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Hoferle PJ, Anderson TK, Kirchdoerfer RN. A genus-specific nsp12 region impacts polymerase assembly in Alphacoronavirus and Gammacoronavirus. J Biol Chem 2024; 300:107802. [PMID: 39307300 DOI: 10.1016/j.jbc.2024.107802] [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: 07/24/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within the Coronavirinae subfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within the Coronavirinae subfamily. We sought to contribute to the limited structural knowledge within the Gammacoronavirus genera and determined the structure of the viral core replication-transcription complex (RTC) from infectious bronchitis virus using single-particle cryo-electron microscopy. Comparison between our infectious bronchitis virus structure with published RTC structures from other Coronavirinae genera reveals structural differences across genera. Using in vitro biochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-genera Coronavirinae studies, as they show genera-specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers.
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Affiliation(s)
- Peter J Hoferle
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Thomas K Anderson
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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Hoferle PJ, Anderson TK, Kirchdoerfer RN. A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604833. [PMID: 39091740 PMCID: PMC11291119 DOI: 10.1101/2024.07.23.604833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within the Coronavirinae subfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within the Coronavirinae subfamily. We sought to contribute to the limited structural knowledge within the Gammacoronavirus genera and determined the structure of the viral core replication-transcription complex (RTC) from Infectious Bronchitis Virus (IBV) using single-particle cryo-EM. Comparison between our IBV structure with published RTC structures from other Coronavirinae genera reveals structural differences across genera. Using in vitro biochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-genera Coronavirinae studies, as they show genera specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers.
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Affiliation(s)
- Peter J. Hoferle
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Thomas K. Anderson
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
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3
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Anderson TK, Hoferle PJ, Chojnacki KJ, Lee K, Coon J, Kirchdoerfer R. An alphacoronavirus polymerase structure reveals conserved replication factor functions. Nucleic Acids Res 2024; 52:5975-5986. [PMID: 38442273 PMCID: PMC11162792 DOI: 10.1093/nar/gkae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine structures of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. One structure shows an unexpected nsp8 stoichiometry despite remaining bound to RNA. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha- and betacoronaviruses. Our work demonstrates the importance of studying diverse coronaviruses in revealing aspects of coronavirus replication and identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter J Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kennan J Chojnacki
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kenneth W Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Robert N Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Nazir MS, Ahmad M, Aslam S, Rafiq A, Al-Hussain SA, Zaki MEA. A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds. Drug Des Devel Ther 2024; 18:1547-1571. [PMID: 38737333 PMCID: PMC11088867 DOI: 10.2147/dddt.s450499] [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: 12/13/2023] [Accepted: 02/24/2024] [Indexed: 05/14/2024] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.
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Affiliation(s)
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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5
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Latosińska M, Latosińska JN. Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure-Property Relationship, and Molecular Docking Study. Molecules 2024; 29:441. [PMID: 38257352 PMCID: PMC10818557 DOI: 10.3390/molecules29020441] [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: 10/31/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor of RNA-dependent RNA polymerase (RdRp), could provide more effective nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, and embryotoxicity. We proposed a set of FVP analogues together with their forms of triphosphate as new SARS-CoV-2 RdRp inhibitors. The main aim of our study was to investigate changes in the mechanism and binding capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, and MD, the differences in the reactivity, toxicity, binding efficiency, and ability to be incorporated by RdRp were assessed. Two new quantum chemical reactivity descriptors, the relative electro-donating and electro-accepting power, were defined and successfully applied. Moreover, a new quantitative method for comparing binding modes was developed based on mathematical metrics and an atypical radar plot. These methods provide deep insight into the set of desirable properties responsible for inhibiting RdRp, allowing ligands to be conveniently screened. The proposed modification of the FVP structure seems to improve its binding ability and enhance the productive mode of binding. In particular, two of the FVP analogues (the trifluoro- and cyano-) bind very strongly to the RNA template, RNA primer, cofactors, and RdRp, and thus may constitute a very good alternative to FVP.
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [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: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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7
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Koch EM, Du J, Dressner M, Alwasti HE, Al Taif Z, Shehab F, Mohamed AM, Ghanem A, Alhajeri A, Alawadhi A, Almoamen N, Ashoor K, Hasan S, Haghighi A, Sunyaev S, Farhat M. Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.08.13.22278740. [PMID: 36032980 PMCID: PMC9413726 DOI: 10.1101/2022.08.13.22278740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.
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Affiliation(s)
- Evan M. Koch
- Department of Biomedical Informatics, Harvard Medical School
| | | | | | | | - Zahra Al Taif
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Fatima Shehab
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Afaf Merza Mohamed
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Amjad Ghanem
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Amani Alhajeri
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Amna Alawadhi
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Nabeel Almoamen
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Khulood Ashoor
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Sara Hasan
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Alireza Haghighi
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital
- Department of Genetics, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital
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8
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Das T, Sikdar S, Chowdhury MHU, Nyma KJ, Adnan M. SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review. Heliyon 2023; 9:e19345. [PMID: 37662720 PMCID: PMC10474441 DOI: 10.1016/j.heliyon.2023.e19345] [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: 01/22/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.
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Affiliation(s)
- Tuhin Das
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Suranjana Sikdar
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md. Helal Uddin Chowdhury
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram, 4331, Bangladesh
| | | | - Md. Adnan
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, 84112, United States
- Department of Pharmacy, International Islamic University Chittagong, Chattogram, 4318, Bangladesh
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9
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Azimi S, Merza MS, Ghasemi F, Dhahi HA, Baradarbarjastehbaf F, Moosavi M, Kargar PG, Len C. Green and rapid and instrumental one-pot method for the synthesis of imidazolines having potential anti-SARS-CoV-2 main protease activity. SUSTAINABLE CHEMISTRY AND PHARMACY 2023; 34:101136. [PMID: 37333050 PMCID: PMC10239909 DOI: 10.1016/j.scp.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is responsible for ongoing epidemics in humans and some other mammals and has been declared a public health emergency of international concern. In this project, several small non-peptide molecules were synthesized to inhibit the major proteinase (Mpro) of SARS-CoV-2 using rational strategies of drug design and medicinal chemistry. Mpro is a key enzyme of coronaviruses and plays an essential role in mediating viral replication and transcription in human lung epithelial and stem cells, making it an attractive drug target for SARS-CoV. The antiviral potential of imidazoline derivatives as inhibitors of (SARS-CoV-2) Mpro was evaluated using in-silico techniques such as molecular docking simulation, molecular dynamics (MD), and ADMET prediction. The docking scores of these imidazoline derivatives were compared to that of the N3 crystal inhibitor and showed that most of these compounds, particularly compound E07, interacted satisfactorily in the active site of the coronavirus and strongly interacted with the residues (Met 165, Gln 166, Met 165, His 41, and Gln 189). Furthermore, the results were confirmed by MD simulations after exposure to long-term MD simulations and ADMET predictions.
