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Sokouti B. A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:994-1026. [PMID: 38023988 PMCID: PMC10651357 DOI: 10.37349/etat.2023.00177] [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: 12/30/2022] [Accepted: 05/22/2023] [Indexed: 12/01/2023] Open
Abstract
The present coronavirus disease 2019 (COVID-19) pandemic scenario has posed a difficulty for cancer treatment. Even under ideal conditions, malignancies like small cell lung cancer (SCLC) are challenging to treat because of their fast development and early metastases. The treatment of these patients must not be jeopardized, and they must be protected as much as possible from the continuous spread of the COVID-19 infection. Initially identified in December 2019 in Wuhan, China, the contagious coronavirus illness 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Finding inhibitors against the druggable targets of SARS-CoV-2 has been a significant focus of research efforts across the globe. The primary motivation for using molecular modeling tools against SARS-CoV-2 was to identify candidates for use as therapeutic targets from a pharmacological database. In the published study, scientists used a combination of medication repurposing and virtual drug screening methodologies to target many structures of SARS-CoV-2. This virus plays an essential part in the maturation and replication of other viruses. In addition, the total binding free energy and molecular dynamics (MD) modeling findings showed that the dynamics of various medications and substances were stable; some of them have been tested experimentally against SARS-CoV-2. Different virtual screening (VS) methods have been discussed as potential means by which the evaluated medications that show strong binding to the active site might be repurposed for use against SARS-CoV-2.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz 5165665813, Iran
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2
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Lea AN, Leyden WA, Sofrygin O, Marafino BJ, Skarbinski J, Napravnik S, Agil D, Augenbraun M, Benning L, Horberg MA, Jefferson C, Marconi VC, Park LS, Gordon KS, Bastarache L, Gangireddy S, Althoff KN, Coburn SB, Gebo KA, Lang R, Williams C, Silverberg MJ. Human Immunodeficiency Virus Status, Tenofovir Exposure, and the Risk of Poor Coronavirus Disease 19 Outcomes: Real-World Analysis From 6 United States Cohorts Before Vaccine Rollout. Clin Infect Dis 2023; 76:1727-1734. [PMID: 36861341 PMCID: PMC10209434 DOI: 10.1093/cid/ciad084] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND People with human immunodeficiency virus (HIV) (PWH) may be at increased risk for severe coronavirus disease 2019 (COVID-19) outcomes. We examined HIV status and COVID-19 severity, and whether tenofovir, used by PWH for HIV treatment and people without HIV (PWoH) for HIV prevention, was associated with protection. METHODS Within 6 cohorts of PWH and PWoH in the United States, we compared the 90-day risk of any hospitalization, COVID-19 hospitalization, and mechanical ventilation or death by HIV status and by prior exposure to tenofovir, among those with severe acute respiratory syndrome coronavirus 2 infection between 1 March and 30 November 2020. Adjusted risk ratios (aRRs) were estimated by targeted maximum likelihood estimation, with adjustment for demographics, cohort, smoking, body mass index, Charlson comorbidity index, calendar period of first infection, and CD4 cell counts and HIV RNA levels (in PWH only). RESULTS Among PWH (n = 1785), 15% were hospitalized for COVID-19 and 5% received mechanical ventilation or died, compared with 6% and 2%, respectively, for PWoH (n = 189 351). Outcome prevalence was lower for PWH and PWoH with prior tenofovir use. In adjusted analyses, PWH were at increased risk compared with PWoH for any hospitalization (aRR, 1.31 [95% confidence interval, 1.20-1.44]), COVID-19 hospitalizations (1.29 [1.15-1.45]), and mechanical ventilation or death (1.51 [1.19-1.92]). Prior tenofovir use was associated with reduced hospitalizations among PWH (aRR, 0.85 [95% confidence interval, .73-.99]) and PWoH (0.71 [.62-.81]). CONCLUSIONS Before COVID-19 vaccine availability, PWH were at greater risk for severe outcomes than PWoH. Tenofovir was associated with a significant reduction in clinical events for both PWH and PWoH.
