-free, at room temperature within short reaction time, giving the α-aminophosphonates derivatives (4a-r) in high chemical yields (up to 80%). Theoretical DFT calculations of three compounds (4p, 4q and 4r) were carried out in a gas phase at CAM-B3LYP 6-31G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. The frontier orbital energies (HOMO/LUMO) were described the charge transfer and used to predict structure-activity relationship study. Molecular electrostatic potential (MEP) has also been analyzed. Molecular docking studies are implemented to analyze the binding energy and compared with Adriamycin against 1ZXM receptor which to be considered as antitumor candidates. In silico pharmacological ADMET properties as Drug likeness and oral activity have been carried out based on Lipinski's rule of five.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Meriem Ferrah
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Mounia Merabet-Khelassi
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Nourhane Touil
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Martial Toffano
- Equipe de Catalyse Moléculaire-ICMMO Bât 420. Université Paris-Saclay, Paris, France
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
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31
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Stakišaitis D, Kapočius L, Tatarūnas V, Gečys D, Mickienė A, Tamošuitis T, Ugenskienė R, Vaitkevičius A, Balnytė I, Lesauskaitė V. Effects of Combined Treatment with Sodium Dichloroacetate and Sodium Valproate on the Genes in Inflammation- and Immune-Related Pathways in T Lymphocytes from Patients with SARS-CoV-2 Infection with Pneumonia: Sex-Related Differences. Pharmaceutics 2024; 16:409. [PMID: 38543303 PMCID: PMC10974540 DOI: 10.3390/pharmaceutics16030409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 12/10/2024] Open
Abstract
The study presents data on the anti-inflammatory effects of a combination of sodium dichloroacetate and sodium valproate (DCA-VPA) on the expression of inflammation- and immune response-related genes in T lymphocytes of SARS-CoV-2 patients. The study aimed to assess the effects of DCA-VPA on the genes of cytokine activity, chemokine-mediated signaling, neutrophil chemotaxis, lymphocyte chemotaxis, T-cell chemotaxis, and regulation of T-cell proliferation pathways. The study included 21 patients with SARS-CoV-2 infection and pneumonia: 9 male patients with a mean age of 68.44 ± 15.32 years and 12 female patients with a mean age of 65.42 ± 15.74 years. They were hospitalized between December 2022 and March 2023. At the time of testing, over 90% of sequences analyzed in Lithuania were found to be of the omicron variant of SARS-CoV-2. The T lymphocytes from patients were treated with 5 mmol DCA and 2 mmol VPA for 24 h in vitro. The effect of the DCA-VPA treatment on gene expression in T lymphocytes was analyzed via gene sequencing. The study shows that DCA-VPA has significant anti-inflammatory effects and apparent sex-related differences. The effect is more potent in T cells from male patients with SARS-CoV-2 infection and pneumonia than in females.
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Affiliation(s)
- Donatas Stakišaitis
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (I.B.)
- Laboratory of Molecular Oncology, National Cancer Institute, 08660 Vilnius, Lithuania
| | - Linas Kapočius
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (I.B.)
| | - Vacis Tatarūnas
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (V.T.); (D.G.); (V.L.)
| | - Dovydas Gečys
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (V.T.); (D.G.); (V.L.)
| | - Auksė Mickienė
- Department of Infectious Diseases, Lithuanian University of Health Sciences, 47116 Kaunas, Lithuania;
| | - Tomas Tamošuitis
- Department of Intensive Care Medicine, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania;
| | - Rasa Ugenskienė
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania;
| | - Arūnas Vaitkevičius
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University Hospital Santaros Klinikos, Vilnius University, 08661 Vilnius, Lithuania;
| | - Ingrida Balnytė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; (L.K.); (I.B.)
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Laboratory of Molecular Cardiology, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (V.T.); (D.G.); (V.L.)