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Affiliation(s)
- Sabikeh Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Muna S Merza
- Prosthetic Dental Techniques Department, Al-Mustaqbal University College, Babylon, 51001, Iraq
| | - Fatemeh Ghasemi
- MSC in Software Engineering, Kowsar, The Institute of Higher Education, Ministry of Science, Research and Technology, Computer Engineering Department, Qazvin, Iran
| | - Hasan Ali Dhahi
- National University of Science and Technology, Dhi Qar, Iraq
| | - Farid Baradarbarjastehbaf
- Faculty of Pharmacy, Department of Pharmaceutical Technology and Biopharmacy, University of Pécs, Pécs, Hungary
| | - Mehdi Moosavi
- Department of Chemistry, Faculty of Chemistry, Mazandaran University, Babolsar, Iran
| | - Pouya Ghamari Kargar
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Christophe Len
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 11 Rue Pierre et Marie Curie, F-75005, Paris, France
- Sorbonne Universités, Universite de Technologie de Compiegne, F- 60200, Compiegne, France
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10
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Han Z, Liu J, Kong L, He Y, Wu H, Xu W. A special satellite-like RNA of a novel hypovirus from Pestalotiopsis fici broadens the definition of fungal satellite. PLoS Pathog 2023; 19:e1010889. [PMID: 37285391 DOI: 10.1371/journal.ppat.1010889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
Satellites associated with plant or animal viruses have been largely detected and characterized, while those from mycoviruses together with their roles remain far less determined. Three dsRNA segments (dsRNA 1 to 3 termed according to their decreasing sizes) were identified in a strain of phytopathogenic fungus Pestalotiopsis fici AH1-1 isolated from a tea leaf. The complete sequences of dsRNAs 1 to 3, with the sizes of 10316, 5511, and 631 bp, were determined by random cloning together with a RACE protocol. Sequence analyses support that dsRNA1 is a genome of a novel hypovirus belonging to genus Alphahypovirus of the family Hypoviridae, tentatively named Pestalotiopsis fici hypovirus 1 (PfHV1); dsRNA2 is a defective RNA (D-RNA) generating from dsRNA1 with septal deletions; and dsRNA3 is the satellite component of PfHV1 since it could be co-precipitated with other dsRNA components in the same sucrose fraction by ultra-centrifuge, suggesting that it is encapsulated together with PfHV1 genomic dsRNAs. Moreover, dsRNA3 shares an identical stretch (170 bp) with dsRNAs 1 and 2 at their 5' termini and the remaining are heterogenous, which is distinct from a typical satellite that generally has very little or no sequence similarity with helper viruses. More importantly, dsRNA3 lacks a substantial open reading frame (ORF) and a poly (A) tail, which is unlike the known satellite RNAs of hypoviruses, as well as unlike those in association with Totiviridae and Partitiviridae since the latters are encapsidated in coat proteins. As up-regulated expression of RNA3, dsRNA1 was significantly down-regulated, suggesting that dsRNA3 negatively regulates the expression of dsRNA1, whereas dsRNAs 1 to 3 have no obvious impact on the biological traits of the host fungus including morphologies and virulence. This study indicates that PfHV1 dsRNA3 is a special type of satellite-like nucleic acid that has substantial sequence homology with the host viral genome without encapsidation in a coat protein, which broadens the definition of fungal satellite.
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Affiliation(s)
- Zhenhao Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Jiwen Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Linghong Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Yunqiang He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Hongqu Wu
- Key Laboratory of Microbial Pesticides, Ministry of Agriculture and Rural Affairs; Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
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11
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Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [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: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
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12
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Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN. An alphacoronavirus polymerase structure reveals conserved co-factor functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532841. [PMID: 36993498 PMCID: PMC10055115 DOI: 10.1101/2023.03.15.532841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K. Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Peter J. Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Kenneth W. Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Joshua J. Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Robert N. Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
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13
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Kandwal S, Fayne D. Genetic conservation across SARS-CoV-2 non-structural proteins - Insights into possible targets for treatment of future viral outbreaks. Virology 2023; 581:97-115. [PMID: 36940641 PMCID: PMC9999249 DOI: 10.1016/j.virol.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
The majority of SARS-CoV-2 therapeutic development work has focussed on targeting the spike protein, viral polymerase and proteases. As the pandemic progressed, many studies reported that these proteins are prone to high levels of mutation and can become drug resistant. Thus, it is necessary to not only target other viral proteins such as the non-structural proteins (NSPs) but to also target the most conserved residues of these proteins. In order to understand the level of conservation among these viruses, in this review, we have focussed on the conservation across RNA viruses, conservation across the coronaviruses and then narrowed our focus to conservation of NSPs across coronaviruses. We have also discussed the various treatment options for SARS-CoV-2 infection. A synergistic melding of bioinformatics, computer-aided drug-design and in vitro/vivo studies can feed into better understanding of the virus and therefore help in the development of small molecule inhibitors against the viral proteins.
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Affiliation(s)
- Shubhangi Kandwal
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland
| | - Darren Fayne
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland.
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14
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [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] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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15
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ElSawy KM, Alminderej FM, Caves LSD. Disruption of 3CLpro protease self-association by short peptides as a potential route to broad spectrum coronavirus inhibitors. J Biomol Struct Dyn 2022; 40:13901-13911. [PMID: 34720051 DOI: 10.1080/07391102.2021.1996462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coronaviruses have posed a persistent threat to human health over the last two decades. Despite the accumulated knowledge about coronavirus-related pathogens, development of an effective treatment for its new variant COVID-19 is highly challenging. For the highly-conserved and main coronavirus protease 3CLpro, dimerization is known to be essential for its catalytic activity and thereby for virus proliferation. Here, we assess the potential of short peptide segments to disrupt dimerization of the 3CLpro protease as a route to block COVID-19 proliferation. Based on the X-ray structure of the 3CLpro dimer, we identified the SPSGVY126QCAMRP dodecapeptide segment as overlapping the hotspot regions on the 3CLpro dimer interface. Using computational blind docking of the peptide to the 3CLpro monomer, we found that the SPSGVY126QCAMRP peptide has favourable thermodynamic binding (ΔG= -5.93 kcal/mol) to the hotspot regions at the 3CLpro dimer interface. Importantly, the peptide was also found to preferentially bind to the hotspot regions compared to other potential binding sites lying away from the dimer interface (ΔΔG=-1.31 kcal/mol). Docking of peptides corresponding to systematic mutation of the V125 and Y126 residues led to the identification of seven peptides, SPSGHAQCAMRP, SPSGVTQCAMRP, SPSGKPQCAMRP, SPSGATQCAMRP, SPSGWLQCAMRP, SPSGAPQCAMRP and SPSGHPQCAMRP, that outperform the wild-type SPSGVY126QCAMRP peptide in terms of preferential binding to the 3CLpro dimer interface. These peptides have the potential to disrupt 3CLpro dimerization and therefore could provide lead structures for the development of broad spectrum COVID-19 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia.,York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK
| | - Fahad M Alminderej
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia
| | - Leo S D Caves
- York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK.,Independent Researcher, São Felix da Marinha, Portugal
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16
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Copertino DC, Casado Lima BC, Duarte RRR, Powell TR, Ormsby CE, Wilkin T, Gulick RM, de Mulder Rougvie M, Nixon DF. Antiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection. J Biomol Struct Dyn 2022; 40:7367-7380. [PMID: 33734021 PMCID: PMC8448789 DOI: 10.1080/07391102.2021.1901144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/24/2021] [Indexed: 12/18/2022]
Abstract
COVID-19 is the disease caused by SARS-CoV-2 which has led to 2,643,000 deaths worldwide, a number which is rapidly increasing. Urgent studies to identify new antiviral drugs, repurpose existing drugs, or identify drugs that can target the overactive immune response are ongoing. Antiretroviral drugs (ARVs) have been tested in past human coronavirus infections, and also against SARS-CoV-2, but a trial of lopinavir and ritonavir failed to show any clinical benefit in COVID-19. However, there is limited data as to the course of COVID-19 in people living with HIV, with some studies showing a decreased mortality for those taking certain ARV regimens. We hypothesized that ARVs other than lopinavir and ritonavir might be responsible for some protection against the progression of COVID-19. Here, we used chemoinformatic analyses to predict which ARVs would bind and potentially inhibit the SARS-CoV-2 main protease (Mpro) or RNA-dependent-RNA-polymerase (RdRp) enzymes in silico. The drugs predicted to bind the SARS-CoV-2 Mpro included the protease inhibitors atazanavir and indinavir. The ARVs predicted to bind the catalytic site of the RdRp included Nucleoside Reverse Transcriptase Inhibitors, abacavir, emtricitabine, zidovudine, and tenofovir. Existing or new combinations of antiretroviral drugs could potentially prevent or ameliorate the course of COVID-19 if shown to inhibit SARS-CoV-2 in vitro and in clinical trials. Further studies are needed to establish the activity of ARVs for treatment or prevention of SARS-CoV-2 infection .Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dennis C. Copertino
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bruno C. Casado Lima
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Rodrigo R. R. Duarte
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Timothy R. Powell
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher E. Ormsby
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Timothy Wilkin
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Roy M. Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Douglas F. Nixon
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
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17
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Ghosh AK, Mishevich JL, Mesecar A, Mitsuya H. Recent Drug Development and Medicinal Chemistry Approaches for the Treatment of SARS-CoV-2 Infection and COVID-19. ChemMedChem 2022; 17:e202200440. [PMID: 36165855 PMCID: PMC9538661 DOI: 10.1002/cmdc.202200440] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/21/2022] [Indexed: 01/14/2023]
Abstract
COVID-19, caused by SARS-CoV-2 infection, continues to be a major public health crisis around the globe. Development of vaccines and the first cluster of antiviral drugs has brought promise and hope for prevention and treatment of severe coronavirus disease. However, continued development of newer, safer, and more effective antiviral drugs are critically important to combat COVID-19 and counter the looming pathogenic variants. Studies of the coronavirus life cycle revealed several important biochemical targets for drug development. In the present review, we focus on recent drug design and medicinal chemistry efforts in small molecule drug discovery, including the development of nirmatrelvir that targets viral protein synthesis and remdesivir and molnupiravir that target viral RdRp. These are recent FDA approved drugs for the treatment of COVID-19.