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Affiliation(s)
- Alexandra N Lea
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Wendy A Leyden
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Oleg Sofrygin
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Ben J Marafino
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Jacek Skarbinski
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
- Oakland Medical Center, Kaiser Permanente Northern California, Oakland, California, USA
| | - Sonia Napravnik
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Deana Agil
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael Augenbraun
- Division of Infectious Diseases, State University of New York Health Sciences University, Brooklyn, USA
| | - Lorie Benning
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael A Horberg
- Mid-Atlantic Permanente Research Institute, Kaiser Permanente Mid-Atlantic States, Rockville, Maryland, USA
| | - Celeena Jefferson
- Mid-Atlantic Permanente Research Institute, Kaiser Permanente Mid-Atlantic States, Rockville, Maryland, USA
| | - Vincent C Marconi
- Emory University School of Medicine and Rollins School of Public Health, Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Lesley S Park
- Stanford Department of Epidemiology & Population Health, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kirsha S Gordon
- VA Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Srushti Gangireddy
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keri N Althoff
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Sally B Coburn
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kelly A Gebo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raynell Lang
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Carolyn Williams
- Epidemiology Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Michael J Silverberg
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
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3
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Cohen S, Hershcovitch M, Taraz M, Kißig O, Issac D, Wood A, Waddington D, Chin P, Friedrich T. Improved and optimized drug repurposing for the SARS-CoV-2 pandemic. PLoS One 2023; 18:e0266572. [PMID: 36928101 PMCID: PMC10019610 DOI: 10.1371/journal.pone.0266572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 09/20/2022] [Indexed: 03/18/2023] Open
Abstract
The active global SARS-CoV-2 pandemic caused more than 426 million cases and 5.8 million deaths worldwide. The development of completely new drugs for such a novel disease is a challenging, time intensive process. Despite researchers around the world working on this task, no effective treatments have been developed yet. This emphasizes the importance of drug repurposing, where treatments are found among existing drugs that are meant for different diseases. A common approach to this is based on knowledge graphs, that condense relationships between entities like drugs, diseases and genes. Graph neural networks (GNNs) can then be used for the task at hand by predicting links in such knowledge graphs. Expanding on state-of-the-art GNN research, Doshi et al. recently developed the Dr-COVID model. We further extend their work using additional output interpretation strategies. The best aggregation strategy derives a top-100 ranking of 8,070 candidate drugs, 32 of which are currently being tested in COVID-19-related clinical trials. Moreover, we present an alternative application for the model, the generation of additional candidates based on a given pre-selection of drug candidates using collaborative filtering. In addition, we improved the implementation of the Dr-COVID model by significantly shortening the inference and pre-processing time by exploiting data-parallelism. As drug repurposing is a task that requires high computation and memory resources, we further accelerate the post-processing phase using a new emerging hardware-we propose a new approach to leverage the use of high-capacity Non-Volatile Memory for aggregate drug ranking.
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Affiliation(s)
- Sarel Cohen
- The Academic College of Tel Aviv-Yaffo, Tel Aviv-Yaffo, Israel
| | | | - Martin Taraz
- Hasso Plattner Institute, University Potsdam, Potsdam, Germany
| | - Otto Kißig
- Hasso Plattner Institute, University Potsdam, Potsdam, Germany
| | - Davis Issac
- Hasso Plattner Institute, University Potsdam, Potsdam, Germany
- * E-mail:
| | - Andrew Wood
- Boston University, Boston, MA, United States of America
| | | | - Peter Chin
- Boston University, Boston, MA, United States of America
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4
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Banik A, Ahmed SR, Sajib EH, Deb A, Sinha S, Azim KF. Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy. Mol Divers 2022; 26:2473-2502. [PMID: 34743299 DOI: 10.1007/s11030-021-10345-w] [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: 02/19/2021] [Accepted: 10/24/2021] [Indexed: 12/31/2022]
Abstract
The deeper understanding of metastasis phenomenon and detection of drug targets could be a potential approach to minimize cancer mortality. In this study, attempts were taken to unmask novel therapeutics to prevent metastasis and cancer progression. Initially, we explored the physiochemical, structural and functional insights of three metastasis tumor antigens (MTAs) and evaluated some plant-based bioactive compounds as potent MTA inhibitors. From 50 plant metabolites screened, isoflavone, gingerol, citronellal and asiatic acid showed maximum binding affinity with all three MTA proteins. The ADME analysis detected no undesirable toxicity that could reduce the drug likeness properties of top plant metabolites. Moreover, molecular dynamics studies revealed that the complexes were stable and showed minimum fluctuation at molecular level. We further performed ligand-based virtual screening to identify similar drug molecules using a large collection of 376,342 compounds from DrugBank. The results suggested that several structural analogs (e.g., tramadol, nabumetone, DGLA and hydrocortisone) may act as agonist to block the MTA proteins and inhibit cancer progression at early stage. The study could be useful to develop effective medications against cancer metastasis in future. Due to encouraging results, we highly recommend further in vitro and in vivo trials for the experimental validation of the findings.