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Ashique S, Mishra N, Mohanto S, Garg A, Taghizadeh-Hesary F, Gowda BJ, Chellappan DK. Application of artificial intelligence (AI) to control COVID-19 pandemic: Current status and future prospects. Heliyon 2024; 10:e25754. [PMID: 38370192 PMCID: PMC10869876 DOI: 10.1016/j.heliyon.2024.e25754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
The impact of the coronavirus disease 2019 (COVID-19) pandemic on the everyday livelihood of people has been monumental and unparalleled. Although the pandemic has vastly affected the global healthcare system, it has also been a platform to promote and develop pioneering applications based on autonomic artificial intelligence (AI) technology with therapeutic significance in combating the pandemic. Artificial intelligence has successfully demonstrated that it can reduce the probability of human-to-human infectivity of the virus through evaluation, analysis, and triangulation of existing data on the infectivity and spread of the virus. This review talks about the applications and significance of modern robotic and automated systems that may assist in spreading a pandemic. In addition, this study discusses intelligent wearable devices and how they could be helpful throughout the COVID-19 pandemic.
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Affiliation(s)
- Sumel Ashique
- Department of Pharmaceutical Sciences, Bengal College of Pharmaceutical Sciences & Research, Durgapur, 713212, West Bengal, India
| | - Neeraj Mishra
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Gwalior, 474005, Madhya Pradesh, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Ashish Garg
- Guru Ramdas Khalsa Institute of Science and Technology, Pharmacy, Jabalpur, M.P, 483001, India
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Clinical Oncology Department, Iran University of Medical Sciences, Tehran, Iran
| | - B.H. Jaswanth Gowda
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, BT9 7BL, UK
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, 57000, Malaysia
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Vijay A, Sreyas Adury VS, Mukherjee A. Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS APPLIED BIO MATERIALS 2024; 7:609-616. [PMID: 37566736 DOI: 10.1021/acsabm.3c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Viruses are known for their extremely high mutation rates, allowing them to evade both the human immune system and many forms of standard medicine. Despite this, the RNA dependent RNA polymerase (RdRp) of the RNA viruses has been largely conserved, and any significant mutation of this protein is unlikely. The recent COVID-19 pandemic presents a need for therapeutics. We have designed a de novo drug design algorithm that generates strong binding ligands from scratch, based on only the structure of the target protein's receptor. In this paper, we applied our method to target SARS-CoV-2 RdRp and generated several de novo molecules. We then chose some drug molecules based on the structural similarity to some of our strongest binding de novo molecules. Subsequently, we showed, using rigorous all-atom explicit-water free energy calculations in near-microsecond time scales using state-of-the-art well-tempered metadynamics simulations, that some of our de novo generated ligands bind more strongly to RdRp than the recent FDA approved drug remdesivir in its active form, remdesivir triphosphate (RTP). We elucidated the binding mechanism for some of the top binders and compared it with RTP. We believe that this work will be useful both by presenting lead structures for RdRp inhibition and by delivering key insights into the residues of the protein potentially involved in the binding/unbinding of these small molecule drugs, leading to more targeted studies in the future.
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Affiliation(s)
- Amal Vijay
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | | | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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Höft MA, Burgers WA, Riou C. The immune response to SARS-CoV-2 in people with HIV. Cell Mol Immunol 2024; 21:184-196. [PMID: 37821620 PMCID: PMC10806256 DOI: 10.1038/s41423-023-01087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
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Affiliation(s)
- Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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Velásquez PA, Hernandez JC, Galeano E, Hincapié-García J, Rugeles MT, Zapata-Builes W. Effectiveness of Drug Repurposing and Natural Products Against SARS-CoV-2: A Comprehensive Review. Clin Pharmacol 2024; 16:1-25. [PMID: 38197085 PMCID: PMC10773251 DOI: 10.2147/cpaa.s429064] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a betacoronavirus responsible for the COVID-19 pandemic, causing respiratory disorders, and even death in some individuals, if not appropriately treated in time. To face the pandemic, preventive measures have been taken against contagions and the application of vaccines to prevent severe disease and death cases. For the COVID-19 treatment, antiviral, antiparasitic, anticoagulant and other drugs have been reused due to limited specific medicaments for the disease. Drug repurposing is an emerging strategy with therapies that have already tested safe in humans. One promising alternative for systematic experimental screening of a vast pool of compounds is computational drug repurposing (in silico assay). Using these tools, new uses for approved drugs such as chloroquine, hydroxychloroquine, ivermectin, zidovudine, ribavirin, lamivudine, remdesivir, lopinavir and tenofovir/emtricitabine have been conducted, showing effectiveness in vitro and in silico against SARS-CoV-2 and some of these, also in clinical trials. Additionally, therapeutic options have been sought in natural products (terpenoids, alkaloids, saponins and phenolics) with promising in vitro and in silico results for use in COVID-19 disease. Among these, the most studied are resveratrol, quercetin, hesperidin, curcumin, myricetin and betulinic acid, which were proposed as SARS-CoV-2 inhibitors. Among the drugs reused to control the SARS-CoV2, better results have been observed for remdesivir in hospitalized patients and outpatients. Regarding natural products, resveratrol, curcumin, and quercetin have demonstrated in vitro antiviral activity against SARS-CoV-2 and in vivo, a nebulized formulation has demonstrated to alleviate the respiratory symptoms of COVID-19. This review shows the evidence of drug repurposing efficacy and the potential use of natural products as a treatment for COVID-19. For this, a search was carried out in PubMed, SciELO and ScienceDirect databases for articles about drugs approved or under study and natural compounds recognized for their antiviral activity against SARS-CoV-2.