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Affiliation(s)
- Arun K Ghosh
- Purdue UniversityDepartments of Chemistry and Medicinal Chemistry560 Oval Drive47907West LafayetteUNITED STATES
| | | | - Andrew Mesecar
- Purdue University College of ScienceBiochemistryUNITED STATES
| | - Hiroaki Mitsuya
- National Cancer InstituteHIV and AIDS Malignancy BranchUNITED STATES
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18
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kerkour R, Chafai N, Moumeni O, Chafaa S. Novel α-aminophosphonate derivates synthesis, theoretical calculation, Molecular docking, and in silico prediction of potential inhibition of SARS-CoV-2. J Mol Struct 2022; 1272:134196. [PMID: 36193287 PMCID: PMC9519172 DOI: 10.1016/j.molstruc.2022.134196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/18/2023]
Abstract
Using the Density Functional Theory approach and in silico docking, the current study analyzes the inhibitory role of a novel α-aminophosphonate derivative against SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) of SARS-CoV-2. FT-IR, UV–Vis, and NMR (1H, 13C, 31P) approaches were used to produce and confirm the novel α-aminophosphonate derivative. The quantum chemical parameters were detremined, and the reactivity of the synthesized molecule was discussed using DFT at the B3LYP/6-31G(d,p) level. In addition, the inhibitory function of the investigated derivative for SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) was estimated using in silico docking. These discoveries could pave the way for novel SARS-CoV-2 therapies to develop and be tested.
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19
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Yang KS, Leeuwon SZ, Xu S, Liu WR. Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir. J Med Chem 2022; 65:8686-8698. [PMID: 35731933 PMCID: PMC9236210 DOI: 10.1021/acs.jmedchem.2c00404] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 12/15/2022]
Abstract
The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease (MPro) of SARS-CoV-2. Since many SARS-CoV-2 variants that resist vaccines and antibodies have emerged, a concern of acquired viral resistance to nirmatrelvir naturally arises. Here, possible mutations in MPro to confer viral evasion of nirmatrelvir are analyzed and discussed from both evolutionary and structural standpoints. The analysis indicates that those mutations will likely reside in the whole aa45-51 helical region and residues including M165, L167, P168, R188, and Q189. Relevant mutations have also been observed in existing SARS-CoV-2 samples. Implications of this analysis to the fight against future drug-resistant viral variants and the development of broad-spectrum antivirals are discussed as well.
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Affiliation(s)
- Kai S. Yang
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Sunshine Z. Leeuwon
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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20
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Alotaibi SH, Amer HH, Touil N, Abdel-Moneim AS, Soliman MM, Zaki YH. Synthesis, Characterization and Molecular Docking of New Nucleosides and Schiff Bases Derived from Ampyrone as Antiviral Agents to Contain the COVID-19 Virus. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2045329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Saad H. Alotaibi
- Department of Chemistry, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Hamada H. Amer
- Department of Chemistry, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
- Unité de Culture Cellulaire, CVMIT, HMI Med V, Rabat, Morocco
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Turabah, Taif, Saudi Arabia
| | - Mohamed M. Soliman
- Department of Clinical Laboratory Sciences, Turabah University College, Taif University, Turabah, Taif, Saudi Arabia
| | - Yasser H. Zaki
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
- Department of Chemistry, Faculty of Science and Humanity Studies at Al-Quwayiyah, Shaqra University, Al Quwayiyah, Saudi Arabia
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21
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Coronavirus enzyme inhibitors-experimentally proven natural compounds from plants. J Microbiol 2022; 60:347-354. [PMID: 35089586 PMCID: PMC8795716 DOI: 10.1007/s12275-022-1499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
Coronavirus disease (COVID-19) can cause critical conditions that require efficient therapeutics. Several medicines are derived from plants, and researchers are seeking natural compounds to ameliorate the symptoms of COVID-19. Viral enzymes are popular targets of antiviral medicines; the genome of coronaviruses encodes several enzymes, including RNA-dependent RNA polymerase and viral proteases. Various screening systems have been developed to identify potential inhibitors. In this review, we describe the natural compounds that have been shown to exert inhibitory effects on coronavirus enzymes. Although computer-aided molecular structural studies have predicted several antiviral compound candidates, the current review focuses on experimentally proven natural compounds.
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22
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Hashemian SMR, Pourhanifeh MH, Hamblin MR, Shahrzad MK, Mirzaei H. RdRp inhibitors and COVID-19: Is molnupiravir a good option? Biomed Pharmacother 2022; 146:112517. [PMID: 34902743 PMCID: PMC8654603 DOI: 10.1016/j.biopha.2021.112517] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Rapid changes in the viral genome allow viruses to evade threats posed by the host immune response or antiviral drugs, and can lead to viral persistence in the host cells. RNA-dependent RNA polymerase (RdRp) is an essential enzyme in RNA viruses, which is involved in RNA synthesis through the formation of phosphodiester bonds. Therefore, in RNA viral infections such as SARS-CoV-2, RdRp could be a crucial therapeutic target. The present review discusses the promising application of RdRp inhibitors, previously approved or currently being tested in human clinical trials, in the treatment of RNA virus infections. Nucleoside inhibitors (NIs) bind to the active site of RdRp, while nonnucleoside inhibitors (NNIs) bind to allosteric sites. Given the absence of highly effective drugs for the treatment of COVID-19, the discovery of an efficient treatment for this pandemic is an urgent concern for researchers around the world. We review the evidence for molnupiravir (MK-4482, EIDD-2801), an antiviral drug originally designed for Alphavirus infections, as a potential preventive and therapeutic agent for the management of COVID-19. At the beginning of this pandemic, molnupiravir was in preclinical development for seasonal influenza. When COVID-19 spread dramatically, the timeline for development was accelerated to focus on the treatment of this pandemic. Real time consultation with regulators took place to expedite this program. We summarize the therapeutic potential of RdRp inhibitors, and highlight molnupiravir as a new small molecule drug for COVID-19 treatment.
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Affiliation(s)
- Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and Endocrinology, ShohadaeTajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran; Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, IR, Iran.
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23
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IMTIAZ F, PASHA MK. A systematic review of RdRp of SARS-CoV-2 through artificial intelligence and machine learning utilizing structure-based drug design strategy. Turk J Chem 2021; 46:583-594. [PMID: 37720604 PMCID: PMC10503974 DOI: 10.55730/1300-0527.3355] [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: 09/10/2021] [Revised: 06/16/2022] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Since the coronavirus disease has been declared a global pandemic, it had posed a challenge among researchers and raised common awareness and collaborative efforts towards finding the solution. Caused by severe acute respiratory coronavirus syndrome-2 (SARS-CoV-2), coronavirus drug design strategy needs to be optimized. It is understandable that cognizance of the pathobiology of COVID-19 can help scientists in the development and discovery of therapeutically effective antiviral drugs by elucidating the unknown viral pathways and structures. Considering the role of artificial intelligence and machine learning with its advancements in the field of science, it is rational to use these methods which can aid in the discovery of new potent candidates in silico. Our review utilizes similar methodologies and focuses on RNA-dependent RNA polymerase (RdRp), based on its importance as an essential element for virus replication and also a promising target for COVID-19 therapeutics. Artificial neural network technique was used to shortlist articles with the support of PRISMA, from different research platforms including Scopus, PubMed, PubChem, and Web of Science, through a combination of keywords. "English language", from the year "2000" and "published articles in journals" were selected to carry out this research. We summarized that structural details of the RdRp reviewed in this analysis will have the potential to be taken into consideration when developing therapeutic solutions and if further multidisciplinary efforts are taken in this domain then potential clinical candidates for RdRp of SARS-CoV-2 could be successfully delivered for experimental validations.