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Affiliation(s)
- Anik Banik
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Plant and Environmental Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Sheikh Rashel Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Plant and Environmental Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Emran Hossain Sajib
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Anamika Deb
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Shiuly Sinha
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Faculté de Pharmacie, Université de Tours, 37200, Tours, France.
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5
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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6
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Singh BG, Gandhi VV, Phadnis PP, Kunwar A. Identification of a pyridine derivative of diselenides as a potent inhibitor of the main protease of SARS-CoV-2 through in silico screening and biochemical evaluation. NEW J CHEM 2022. [DOI: 10.1039/d2nj02744e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Among the 22 organoselenium compounds studied, 2-Py2Se2 & Nict2Se2 showed the highest affinity for Mpro. The biochemical studies confirmed their superiority as compared to standard compound like Ebselen in terms of the IC50 required for Mpro inhibition.
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Affiliation(s)
- B. G. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - V. V. Gandhi
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - P. P. Phadnis
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - A. Kunwar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai-400085, India
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7
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Immunoinformatics approach for designing a universal multiepitope vaccine against Chandipura Virus. Microb Pathog 2021; 162:105358. [PMID: 34902539 DOI: 10.1016/j.micpath.2021.105358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 12/23/2022]
Abstract
Chandipura vesiculovirus (CHPV) is a fast-emerging virus that causes acute encephalitis with a high death rate. Because of its extensive prevalence in African and Asian countries, this infection has become a global hazard, and there is an urgent need to create an effective and non-allergenic vaccine or appropriate treatment to combat it. A vaccine candidate is offered utilizing a computational technique in this study. To build a potential vaccine candidate, viral protein sequences were acquired from the National Center for Biotechnology Information database and evaluated with several bioinformatics techniques to identify B-cell and T-cell epitopes. V1 was shown to be superior in terms of various physicochemical qualities, as well as highly immunogenic and non-allergic. Molecular docking revealed that the CHPV vaccine construct had a greater binding affinity with human Toll-like receptors (TLR-3 and TLR-8) and that it was stable in molecular dynamics simulations. MEC-CHPV was in silico cloned in the pET28a (+) expression vector using codon optimization. The current research identifies potential antigenic epitopes that could be used as vaccine candidates to eradicate the CHPV. This in-silico development of a CHPV vaccine with multiple epitopes could open the path for future rapid laboratory tests.
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8
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Abd El Hadi SR, Zien El-Deen EE, Bahaa MM, Sadakah AA, Yassin HA. COVID-19: Vaccine Delivery System, Drug Repurposing and Application of Molecular Modeling Approach. Drug Des Devel Ther 2021; 15:3313-3330. [PMID: 34366663 PMCID: PMC8335551 DOI: 10.2147/dddt.s320320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022] Open
Abstract
The acute respiratory syndrome coronavirus (SARS-CoV-2) has spread across the world, resulting in a pandemic COVID-19 which is a human zoonotic disease that is caused by a novel coronavirus (CoV) strain thought to have originated in wild or captive bats in the initial COVID outbreak region. The global COVID-19 outbreak started in Guangdong Province, China's southernmost province. The global response to the COVID-19 pandemic has been hampered by the sheer number of infected people, many of whom need intensive care before succumbing to the disease. The epidemic is being handled by a combination of disease control by public health interventions and compassionate treatment for those who have been impacted. There is no clear anti-COVID-19 medication available at this time. However, the need to find medications that can turn the tide has led to the development of a number of investigational drugs as potential candidates for improving outcomes, especially in the severely and critically ill. Although many of these adjunctive medications are still being studied in clinical trials, professional organizations have attempted to define the circumstances in which their use is deemed off-label or compassionate. It is important to remind readers that new information about COVID-19's clinical features, treatment options, and outcomes is released on a regular basis. The mainstay of treatment remains optimized supportive care, and the therapeutic effectiveness of the subsequent agents is still being studied.