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Affiliation(s)
- Paula Andrea Velásquez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Elkin Galeano
- Grupo Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jaime Hincapié-García
- Grupo de investigación, Promoción y prevención farmacéutica, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
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Wang Y, Lai Y. The Interrelationship between HIV Infection and COVID-19: A Review of the Literature. Curr HIV Res 2024; 22:6-15. [PMID: 38151836 DOI: 10.2174/011570162x282739231222062830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
The Corona Virus Disease 2019 (COVID-19) pandemic resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to significant morbidity and mortality in patients and put a strain on healthcare systems worldwide. The clinical characteristics and results of COVID-19 in immunosuppressed patients, such as people living with human immunodeficiency virus (PLWH), considered at higher risk of severe disease, are not well-characterized. Accumulated evidence indicates that COVID-19 and the human immunodeficiency virus (HIV) can interact in various ways. This review explored the similarities and differences in virology between SARS-CoV-2 and HIV, the effect of the COVID-19 vaccine on PLWH, the impact of the COVID-19 pandemic on PLWH care and prevention, and the influence of HIV-related factors on COVID-19. Discovering the potential link between HIV and COVID-19 may provide a novel way to avoid the factors of HIV and SARS-CoV-2 co-infection and advance future research.
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Affiliation(s)
- Yiyu Wang
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yu Lai
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
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Gasmi A, Noor S, Menzel A, Khanyk N, Semenova Y, Lysiuk R, Beley N, Bolibrukh L, Gasmi Benahmed A, Storchylo O, Bjørklund G. Potential Drugs in COVID-19 Management. Curr Med Chem 2024; 31:3245-3264. [PMID: 37461346 DOI: 10.2174/0929867331666230717154101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/27/2023] [Accepted: 06/05/2023] [Indexed: 11/18/2023]
Abstract
The SARS-CoV-2 virus first emerged in China in December 2019 and quickly spread worldwide. Despite the absence of a vaccination or authorized drug specifically developed to combat this infection, certain medications recommended for other diseases have shown potential effectiveness in treating COVID-19, although without definitive confirmation. This review aims to evaluate the existing literature on the efficacy of these medications against COVID-19. The review encompasses various potential treatments, including antiviral medications, anti-malaria and anti-rheumatic drugs, vaccines, corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDs), antipyretic and analgesic medicines, antiparasitic drugs, and statins. The analysis also addresses the potential benefits and drawbacks of these medications, as well as their effects on hypertension and diabetes. Although these therapies hold promise against COVID-19, further research, including suitable product production or clinical testing, is needed to establish their therapeutic efficacy.