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Affiliation(s)
- Fariha IMTIAZ
- Punjab University College of Pharmacy, University of the Punjab, Lahore,
Pakistan
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24
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Murugan C, Ramamoorthy S, Kuppuswamy G, Murugan RK, Sivalingam Y, Sundaramurthy A. COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks. Int J Biol Macromol 2021; 193:1165-1200. [PMID: 34710479 PMCID: PMC8545698 DOI: 10.1016/j.ijbiomac.2021.10.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023]
Abstract
Today, the world population is facing an existential threat by an invisible enemy known as severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) or COVID-19. It is highly contagious and has infected a larger fraction of human population across the globe on various routes of transmission. The detailed knowledge of the SARS-CoV-2 structure and clinical aspects offers an important insight into the evolution of infection, disease progression and helps in executing the different therapies effectively. Herein, we have discussed in detail about the genome structure of SARS-CoV-2 and its role in the proteomic rational spread of different muted species and pathogenesis in infecting the host cells. The mechanisms behind the viral outbreak and its immune response, the availability of existing diagnostics techniques, the treatment efficacy of repurposed drugs and the emerging vaccine trials for the SARS-CoV-2 outbreak also have been highlighted. Furthermore, the possible antiviral effects of various herbal products and their extracted molecules in inhibiting SARS-CoV-2 replication and cellular entry are also reported. Finally, we conclude our opinion on current challenges involved in the drug development, bulk production of drug/vaccines and their storage requirements, logistical procedures and limitations related to dosage trials for larger population.
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Affiliation(s)
- Chandran Murugan
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Sharmiladevi Ramamoorthy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Guruprasad Kuppuswamy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Rajesh Kumar Murugan
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Yuvaraj Sivalingam
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Anandhakumar Sundaramurthy
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India; Department of Chemical Engineering, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India.
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25
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Dhankhar P, Dalal V, Kumar V. Screening of Severe Acute Respiratory Syndrome Coronavirus 2 RNA-Dependent RNA Polymerase Inhibitors Using Computational Approach. J Comput Biol 2021; 28:1228-1247. [PMID: 34847746 PMCID: PMC8819516 DOI: 10.1089/cmb.2020.0639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The detrimental effect of coronavirus disease 2019 (COVID-19) pandemic has manifested itself as a global crisis. Currently, no specific treatment options are available for COVID-19, so therapeutic interventions to tackle the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection must be urgently established. Therefore, cohesive and multidimensional efforts are required to identify new therapies or investigate the efficacy of small molecules and existing drugs against SARS-CoV-2. Since the RNA-dependent RNA Polymerase (RdRP) of SARS-CoV-2 is a promising therapeutic target, this study addresses the identification of antiviral molecules that can specifically target SARS-CoV-2 RdRP. The computational approach of drug development was used to screen the antiviral molecules from two antiviral libraries (Life Chemicals [LC] and ASINEX) against RdRP. Here, we report six antiviral molecules (F3407-4105, F6523-2250, F6559-0746 from LC and BDG 33693278, BDG 33693315, LAS 34156196 from ASINEX), which show substantial interactions with key amino acid residues of the active site of SARS-CoV-2 RdRP and exhibit higher binding affinity (>7.5 kcalmol-1) than Galidesivir, an Food and Drug Administration-approved inhibitor of the same. Further, molecular dynamics simulation and Molecular Mechanics Poisson-Boltzmann Surface Area results confirmed that identified molecules with RdRP formed higher stable RdRP-inhibitor(s) complex than RdRP-Galidesvir complex. Our findings suggest that these molecules could be potential inhibitors of SARS-CoV-2 RdRP. However, further in vitro and preclinical experiments would be required to validate these potential inhibitors of SARS-CoV-2 protein.
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Affiliation(s)
- Poonam Dhankhar
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Viney Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
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26
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Shah MA, Rasul A, Yousaf R, Haris M, Faheem HI, Hamid A, Khan H, Khan AH, Aschner M, Batiha GE. Combination of natural antivirals and potent immune invigorators: A natural remedy to combat COVID-19. Phytother Res 2021; 35:6530-6551. [PMID: 34396612 PMCID: PMC8441799 DOI: 10.1002/ptr.7228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/14/2021] [Accepted: 04/10/2021] [Indexed: 12/23/2022]
Abstract
The flare-up in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in December 2019 in Wuhan, China, and spread expeditiously worldwide has become a health challenge globally. The rapid transmission, absence of anti-SARS-CoV-2 drugs, and inexistence of vaccine are further exacerbating the situation. Several drugs, including chloroquine, remdesivir, and favipiravir, are presently undergoing clinical investigation to further scrutinize their effectiveness and validity in the management of COVID-19. Natural products (NPs) in general, and plants constituents specifically, are unique sources for various effective and novel drugs. Immunostimulants, including vitamins, iron, zinc, chrysin, caffeic acid, and gallic acid, act as potent weapons against COVID-19 by reinvigorating the defensive mechanisms of the immune system. Immunity boosters prevent COVID-19 by stimulating the proliferation of T-cells, B-cells, and neutrophils, neutralizing the free radicals, inhibiting the immunosuppressive agents, and promoting cytokine production. Presently, antiviral therapy includes several lead compounds, such as baicalin, glycyrrhizin, theaflavin, and herbacetin, all of which seem to act against SARS-CoV-2 via particular targets, such as blocking virus entry, attachment to host cell receptor, inhibiting viral replication, and assembly and release.
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Affiliation(s)
- Muhammad Ajmal Shah
- Department of Pharmacognosy, Faculty of Pharmaceutical SciencesGovernment College UniversityFaisalabadPakistan
| | - Azhar Rasul
- Department of Zoology, Faculty of Life SciencesGovernment College UniversityFaisalabadPakistan
| | - Rimsha Yousaf
- Department of Pharmacognosy, Faculty of Pharmaceutical SciencesGovernment College UniversityFaisalabadPakistan
| | - Muhammad Haris
- Department of Pharmacognosy, Faculty of Pharmaceutical SciencesGovernment College UniversityFaisalabadPakistan
| | - Hafiza Ishmal Faheem
- Department of Pharmacognosy, Faculty of Pharmaceutical SciencesGovernment College UniversityFaisalabadPakistan
| | - Ayesha Hamid
- Department of Pharmacognosy, Faculty of Pharmaceutical SciencesGovernment College UniversityFaisalabadPakistan
| | - Haroon Khan
- Department of PharmacyAbdul Wali Khan UniversityMardanPakistan
| | - Abdul Haleem Khan
- Department of PharmacyForman Christian College (A Chartered University)LahorePakistan
| | - Michael Aschner
- Department of Molecular PharmacologyAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Gaber El‐Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary MedicineDamanhour UniversityDamanhourAl‐BeheiraEgypt
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27
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Szabó PB, Sabanés Zariquiey F, Nogueira JJ. Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations. J Chem Inf Model 2021; 61:5508-5523. [PMID: 34730967 PMCID: PMC8659376 DOI: 10.1021/acs.jcim.1c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Indexed: 11/30/2022]
Abstract
The lack of conformational sampling in virtual screening projects can lead to inefficient results because many of the potential drugs may not be able to bind to the target protein during the static docking simulations. Here, we performed ensemble docking for around 2000 United States Food and Drug Administration (FDA)-approved drugs with the RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a target. The representative protein structures were generated by clustering classical molecular dynamics trajectories, which were evolved using three solvent scenarios, namely, pure water, benzene/water and phenol/water mixtures. The introduction of dynamic effects in the theoretical model showed improvement in docking results in terms of the number of strong binders and binding sites in the protein. Some of the discovered pockets were found only for the cosolvent simulations, where the nonpolar probes induced local conformational changes in the protein that lead to the opening of transient pockets. In addition, the selection of the ligands based on a combination of the binding free energy and binding free energy gap between the best two poses for each ligand provided more suitable binders than the selection of ligands based solely on one of the criteria. The application of cosolvent molecular dynamics to enhance the sampling of the configurational space is expected to improve the efficacy of virtual screening campaigns of future drug discovery projects.