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Affiliation(s)
- Soha R Abd El Hadi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Esmat E Zien El-Deen
- Pharmaceutical Technology Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- Pharmaceutics Department, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Mostafa M Bahaa
- Pharmacy Practice Department, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Abdelfattah A Sadakah
- Oral and Maxillofacial Surgery, Department, Faculty of Dentistry, Tanta University, Tanta, Egypt
- Oral and Maxillofacial Surgery, Department, Faculty of Dentistry, AlSalam University, Tanta, Egypt
| | - Heba A Yassin
- Pharmaceutics Department. Faculty of Pharmacy, AlSalam University, Tanta, Egypt
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9
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De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation. Int J Mol Sci 2021; 22:ijms22136874. [PMID: 34206794 PMCID: PMC8267631 DOI: 10.3390/ijms22136874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we have generated ssRNA aptamers to inhibit SARS-CoV-2 Mpro, a protease necessary for the SARS-CoV-2 coronavirus replication. Because there is no aptamer 3D structure currently available in the databanks for this protein, first, we modeled an ssRNA aptamer using an entropic fragment-based strategy. We refined the initial sequence and 3D structure by using two sequential approaches, consisting of an elitist genetic algorithm and an RNA inverse process. We identified three specific aptamers against SARS-CoV-2 Mpro, called MAptapro, MAptapro-IR1, and MAptapro-IR2, with similar 3D conformations and that fall in the dimerization region of the SARS-CoV-2 Mpro necessary for the enzymatic activity. Through the molecular dynamic simulation and binding free energy calculation, the interaction between the MAptapro-IR1 aptamer and the SARS-CoV-2 Mpro enzyme resulted in the strongest and the highest stable complex; therefore, the ssRNA MAptapro-IR1 aptamer was selected as the best potential candidate for the inhibition of SARS-CoV-2 Mpro and a perspective therapeutic drug for the COVID-19 disease.
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10
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Renz A, Widerspick L, Dräger A. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. Genes (Basel) 2021; 12:796. [PMID: 34073716 PMCID: PMC8225150 DOI: 10.3390/genes12060796] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022] Open
Abstract
The current SARS-CoV-2 pandemic is still threatening humankind. Despite first successes in vaccine development and approval, no antiviral treatment is available for COVID-19 patients. The success is further tarnished by the emergence and spreading of mutation variants of SARS-CoV-2, for which some vaccines have lower efficacy. This highlights the urgent need for antiviral therapies even more. This article describes how the genome-scale metabolic model (GEM) of the host-virus interaction of human alveolar macrophages and SARS-CoV-2 was refined by incorporating the latest information about the virus's structural proteins and the mutant variants B.1.1.7, B.1.351, B.1.28, B.1.427/B.1.429, and B.1.617. We confirmed the initially identified guanylate kinase as a potential antiviral target with this refined model and identified further potential targets from the purine and pyrimidine metabolism. The model was further extended by incorporating the virus' lipid requirements. This opened new perspectives for potential antiviral targets in the altered lipid metabolism. Especially the phosphatidylcholine biosynthesis seems to play a pivotal role in viral replication. The guanylate kinase is even a robust target in all investigated mutation variants currently spreading worldwide. These new insights can guide laboratory experiments for the validation of identified potential antiviral targets. Only the combination of vaccines and antiviral therapies will effectively defeat this ongoing pandemic.
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Affiliation(s)
- Alina Renz
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Lina Widerspick
- Bernhard Nocht Institute for Tropical Medicine, Virus Immunology, 20359 Hamburg, Germany;
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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11
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Tenofovir, Another Inexpensive, Well-Known and Widely Available Old Drug Repurposed for SARS-COV-2 Infection. Pharmaceuticals (Basel) 2021; 14:ph14050454. [PMID: 34064831 PMCID: PMC8150375 DOI: 10.3390/ph14050454] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 12/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is spreading worldwide with different clinical manifestations. Age and comorbidities may explain severity in critical cases and people living with human immunodeficiency virus (HIV) might be at particularly high risk for severe progression. Nonetheless, current data, although sometimes contradictory, do not confirm higher morbidity, risk of more severe COVID-19 or higher mortality in HIV-infected people with complete access to antiretroviral therapy (ART). A possible protective role of ART has been hypothesized to explain these observations. Anti-viral drugs used to treat HIV infection have been repurposed for COVID-19 treatment; this is also based on previous studies on severe acute respiratory syndrome virus (SARS-CoV) and Middle East respiratory syndrome virus (MERS-CoV). Among them, lopinavir/ritonavir, an inhibitor of viral protease, was extensively used early in the pandemic but it was soon abandoned due to lack of effectiveness in clinical trials. However, remdesivir, a nucleotide analog that acts as reverse-transcriptase inhibitor, which was tested early during the pandemic because of its wide range of antiviral activity against several RNA viruses and its safety profile, is currently the only antiviral medication approved for COVID-19. Tenofovir, another nucleotide analog used extensively for HIV treatment and pre-exposure prophylaxis (PrEP), has also been hypothesized as effective in COVID-19. No data on tenofovir's efficacy in coronavirus infections other than COVID-19 are currently available, although information relating to SARS-CoV-2 infection is starting to come out. Here, we review the currently available evidence on tenofovir's efficacy against SARS-CoV-2.
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