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Affiliation(s)
- Amin Gasmi
- Société Francophone de Nutrithérapie et de Nutrigénétique Appliquée, Villeurbanne, France
| | - Sadaf Noor
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Nataliia Khanyk
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Yuliya Semenova
- Nazarbayev University School of Medicine, Astana, Kazakhstan
| | - Roman Lysiuk
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
- CONEM Ukraine Life Science Research Group, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Nataliya Beley
- I. Ya. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | | | | | - Olha Storchylo
- Medical Chemistry Department, Odessa National Medical University, Odesa, Ukraine
| | - Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Mo i Rana, Norway
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38
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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Hodel K, Fonseca A, Barbosa I, Medina C, Alves B, Maciel C, Nascimento D, Oliveira-Junior G, Pedreira L, de Souza M, Godoy AL. Obesity and its Relationship with Covid-19: A Review of the Main Pharmaceutical Aspects. Curr Pharm Biotechnol 2024; 25:1651-1663. [PMID: 38258769 DOI: 10.2174/0113892010264503231108070917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 01/24/2024]
Abstract
Important physiological changes are observed in patients with obesity, such as intestinal permeability, gastric emptying, cardiac output, and hepatic and renal function. These differences can determine variations in the pharmacokinetics of different drugs and can generate different concentrations at the site of action, which can lead to sub therapeutic or toxic concentrations. Understanding the physiological and immunological processes that lead to the clinical manifestations of COVID-19 is essential to correlate obesity as a risk factor for increasing the prevalence, severity, and lethality of the disease. Several drugs have been suggested to control COVID- 19 like Lopinavir, Ritonavir, Ribavirin, Sofosbuvir, Remdesivir, Oseltamivir, Oseltamivir phosphate, Oseltamivir carboxylate, Hydroxychloroquine, Chloroquine, Azithromycin, Teicoplanin, Tocilizumab, Anakinra, Methylprednisolone, Prednisolone, Ciclesonide and Ivermectin. Similarly, these differences between healthy people and obese people can be correlated to mechanical factors, such as insufficient doses of the vaccine for high body mass, impairing the absorption and distribution of the vaccine that will be lower than desired or can be linked to the inflammatory state in obese patients, which can influence the humoral immune response. Additionally, different aspects make the obese population more prone to persistent symptoms of the disease (long COVID), which makes understanding these mechanisms fundamental to addressing the implications of the disease. Thus, this review provides an overview of the relationship between COVID-19 and obesity, considering aspects related to pharmacokinetics, immunosuppression, immunization, and possible implications of long COVID in these individuals.
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Affiliation(s)
- Katharine Hodel
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Ananda Fonseca
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Islania Barbosa
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Caio Medina
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Brenda Alves
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Carine Maciel
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Daniel Nascimento
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Gessualdo Oliveira-Junior
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Lorena Pedreira
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Monielly de Souza
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
| | - Ana Leonor Godoy
- Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador, Brazil
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Rago V, Bossio S, Lofaro D, Perri A, Di Agostino S. New Insights into the Link between SARS-CoV-2 Infection and Renal Cancer. Life (Basel) 2023; 14:52. [PMID: 38255667 PMCID: PMC10817602 DOI: 10.3390/life14010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Cancer has been described as a risk factor for greater susceptibility to SARS-CoV-2 infection and severe COVID-19, mainly for patients with metastatic disease. Conversely, to that reported for most solid and hematological malignancies, the few available clinical studies reported that the infection did not increase the risk of death in renal cancer patients. The expression on proximal tubular renal cells of the key players in cellular viral uptake, ACE2, TMPRSS2, and NRP1, seems to be the mechanism for the direct kidney injury seen in patients with COVID-19. Interestingly, data from The Cancer Genome Atlas and experimental analyses on various renal cancer cell lines demonstrated that the above-reported receptors/cofactors are maintained by renal cancer cells. However, whether SARS-CoV-2 infection directly kills renal cancer cells or generates enhanced immunogenicity is a question worth investigating. In addition, some researchers have further addressed the topic by studying the expression and prognostic significance of gene signatures related to SARS-CoV-2 infection in renal cancer patients. The emerging data highlights the importance of better understanding the existence of a link between renal cancer and COVID-19 since it could lead to the identification of new prognostic factors and the development of new therapeutic targets in the management of renal cancer patients.
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Affiliation(s)
- Vittoria Rago
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| | - Sabrina Bossio
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
| | - Danilo Lofaro
- de-Health Lab, Department of Mechanical, Energy, Management Engineering, University of Calabria, 87036 Rende, Italy;
| | - Anna Perri
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
| | - Silvia Di Agostino
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy;
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Ao D, He X, Liu J, Xu L. Strategies for the development and approval of COVID-19 vaccines and therapeutics in the post-pandemic period. Signal Transduct Target Ther 2023; 8:466. [PMID: 38129394 PMCID: PMC10739883 DOI: 10.1038/s41392-023-01724-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in significant casualties and put immense strain on public health systems worldwide, leading to economic recession and social unrest. In response, various prevention and control strategies have been implemented globally, including vaccine and drug development and the promotion of preventive measures. Implementing these strategies has effectively curbed the transmission of the virus, reduced infection rates, and gradually restored normal social and economic activities. However, the mutations of SARS-CoV-2 have led to inevitable infections and reinfections, and the number of deaths continues to rise. Therefore, there is still a need to improve existing prevention and control strategies, mainly focusing on developing novel vaccines and drugs, expediting medical authorization processes, and keeping epidemic surveillance. These measures are crucial to combat the Coronavirus disease (COVID-19) pandemic and achieve sustained, long-term prevention, management, and disease control. Here, we summarized the characteristics of existing COVID-19 vaccines and drugs and suggested potential future directions for their development. Furthermore, we discussed the COVID-19-related policies implemented over the past years and presented some strategies for the future.