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Affiliation(s)
- P. Bernát Szabó
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
- Department
of Chemistry, Universidad Autónoma
de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
| | | | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
- IADCHEM,
Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain
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28
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Gul S, Ozcan O, Asar S, Okyar A, Barıs I, Kavakli IH. In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials. J Biomol Struct Dyn 2021; 39:6772-6791. [PMID: 32752938 PMCID: PMC7484590 DOI: 10.1080/07391102.2020.1802346] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxychloroquine. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CLpro) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CLpro based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Onur Ozcan
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Sinan Asar
- Department of Anesthesiology and Reanimation, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Alper Okyar
- Department of Pharmacology, Istanbul University Faculty of Pharmacy, Istanbul, Turkey
| | - Ibrahim Barıs
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
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29
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Kumar S, Çalışkan DM, Janowski J, Faist A, Conrad BCG, Lange J, Ludwig S, Brunotte L. Beyond Vaccines: Clinical Status of Prospective COVID-19 Therapeutics. Front Immunol 2021; 12:752227. [PMID: 34659259 PMCID: PMC8519339 DOI: 10.3389/fimmu.2021.752227] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Since November 2019 the SARS-CoV-2 pandemic has caused nearly 200 million infection and more than 4 million deaths globally (Updated information from the World Health Organization, as on 2nd Aug 2021). Within only one year into the pandemic, several vaccines were designed and reached approval for the immunization of the world population. The remarkable protective effects of the manufactured vaccines are demonstrated in countries with high vaccination rates, such as Israel and UK. However, limited production capacities, poor distribution infrastructures and political hesitations still hamper the availability of vaccines in many countries. In addition, due to the emergency of SARS-CoV-2 variants with immune escape properties towards the vaccines the global numbers of new infections as well as patients developing severe COVID-19, remains high. New studies reported that about 8% of infected individuals develop long term symptoms with strong personal restrictions on private as well as professional level, which contributes to the long socioeconomic problems caused by this pandemic. Until today, emergency use-approved treatment options for COVID-19 are limited to the antiviral Remdesivir, a nucleoside analogue targeting the viral polymerase, the glucocorticosteroide Dexamethasone as well as neutralizing antibodies. The therapeutic benefits of these treatments are under ongoing debate and clinical studies assessing the efficiency of these treatments are still underway. To identify new therapeutic treatments for COVID-19, now and by the post-pandemic era, diverse experimental approaches are under scientific evaluation in companies and scientific research teams all over the world. To accelerate clinical translation of promising candidates, repurposing approaches of known approved drugs are specifically fostered but also novel technologies are being developed and are under investigation. This review summarizes the recent developments from the lab bench as well as the clinical status of emerging therapeutic candidates and discusses possible therapeutic entry points for the treatment strategies with regard to the biology of SARS-CoV-2 and the clinical course of COVID-19.
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Affiliation(s)
- Sriram Kumar
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
| | - Duygu Merve Çalışkan
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
| | - Josua Janowski
- Institute of Virology, University of Münster, Münster, Germany
- SP BioSciences Graduate Program, University of Münster, Münster, Germany
| | - Aileen Faist
- Institute of Virology, University of Münster, Münster, Germany
- CiM-IMPRS Graduate Program, University of Münster, Münster, Germany
| | | | - Julius Lange
- Institute of Virology, University of Münster, Münster, Germany
| | - Stephan Ludwig
- Institute of Virology, University of Münster, Münster, Germany
- EvoPAD Research Training Group 2220, University of Münster, Münster, Germany
- CiM-IMPRS Graduate Program, University of Münster, Münster, Germany
- Interdisciplinary Centre for Medical Research, University of Münster, Münster, Germany
| | - Linda Brunotte
- Institute of Virology, University of Münster, Münster, Germany
- Interdisciplinary Centre for Medical Research, University of Münster, Münster, Germany
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30
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Farooqi T, Malik JA, Mulla AH, Al Hagbani T, Almansour K, Ubaid MA, Alghamdi S, Anwar S. An overview of SARS-COV-2 epidemiology, mutant variants, vaccines, and management strategies. J Infect Public Health 2021; 14:1299-1312. [PMID: 34429257 PMCID: PMC8366110 DOI: 10.1016/j.jiph.2021.08.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Over the last two decades, humanity has observed the extraordinary anomaly caused by novel, weird coronavirus strains, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). As the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has made its entry into the world, it has dramatically affected life in every domain by continuously producing new variants. The vaccine development is an ongoing process, although some vaccines got marketed. The big challenge is now whether the vaccine candidates can provide long-lasting protection or prevention against mutant variants. METHODS The information was gathered from various journals, electronic searches via Internet-based information such as PubMed, Google Scholar, Science Direct, online electronic journals, WHO landscape, world meters, WHO website, and News. RESULTS This review will present and discuss some coronavirus disease 19 (COVID-19) related aspects including: the pathophysiology, epidemiology, mutant variants vaccine candidates, vaccine efficacy, and management strategies. Due to the high death rate, continuous spread, an inadequate workforce, lack of required therapeutics, and incomplete understanding of the viral strain, it becomes crucial to build the knowledge of its biological characteristics and make available the rapid diagnostic and vital therapeutic machinery for the combat and management of an infection. CONCLUSION The data summarizes current research on the COVID 19 infection and therapeutic interventions, which will direct future decision-making on the effort-worthy phases of the COVID 19 and the development of critical therapeutics. The only possible solution is the vaccine development targeting against all variant strains to halt its progress; the identified theoretical and practical knowledge can eliminate the gaps to improve a better understanding of the novel coronavirus structure and its design of a vaccine. In addition, to that the long-lasting protection is another challenging objective that need to be looked into.
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Affiliation(s)
- Tahmeena Farooqi
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Jonaid Ahmad Malik
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Guwahati, India; Department of Biomedical Engineering, Indian Institute of Technology (IIT), Ropar, Punjab, India
| | | | - Turki Al Hagbani
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Khaled Almansour
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | | | - Saleh Alghamdi
- Department of Clinical Pharmacy, Faculty of Clinical Pharmacy, Albaha University, Albaha, Saudi Arabia
| | - Sirajudheen Anwar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia.
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31
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Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2021; 65:2866-2879. [PMID: 34570513 PMCID: PMC8491550 DOI: 10.1021/acs.jmedchem.1c00566] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.
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Affiliation(s)
- Sarah Huff
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Indrasena Reddy Kummetha
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Matthew B Huante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shaobo Wang
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - William Bray
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Mark Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
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32
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Kumar RP, Siddique S. 22-Hydroxyhopane, a novel multitargeted phytocompound against SARS-CoV-2 from Adiantum latifolium Lam. Nat Prod Res 2021; 36:4276-4281. [PMID: 34544287 DOI: 10.1080/14786419.2021.1976177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The present pandemic disease COVID-19 demands an urgent need for more efficient antiviral drugs against SARS-CoV-2. 22-Hydroxyhopane is a bioactive triterpenoid compound with antibacterial activity, present in the leaves of Adiantum latifolium. In this study, molecular docking method revealed strong binding affinity of the compound for ten proteins essential for SARS-CoV-2 multiplication in host cells, including seven nonstructural proteins, two structural proteins and one receptor protein, with a binding energy of -7.61 to -9.82 kcal/mol and inhibition constant <1 μM. MDS and MM-PBSA analysis of the best ranked complex further confirmed the results. The targets selected include six enzymes, RNA binding protein, spike protein, membrane protein and ACE2 receptor of SARS-CoV-2. It is the first report of a natural compound from A. latifolium having multitargeted activity against SARS-CoV-2. We conclude that 22-hydroxyhopane may be used as a best source for the development of novel therapeutic drugs for COVID-19, but requires further evaluations.
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Affiliation(s)
- R Pradeep Kumar
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
| | - Simna Siddique
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
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33
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Schmidt J, Berghaus S, Blessing F, Wenzel F, Herbeck H, Blessing J, Schierack P, Rödiger S, Roggenbuck D. Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. GeroScience 2021; 43:2249-2264. [PMID: 34468954 PMCID: PMC8408040 DOI: 10.1007/s11357-021-00443-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022] Open
Abstract
To study host-virus interactions after SARS coronavirus-2 (SARS-CoV-2) infection, genetic virus characteristics and the ensued humoral immune response were investigated for the first time. Fifty-five SARS-CoV-2-infected patients from the early pandemic phase were followed up including serological testing and whole genome sequencing. Anti-spike and nucleocapsid protein (S/N) IgG and IgM levels were determined by screening ELISA and IgG was further characterized by reactivity to S-subunit 1 (anti-S1), S-subunit 2 (anti-S2) and anti-N. In 55 patients, 90 genetic SARS-CoV-2 changes including 48 non-synonymous single nucleotide variants were identified. Phylogenetic analysis of the sequencing data showed a cluster representing a local outbreak and various family clusters. Anti-S/N and anti-N IgG were detected in 49 patients at an average of 83 days after blood collection. Anti-S/N IgM occurred significantly less frequently than IgG whereas anti-S2 was the least prevalent IgG reactivity (P < 0.05, respectively). Age and overweight were significantly associated with higher anti-S/N and anti-S1 IgG levels while age only with anti-N IgG (multiple regression, P < 0.05, respectively). Anti-S/N IgG/IgM levels, blood group A + , cardiovascular and tumour disease, NSP12 Q444H and ORF3a S177I were independent predictors of clinical characteristics with anti-S/N IgM being associated with the need for hospitalization (multivariate regression, P < 0.05, respectively). Anti-SARS-CoV-2 antibody generation was mainly affected by higher age and overweight in the present cohort. COVID-19 traits were associated with genetic SARS-CoV-2 variants, anti-S/N IgG/IgM levels, blood group A + and concomitant disease. Anti-S/N IgM was the only antibody associated with the need for hospitalization.
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Affiliation(s)
- Jonas Schmidt
- Institute for Laboratory Medicine, Singen, Germany
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | | | - Frithjof Blessing
- Institute for Laboratory Medicine, Singen, Germany
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
| | - Folker Wenzel
- Faculty of Medical and Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany
| | | | | | - Peter Schierack
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Faculty Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany.
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany.
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [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: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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Khursheed A, Jain V, Rasool A, Rather MA, Malik NA, Shalla AH. Molecular scaffolds from mother nature as possible lead compounds in drug design and discovery against coronaviruses: A landscape analysis of published literature and molecular docking studies. Microb Pathog 2021; 157:104933. [PMID: 33984466 PMCID: PMC8110334 DOI: 10.1016/j.micpath.2021.104933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
The recent outbreak of viral infection and its transmission has highlighted the importance of its slowdown for the safeguard of public health, globally. The identification of novel drugs and efficient therapies against these infectious viruses is need of the hour. The eruption of COVID-19 is caused by a novel acute respiratory syndrome virus SARS-CoV-2 which has taken the whole world by storm as it has transformed into a global pandemic. This lethal syndrome is a global health threat to general public which has already affected millions of people. Despite the development of some potential vaccines and repurposed drugs by some Pharma companies, this health emergency needs more attention due to the less efficacy of these vaccines coupled with the emergence of novel and resistant strains of SARS-CoV-2. Due to enormous structural diversity and biological applications, natural products are considered as a wonderful source of drugs for such diseases. Natural product based drugs constitute a substantial proportion of the pharmaceutical market particularly in the therapeutic areas of infectious diseases and oncology. The naturally occurring bioactive antiviral phytochemicals including alkaloids, flavonoids and peptides have been subjected to virtual screening against COVID-19. Since there is no specific medicine available for the treatment of Covid-19, designing new drugs using in silico methods plays an all important role to find that magic bullet which can target this lethal virus. The in silico method is not only quick but economical also when compared to the other conventional methods which are hit and trial methods. Based on this in silico approach, various natural products have been recently identified which might have a potential to inhibit COVID-19 outbreak. These natural products have been shown by these docking studies to interact with the spike protein of the novel coronavirus. This spike protein has been shown to bind to a transmembrane protein called Angiotensin converting enzyme 2 (ACE2), this protein acts as a receptor for the viral spike protein. This comprehensive review article anticipates providing a summary of the authentic and peer reviewed published literature about the potential of natural metabolites that can be developed into possible lead compounds against this new threat of Covid-19. Main focus of the article will be to highlight natural sources of potential anti-coronavirus molecules, mechanism of action, docking studies and the target proteins as well as their toxicity profiles. This review article intends to provide a starting point for the research endeavors that are needed for the design and development of drugs based on pure natural products, their synthetic or semi-synthetic derivatives and standardized plant extracts. This review article will be highly helpful for scientists who are working or intend to work on antiviral drugs from natural sources.
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Affiliation(s)
- Aadil Khursheed
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Vikrant Jain
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Ajaz Rasool
- Department of Zoology, University of Kashmir, Srinagar, 190006, India
| | - Manzoor A Rather
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India.
| | - Nisar Ahmad Malik
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
| | - Aabid Hussain Shalla
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
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García-Trejo JJ, Ortega R, Zarco-Zavala M. Putative Repurposing of Lamivudine, a Nucleoside/Nucleotide Analogue and Antiretroviral to Improve the Outcome of Cancer and COVID-19 Patients. Front Oncol 2021; 11:664794. [PMID: 34367956 PMCID: PMC8335563 DOI: 10.3389/fonc.2021.664794] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Lamivudine, also widely known as 3TC belongs to a family of nucleotide/nucleoside analogues of cytidine or cytosine that inhibits the Reverse Transcriptase (RT) of retroviruses such as HIV. Lamivudine is currently indicated in combination with other antiretroviral agents for the treatment of HIV-1 infection or for chronic Hepatitis B (HBV) virus infection associated with evidence of hepatitis B viral replication and active liver inflammation. HBV reactivation in patients with HBV infections who receive anticancer chemotherapy can be a life-threatening complication during and after the completion of chemotherapy. Lamivudine is used, as well as other antiretrovirals, to prevent the reactivation of the Hepatitis B virus during and after chemotherapy. In addition, Lamivudine has been shown to sensitize cancer cells to chemotherapy. Lamivudine and other similar analogues also have direct positive effects in the prevention of cancer in hepatitis B or HIV positive patients, independently of chemotherapy or radiotherapy. Recently, it has been proposed that Lamivudine might be also repurposed against SARS-CoV-2 in the context of the COVID-19 pandemic. In this review we first examine recent reports on the re-usage of Lamivudine or 3TC against the SARS-CoV-2, and we present docking evidence carried out in silico suggesting that Lamivudine may bind and possibly work as an inhibitor of the SARS-CoV-2 RdRp RNA polymerase. We also evaluate and propose assessment of repurposing Lamivudine as anti-SARS-CoV-2 and anti-COVID-19 antiviral. Secondly, we summarize the published literature on the use of Lamivudine or (3TC) before or during chemotherapy to prevent reactivation of HBV, and examine reports of enhanced effectiveness of radiotherapy in combination with Lamivudine treatment against the cancerous cells or tissues. We show that the anti-cancer properties of Lamivudine are well established, whereas its putative anti-COVID effect is under investigation. The side effects of lamivudine and the appearance of resistance to 3TC are also discussed.