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Affiliation(s)
- Danyi Ao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Sichuan, People's Republic of China
| | - Xuemei He
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Sichuan, People's Republic of China
| | - Jian Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Sichuan, People's Republic of China
| | - Li Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Sichuan, People's Republic of China.
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Hsu CW, Yang WW, Hou CY, Feng IJ, Huang TY, Lee PL, Guo HR, Huang CY, Su SB. Patients with Hepatitis C Undergoing Direct-Acting Antiviral Treatment Have a Lower SARS-CoV-2 Infection Rate. Life (Basel) 2023; 13:2326. [PMID: 38137927 PMCID: PMC10745044 DOI: 10.3390/life13122326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
This study retrospectively analyzed the medical records of 602 patients with first-time positive results for the HCV nucleic acid test between 1 May 2021 and 31 March 2023, exploring the association between DAA treatment and SARS-CoV-2 infection. The results showed that 9.8% of HCV patients were co-infected with SARS-CoV-2. Gender, age, vaccination status, and HCV genotype did not significantly affect SARS-CoV-2 infection. However, patients undergoing DAA treatment showed significantly lower rates of SARS-CoV-2 infection and mortality compared to those not undergoing DAA treatment. The analysis also compared patients undergoing different DAA treatments, with Epclusa and Maviret showing superior protection against SARS-CoV-2. Furthermore, this study explored the severity and mortality of SARS-CoV-2 infection in patients undergoing and having completed DAA treatment. It revealed that patients diagnosed with COVID-19 during DAA treatment experienced only mild symptoms, and none died, suggesting a potential protective effect of DAA treatment against severe outcomes of SARS-CoV-2 infection. The findings contribute to the understanding of the interplay between HCV, DAA treatment, and SARS-CoV-2 infection, highlighting the need for continued monitoring and healthcare measures for individuals with chronic conditions during the ongoing COVID-19 pandemic.
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Affiliation(s)
- Chin-Wen Hsu
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Wan-Wen Yang
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Chia-Yi Hou
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - I-Jung Feng
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung 804201, Taiwan
| | - Ting-Yi Huang
- Department of Hepato-Gastroenterology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Pei-Lun Lee
- Department of Hepato-Gastroenterology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - How-Ran Guo
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan;
| | - Chien-Yuan Huang
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Shih-Bin Su
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
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Xie NN, Zhang WC, Chen J, Tian FB, Song JX. Clinical Characteristics, Diagnosis, and Therapeutics of COVID-19: A Review. Curr Med Sci 2023; 43:1066-1074. [PMID: 37837572 DOI: 10.1007/s11596-023-2797-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/03/2023] [Indexed: 10/16/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that suddenly emerged at the end of December 2019 and caused coronavirus disease 2019 (COVID-19) continues to afflict humanity, not only seriously affecting healthcare systems but also leading to global social and economic imbalances. As of August 2022, there were approximately 580 million confirmed cases of COVID-19 and approximately 6.4 million confirmed deaths due to this disease. The data are sufficient to highlight the seriousness of SARS-CoV-2 infection. Although most patients with COVID-19 present primarily with respiratory symptoms, an increasing number of extrapulmonary systemic symptoms and manifestations have been associated with COVID-19. Since the outbreak of COVID-19, much has been learned about the disease and its causative agent. Therefore, great effort has been aimed at developing treatments and drug interventions to treat and reduce the incidence of COVID-19. In this narrative review, we provide a brief overview of the epidemiology, mechanisms, clinical manifestations, diagnosis, and therapeutics of COVID-19.