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Affiliation(s)
- José J García-Trejo
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Raquel Ortega
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Mariel Zarco-Zavala
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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Khater S, Kumar P, Dasgupta N, Das G, Ray S, Prakash A. Combining SARS-CoV-2 Proofreading Exonuclease and RNA-Dependent RNA Polymerase Inhibitors as a Strategy to Combat COVID-19: A High-Throughput in silico Screening. Front Microbiol 2021; 12:647693. [PMID: 34354677 PMCID: PMC8329495 DOI: 10.3389/fmicb.2021.647693] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people worldwide. Currently, many clinical trials in search of effective COVID-19 drugs are underway. Viral RNA-dependent RNA polymerase (RdRp) remains the target of choice for prophylactic or curative treatment of COVID-19. Nucleoside analogs are the most promising RdRp inhibitors and have shown effectiveness in vitro, as well as in clinical settings. One limitation of such RdRp inhibitors is the removal of incorporated nucleoside analogs by SARS-CoV-2 exonuclease (ExoN). Thus, ExoN proofreading activity accomplishes resistance to many of the RdRp inhibitors. We hypothesize that in the absence of highly efficient antivirals to treat COVID-19, combinatorial drug therapy with RdRp and ExoN inhibitors will be a promising strategy to combat the disease. To repurpose drugs for COVID-19 treatment, 10,397 conformers of 2,240 approved drugs were screened against the ExoN domain of nsp14 using AutoDock VINA. The molecular docking approach and detailed study of interactions helped us to identify dexamethasone metasulfobenzoate, conivaptan, hesperidin, and glycyrrhizic acid as potential inhibitors of ExoN activity. The results were further confirmed using molecular dynamics (MD) simulations and molecular mechanics combined with generalized Born model and solvent accessibility method (MM-GBSA) calculations. Furthermore, the binding free energy of conivaptan and hesperidin, estimated using MM-GBSA, was -85.86 ± 0.68 and 119.07 ± 0.69 kcal/mol, respectively. Based on docking, MD simulations and known antiviral activities, and conivaptan and hesperidin were identified as potential SARS-CoV-2 ExoN inhibitors. We recommend further investigation of this combinational therapy using RdRp inhibitors with a repurposed ExoN inhibitor as a potential COVID-19 treatment.
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Affiliation(s)
- Shradha Khater
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- miBiome Therapeutics LLP, Mumbai, India
| | - Pawan Kumar
- National Institute of Immunology, New Delhi, India
| | | | | | - Shashikant Ray
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
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In silico investigation on the inhibitory effect of fungal secondary metabolites on RNA dependent RNA polymerase of SARS-CoV-II: A docking and molecular dynamic simulation study. Comput Biol Med 2021; 135:104613. [PMID: 34242870 PMCID: PMC8256662 DOI: 10.1016/j.compbiomed.2021.104613] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/27/2021] [Accepted: 06/27/2021] [Indexed: 12/21/2022]
Abstract
The newly emerged Coronavirus Disease 2019 (COVID-19) rapidly outspread worldwide and now is one of the biggest infectious pandemics in human society. In this study, the inhibitory potential of 99 secondary metabolites obtained from endophytic fungi was investigated against the new coronavirus RNA-dependent RNA polymerase (RdRp) using computational methods. A sequence of blind and targeted molecular dockings was performed to predict the more potent compounds on the viral enzyme. In the next step, the five selected compounds were further evaluated by molecular dynamics (MD) simulation. Moreover, the pharmacokinetics of the metabolites was assessed using SwissADME server. The results of molecular docking showed that compounds 18-methoxy cytochalasin J, (22E,24R)-stigmasta-5,7,22-trien-3-β-ol, beauvericin, dankasterone B, and pyrrocidine A had higher binding energy than others. The findings of MD and SwissADME demonstrated that two fungal metabolites, 18-methoxy cytochalasin J and pyrrocidine A had better results than others in terms of protein instability, strong complex formation, and pharmacokinetic properties. In conclusion, it is recommended to further evaluate the compounds 18-methoxy cytochalasin J and pyrrocidine A in the laboratory as good candidates for inhibiting COVID-19.
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Liang H, Zhao L, Gong X, Hu M, Wang H. Virtual screening FDA approved drugs against multiple targets of SARS-CoV-2. Clin Transl Sci 2021; 14:1123-1132. [PMID: 33606912 PMCID: PMC8014887 DOI: 10.1111/cts.13007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/07/2021] [Accepted: 01/27/2021] [Indexed: 01/18/2023] Open
Abstract
The outbreak of the novel coronavirus severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) respiratory disease, led to a global pandemic with high morbidity and mortality. Despite frenzied efforts in therapeutic development, there are currently no effective drugs for treatment, nor are there vaccines for its prevention. Drug repurposing, representing as an effective drug discovery strategy from existing drugs, is one of the most practical treatment options against the outbreak. In this study, we present a novel strategy for in silico molecular modeling screening for potential drugs that may interact with multiple main proteins of SARS-CoV-2. Targeting multiple viral proteins is a novel drug discovery concept in that it enables the potential drugs to act on different stages of the virus' life cycle, thereby potentially maximizing the drug potency. We screened 2631 US Food and Drug Administration (FDA)-approved small molecules against 4 key proteins of SARS-CoV-2 that are known as attractive targets for antiviral drug development. In total, we identified 29 drugs that could actively interact with 2 or more target proteins, with 5 drugs (avapritinib, bictegravir, ziprasidone, capmatinib, and pexidartinib) being common candidates for all 4 key host proteins and 3 of them possessing the desirable molecular properties. By overlaying docked positions of drug candidates onto individual host proteins, it has been further confirmed that the binding site conformations are conserved. The drugs identified in our screening provide potential guidance for experimental confirmation, such as in vitro molecular assays and in vivo animal testing, as well as incorporation into ongoing clinical studies.
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Affiliation(s)
- Hualou Liang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Liang Zhao
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Xiajing Gong
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Meng Hu
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Hongbin Wang
- Center for Biomedical Informatics, College of Medicine, Texas A&M University Health Science Center, Houston, TX, USA
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40
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Wang R, Stephen P, Tao Y, Zhang W, Lin SX. Human endeavor for anti-SARS-CoV-2 pharmacotherapy: A major strategy to fight the pandemic. Biomed Pharmacother 2021; 137:111232. [PMID: 33486202 PMCID: PMC7834004 DOI: 10.1016/j.biopha.2021.111232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/22/2022] Open
Abstract
The global spread of COVID-19 constitutes the most dangerous pandemic to emerge during the last one hundred years. About seventy-nine million infections and more than 1.7 million death have been reported to date, along with destruction of the global economy. With the uncertainty evolved by alarming level of genome mutations, coupled with likelihood of generating only a short lived immune response by the vaccine injections, the identification of antiviral drugs for direct therapy is the need of the hour. Strategies to inhibit virus infection and replication focus on targets such as the spike protein and non-structural proteins including the highly conserved RNA-dependent-RNA-polymerase, nucleotidyl-transferases, main protease and papain-like proteases. There is also an indirect option to target the host cell recognition systems such as angiotensin-converting enzyme 2 (ACE2), transmembrane protease, serine 2, host cell expressed CD147, and the host furin. A drug search strategy consensus in tandem with analysis of currently available information is extremely important for the rapid identification of anti-viral. An unprecedented display of cooperation among the scientific community regarding SARS-CoV-2 research has resulted in the accumulation of an enormous amount of literature that requires curation. Drug repurposing and drug combinations have drawn tremendous attention for rapid therapeutic application, while high throughput screening and virtual searches support de novo drug identification. Here, we examine how certain approved drugs targeting different viruses can play a role in combating this new virus and analyze how they demonstrate efficacy under clinical assessment. Suggestions on repurposing and de novo strategies are proposed to facilitate the fight against the COVID-19 pandemic.
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Affiliation(s)
- Ruixuan Wang
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Preyesh Stephen
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Yi Tao
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Wenfa Zhang
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada
| | - Sheng-Xiang Lin
- Axe Molecular Endocrinology and Nephrology, CHU Research Center and Laval University, Quebec City, Quebec, G1V 4G2, Canada.
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Pirzada RH, Haseeb M, Batool M, Kim M, Choi S. Remdesivir and Ledipasvir among the FDA-Approved Antiviral Drugs Have Potential to Inhibit SARS-CoV-2 Replication. Cells 2021; 10:1052. [PMID: 33946869 PMCID: PMC8146643 DOI: 10.3390/cells10051052] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
The rapid spread of the virus, the surge in the number of deaths, and the unavailability of specific SARS-CoV-2 drugs thus far necessitate the identification of drugs with anti-COVID-19 activity. SARS-CoV-2 enters the host cell and assembles a multisubunit RNA-dependent RNA polymerase (RdRp) complex of viral nonstructural proteins that plays a substantial role in the transcription and replication of the viral genome. Therefore, RdRp is among the most suitable targets in RNA viruses. Our aim was to investigate the FDA approved antiviral drugs having potential to inhibit the viral replication. The methodology adopted was virtual screening and docking of FDA-approved antiviral drugs into the RdRp protein. Top hits were selected and subjected to molecular dynamics simulations to understand the dynamics of RdRp in complex with these drugs. The antiviral activity of the drugs against SARS-CoV-2 was assessed in Vero E6 cells. Notably, both remdesivir (half-maximal effective concentration (EC50) 6.6 μM, 50% cytotoxicity concentration (CC50) > 100 µM, selectivity index (SI) = 15) and ledipasvir (EC50 34.6 μM, CC50 > 100 µM, SI > 2.9) exerted antiviral action. This study highlights the use of direct-acting antiviral drugs, alone or in combination, for better treatments of COVID-19.