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Affiliation(s)
- Na-Na Xie
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wen-Cong Zhang
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jia Chen
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fang-Bing Tian
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jian-Xin Song
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Liao X, Fan Y, Zhong C, Zhao S, Guo L, Tan W, Yin J, Fan R. Effects of entecavir and tenofovir disoproxil fumarate on the incidence and severity of COVID-19 in patients with chronic hepatitis B. BMC Infect Dis 2023; 23:843. [PMID: 38036959 PMCID: PMC10688146 DOI: 10.1186/s12879-023-08838-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Whether different anti-hepatitis B virus (HBV) drugs have different effects on COVID-19 is controversial. We aimed to evaluate the incidence of COVID-19 in chronic hepatitis B (CHB) patients receiving anti-HBV treatment, and to compare the impact of entecavir (ETV) and tenofovir disoproxil fumarate (TDF) on the severity of COVID-19. METHODS CHB outpatients were enrolled from December 2022 to February 2023. Questionnaires were used to collect whether subjects were currently or previously had COVID-19 within the past 2 months, and the information of symptoms, duration, and severity if infected. RESULTS Six hundred thirty CHB patients were enrolled, 64.3% (405/630) patients were currently or previously had COVID-19. No COVID-19 patient required hospitalization, intensive care unit admission, oxygen support or died. Majority of patients reported mild (32.8% [133/405]) and moderate (48.1% [195/405]) symptoms. After propensity score matching, 400 matched patients were obtained (ETV: 238; TDF: 162), among which the incidences of COVID-19 were comparable between ETV and TDF-treated patients (60.1% [143/238] vs. 64.2% [104/162], p = 0.468). The proportion of patients complicated with any symptom caused by COVID-19 were also similar (ETV vs. TDF: 90.9% [130/143] vs. 91.3% [95/104], p = 1.000). In addition, the severity of overall symptom was comparable between ETV and TDF-treated patients, in terms of proportion of patients complicated with severe symptom (9.8% vs. 8.7%, p = 0.989), symptom duration (4.3 vs. 4.3 days, p = 0.927), and symptom severity score (4.1 vs. 4.0, p = 0.758). Subgroup analysis supported these results. CONCLUSIONS During the current pandemic, the vast majority of CHB patients experienced non-severe COVID-19, and ETV and TDF did not affect COVID-19 severity differently.
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Affiliation(s)
- Xingmei Liao
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yujie Fan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chunxiu Zhong
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siru Zhao
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liangxu Guo
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenjuan Tan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junhua Yin
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Fan
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Clinical Research Center for Viral Hepatitis, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Khalil A, Mohamed A, Hassan M, Magboul S, Ali H, Elmasoudi AS, Ellithy K, Qusad M, Alhothi A, Al Maslamani E, Al Amri M, Soliman A. Efficacy and Safety of Remdesivir in Hospitalized Pediatric COVID-19: A Retrospective Case-Controlled Study. Ther Clin Risk Manag 2023; 19:949-958. [PMID: 38023628 PMCID: PMC10680468 DOI: 10.2147/tcrm.s432565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction While most children experience mild coronavirus disease 2019 (COVID-19) infections, a minority of cases progress to severe or critical illness. This study aimed to assess the efficacy and safety of Remdesivir (RDV) therapy in children with moderate to severe COVID-19, enhancing clinical decision-making and expanding our understanding of antiviral treatments for pediatric patients. Methods The study included 60 patients, 38 receiving RDV treatment and 22 serving as the control group. Data was collected retrospectively from January 2021 to January 2022 through electronic hospital records. Results Regarding the main clinical symptoms reported, most patients experienced Upper Respiratory Tract Infections (93.3%), indicating respiratory involvement. Additional symptoms included Central Nervous System (11.7%) and Gastrointestinal (10.0%). Among the 38 cases in the RDV group included in the study, the adverse effects associated with using RDV: Hypoalbuminemia in 19 cases (50.0%) and anemia in 18 cases (47.4%), making them the most common adverse effects. Only one case in the RDV group experienced non-RDV-related death with a different clinical diagnosis. The results showed that RDV treatment was well-tolerated in pediatric patients, with no significant differences in hospital stay and oxygen treatment compared to the control group with P values (0.2, 0.18), respectively. Conclusion The outcomes indicate that Remdesivir may represent a safe and therapeutic choice for children with coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Ahmed Khalil
- Section of Pediatric Clinical Pharmacy, Pharmacy Department, Hamad General Hospital, Doha, Qatar
| | - Asmaa Mohamed
- Section of Pediatric Clinical Pharmacy, Pharmacy Department, Hamad General Hospital, Doha, Qatar
| | - Manasik Hassan
- Section of Academic General Pediatrics, Department of Pediatrics, Hamad General Hospital, Doha, Qatar
| | - Samar Magboul
- Section of Academic General Pediatrics, Department of Pediatrics, Hamad General Hospital, Doha, Qatar
| | - Hossamaldein Ali
- Section of Pediatric Clinical Pharmacy, Pharmacy Department, Hamad General Hospital, Doha, Qatar
| | - Ahmed Salah Elmasoudi
- Section of Pediatric Clinical Pharmacy, Pharmacy Department, Hamad General Hospital, Doha, Qatar
| | - Khaled Ellithy
- Section of Pediatric Intensive Care Unit, Department of Pediatrics, Hamad General Hospital, Doha, Qatar
| | - Mohammad Qusad
- Section of Academic General Pediatrics, Department of Pediatrics, Hamad General Hospital, Doha, Qatar
| | - Abdulla Alhothi
- Section of Academic General Pediatrics, Department of Pediatrics, Hamad General Hospital, Doha, Qatar
| | - Eman Al Maslamani
- Section of Infectious Diseases, Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | | | - Ashraf Soliman
- Department of Pediatrics, Hamad General Hospital, Doha, Qatar
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46
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Shoraka S, Mohebbi SR, Hosseini SM, Ghaemi A, Zali MR. SARS-CoV-2 and chronic hepatitis B: Focusing on the possible consequences of co-infection. JOURNAL OF CLINICAL VIROLOGY PLUS 2023; 3:100167. [DOI: 10.1016/j.jcvp.2023.100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025] Open
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Ma Y, Zhong J, Zhu N. Weighted hypergraph learning and adaptive inductive matrix completion for SARS-CoV-2 drug repositioning. Methods 2023; 219:102-110. [PMID: 37804962 DOI: 10.1016/j.ymeth.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023] Open
Abstract
MOTIVATION The outbreak of the human coronavirus (SARS-CoV-2) has placed a huge burden on public health and the world economy. Compared with de novo drug discovery, drug repurposing is a promising therapeutic strategy that facilitates rapid clinical treatment decisions, shortens the development process, and reduces costs. RESULTS In this study, we propose a weighted hypergraph learning and adaptive inductive matrix completion method, WHAIMC, for predicting potential virus-drug associations. Firstly, we integrate multi-source data to describe viruses and drugs from multiple perspectives, including drug chemical structures, drug targets, virus complete genome sequences, and virus-drug associations. Then, WHAIMC establishes an adaptive inductive matrix completion model to improve performance through adaptive learning of similarity relations. Finally, WHAIMC introduces weighted hypergraph learning into adaptive inductive matrix completion to capture higher-order relationships of viruses (or drugs). The results showed that WHAIMC had a strong predictive performance for new virus-drug associations, new viruses, and new drugs. The case study further demonstrates that WHAIMC is highly effective for repositioning antiviral drugs against SARS-CoV-2 and provides a new perspective for virus-drug association prediction. The code and data in this study is freely available at https://github.com/Mayingjun20179/WHAIMC.
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Affiliation(s)
- Yingjun Ma
- School of Mathematics and Statistics, Xiamen University of Technology, Xiamen 361024, China.
| | - Junjiang Zhong
- School of Mathematics and Statistics, Xiamen University of Technology, Xiamen 361024, China
| | - Nenghui Zhu
- School of Mathematics and Statistics, Xiamen University of Technology, Xiamen 361024, China
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Lachhab S, El Mansouri AE, Mehdi A, Dennemont I, Neyts J, Jochmans D, Andrei G, Snoeck R, Sanghvi YS, Ait Ali M, Loiseau PM, Lazrek HB. Synthesis of new 3-acetyl-1,3,4-oxadiazolines combined with pyrimidines as antileishmanial and antiviral agents. Mol Divers 2023; 27:2147-2159. [PMID: 36251201 PMCID: PMC9573813 DOI: 10.1007/s11030-022-10548-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022]
Abstract
A new series of 3-acetyl-1,3,4-oxadiazoline hybrid molecules was designed and synthesized using a condensation between acyclonucleosides and substituted phenylhydrazone. All intermediates and final products were screened against Leishmania donovani, a Protozoan parasite and against three viruses SARS-CoV-2, HCMV and VZV. While no significant activity was observed against the viruses, the intermediate with 6-azatymine as thymine and 5-azathymine-3-acetyl-1,3,4-oxadiazoline hybrid exhibited a significant antileishmanial activity. The later compound was the most promising, exhibiting an IC50 value at 8.98 µM on L. donovani intramacrophage amastigotes and a moderate selectivity index value at 2.4.
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Affiliation(s)
- Saida Lachhab
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Az-Eddine El Mansouri
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Ahmad Mehdi
- ICGM, Université Montpellier, CNRS, ENSCM, Montpellier, France
| | - Indira Dennemont
- Antiparasite Chemotherapy, CNRS, BioCIS, Université Paris-Saclay, Chatenay-Malabry, 92290, Paris, France
| | - Johan Neyts
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Dirk Jochmans
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KULeuven, Louvain, Belgium
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, CA, 92024-6615, USA
| | - Mustapha Ait Ali
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Philippe M Loiseau
- Antiparasite Chemotherapy, CNRS, BioCIS, Université Paris-Saclay, Chatenay-Malabry, 92290, Paris, France
| | - Hassan B Lazrek
- Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia, University Cadi Ayyad, Marrakech, Morocco.
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Abduljalil JM, Elfiky AA, Sayed ESTA, AlKhazindar MM. In silico structural elucidation of Nipah virus L protein and targeting RNA-dependent RNA polymerase domain by nucleoside analogs. J Biomol Struct Dyn 2023; 41:8215-8229. [PMID: 36205638 DOI: 10.1080/07391102.2022.2130987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/25/2022] [Indexed: 10/10/2022]
Abstract
The large (L) protein of Mononegavirales is a multi-domain protein that performs transcription and genome replication. One of the important domains in L is the RNA-dependent RNA polymerase (RdRp), a promising target for antiviral drugs. In this work, we employed rigorous computational comparative modeling to predict the structure of L protein of Nipah virus (NiV). The RdRp domain was targeted by a panel of nucleotide analogs, previously reported to inhibit different viral RNA polymerases, using molecular docking. Best binder compounds were subjected to molecular dynamics simulation to validate their binding. Molecular mechanics/generalized-born surface area (MM/GBSA) calculations estimated the binding free energy. The predicted model of NiV L has an excellent quality as judged by physics- and knowledge-based validation tests. Galidesivir, AT-9010 and Norov-29 scored the top nucleotide analogs to bind to the RdRp. Their binding free energies obtained by MM/GBSA (-31.01 ± 3.9 to -38.37 ± 4.8 kcal/mol) ranked Norov-29 as the best potential inhibitor. Purine nucleotide analogs are expected to harbor the scaffold for an effective drug against NiV. Finally, this study is expected to provide a start point for medicinal chemistry and drug discovery campaigns toward identification of effective chemotherapeutic agent(s) against NiV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - El-Sayed T A Sayed
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Maha M AlKhazindar
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
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50
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Awad AM, Hansen K, Del Rio D, Flores D, Barghash RF, Kakkola L, Julkunen I, Awad K. Insights into COVID-19: Perspectives on Drug Remedies and Host Cell Responses. Biomolecules 2023; 13:1452. [PMID: 37892134 PMCID: PMC10604481 DOI: 10.3390/biom13101452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In light of the COVID-19 global pandemic caused by SARS-CoV-2, ongoing research has centered on minimizing viral spread either by stopping viral entry or inhibiting viral replication. Repurposing antiviral drugs, typically nucleoside analogs, has proven successful at inhibiting virus replication. This review summarizes current information regarding coronavirus classification and characterization and presents the broad clinical consequences of SARS-CoV-2 activation of the angiotensin-converting enzyme 2 (ACE2) receptor expressed in different human cell types. It provides publicly available knowledge on the chemical nature of proposed therapeutics and their target biomolecules to assist in the identification of potentially new drugs for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Ahmed M. Awad
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Kamryn Hansen
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Diana Del Rio
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Derek Flores
- Department of Chemistry, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Reham F. Barghash
- Institute of Chemical Industries Research, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Laura Kakkola
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
| | - Ilkka Julkunen
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
- Clinical Microbiology, Turku University Hospital, 20521 Turku, Finland
| | - Kareem Awad
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20014 Turku, Finland
- Department of Therapeutic Chemistry, Institute of Pharmaceutical and Drug Industries Research, National Research Center, Dokki, Cairo 12622, Egypt
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