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Affiliation(s)
- Rameez Hassan Pirzada
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
- S&K Therapeutics, Woncheon Hall 135, Ajou University, Suwon 16499, Korea
| | - MoonSuk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (R.H.P.); (M.H.); (M.B.); (M.K.)
- S&K Therapeutics, Woncheon Hall 135, Ajou University, Suwon 16499, Korea
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Kumar D T, Shaikh N, Kumar S U, Doss C GP, Zayed H. Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Front Mol Biosci 2021; 8:645216. [PMID: 33898520 PMCID: PMC8062963 DOI: 10.3389/fmolb.2021.645216] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 01/18/2023] Open
Abstract
The number of confirmed COVID-19 cases is rapidly increasing with no direct treatment for the disease. Few repurposed drugs, such as Remdesivir, Chloroquine, Hydroxychloroquine, Lopinavir, and Ritonavir, are being tested against SARS-CoV-2. Remdesivir is the drug of choice for Ebola virus disease and has been authorized for emergency use. This drug acts against SARS-CoV-2 by inhibiting the RNA-dependent-RNA-polymerase (RdRp) of SARS-CoV-2. RdRp of viruses is prone to mutations that confer drug resistance. A recent study by Pachetti et al. in 2020 identified the P323L mutation in the RdRp protein of SARS-CoV-2. In this study, we aimed to determine the potency of lead compounds similar to Remdesivir, which can be used as an alternative when variants of SARS-CoV-2 develop resistance due to RdRp mutations. The initial screening yielded 704 compounds that were 90% similar to the control drug, Remdesivir. On further evaluation through drugability and antiviral inhibition percentage analyses, we shortlisted 32 and seven compounds, respectively. These seven compounds were further analyzed for their molecular interactions, which revealed that all seven compounds interacted with RdRp with higher affinity than Remdesivir under native conditions. However, three compounds failed to interact with the mutant protein with higher affinity than Remdesivir. Dynamic cross-correlation matrix (DCCM) and vector field collective motions analyses were performed to identify the precise movements of docked complexes' residues. Furthermore, the compound SCHEMBL20144212 showed a high affinity for native and mutant proteins and might provide an alternative against SARS-CoV-2 variants that might confer resistance to Remdesivir. Further validations by in vitro and in vivo studies are needed to confirm the efficacy of our lead compounds for their inhibition against SARS-CoV-2.
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Affiliation(s)
- Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Nishaat Shaikh
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Udhaya Kumar S
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - George Priya Doss C
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
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Saakre M, Mathew D, Ravisankar V. Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:21. [PMID: 33782651 PMCID: PMC7989718 DOI: 10.1186/s43088-021-00107-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
Background The world pandemic COVID-19 caused by SARS-CoV-2 is currently claiming thousands of lives. Flavonoids abundantly present in the fruits and vegetables, especially quercetin, are shown to have antiviral activities. Main text This paper reviews the capability of the plant flavonoid quercetin to fight the novel coronavirus and the possibility for drug development based on this. The mode of action explaining the known pathways through which this molecule succeeds in the antiviral activity, action of quercetin on SARS-CoV-2 main protease 3CLpro, antiviral activities of its derivatives on human viruses, effect of combination of zinc co-factor along with quercetin in the COVID-19 treatment, and the regulation of miRNA genes involved in the viral pathogenesis are discussed. Proof for this concept is provided following the virtual screening using ten key enzymes of SARS-CoV-2 and assessing their interactions. Active residues in the 3D structures have been predicted using CASTp and were docked against quercetin. Key proteins 3CLpro, spike glycoprotein/ human ACE2-BOAT1 complex, RNA-dependent RNA polymerase, main peptidase, spike glycoprotein, RNA replicase, RNA binding protein, papain-like protease, SARS papain-like protease/ deubiquitinase, and complex of main peptidase with an additional Ala at the N-terminus of each protomer, have shown the binding energies ranging between − 6.71 and − 3.37 kcal/ Mol, showing that quercetin is a potential drug candidate inhibiting multiple SARS-CoV-2 enzymes. Conclusion The antiviral properties of flavonoid and the molecular mechanisms involved are reviewed. Further, proof for this concept is given by docking of key proteins from SARS-CoV-2 with quercetin. Graphical abstract ![]()
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Affiliation(s)
- Manjesh Saakre
- National Institute for Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi, 110 012 India
| | - Deepu Mathew
- Bioinformatics Centre, Kerala Agricultural University, Thrissur, 680 656 India
| | - V Ravisankar
- Bioinformatics Centre, Kerala Agricultural University, Thrissur, 680 656 India
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Xie Y, Guo X, Hu T, Wei D, Ma X, Wu J, Huang B, Shen J. Significant Inhibition of Porcine Epidemic Diarrhea Virus In Vitro by Remdesivir, Its Parent Nucleoside and β-D-N 4-hydroxycytidine. Virol Sin 2021; 36:997-1005. [PMID: 33751399 PMCID: PMC7983969 DOI: 10.1007/s12250-021-00362-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/22/2021] [Indexed: 12/03/2022] Open
Abstract
Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) is widespread in the world. In recent years, the increased virulence of the virus due to viral variations, has caused great economic losses to the pig industry in many countries. It is always worthy to find effective therapeutic methods for PED. As an important class of antivirals, nucleoside drugs which target viral polymerases have been applied in treating human viral infections for half a century. Herein, we evaluated the anti-PEDV potential of three broad-spectrum antiviral nucleoside analogs, remdesivir (RDV), its parent nucleoside (RDV-N) and β-d-N4-hydroxycytidine (NHC). Among them, RDV-N was the most active agent in Vero E6 cells with EC50 of 0.31 μmol/L, and more potent than RDV (EC50 = 0.74 μmol/L) and NHC (EC50 = 1.17 μmol/L). The activity of RDV-N was further confirmed using an indirect immuno-fluorescence assay. Moreover, RDV-N exhibited a good safety profile in cells and in mice. The high sequence similarity of the polymerase functional domains of PEDV with other five porcine coronaviruses indicated a broader antiviral spectrum for the three compounds. Generally, RDV-N is a promising broad-spectrum antiviral nucleoside, and it would be worthy to make some structural modifications to increase its oral bioavailability.
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Affiliation(s)
- Yuanchao Xie
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiaozhen Guo
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China
| | - Tianwen Hu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Daibao Wei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China
| | - Jiaqiang Wu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, 250023, China.
| | - Jingshan Shen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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45
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Koulgi S, Jani V, V N MU, Sonavane U, Joshi R. Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2021; 40:7230-7244. [PMID: 33682633 DOI: 10.1080/07391102.2021.1894985] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA dependent RNA polymerase (RdRP) from positive-stranded RNA viruses has always been a hot target for designing of new drugs. Major class of drugs that are targeted against RdRP are nucleotide analogues. Extensive docking and molecular dynamics study describing the binding of natural nucleotides (NTPs) and its analogues leading to significant structural variation in the RdRP has been presented here. RdRP simulations in its apo, NTP-bound, and analogue-bound form have been performed. Nucleotide analogues included in this study were, favipiravir, galidesivir, lamivudine, ribavirin, remdesivir and sofosbuvir. The conformational flexibility of the RdRP molecule has been explored using principal component (PCA) and Markov state modeling (MSM) analysis. PCA inferred the presence of correlated motions among the conserved motifs of RdRP. Inter-domain distances between the finger and thumb subdomain flanking the nascent RNA template entry site sampled open and closed conformations. The ligand and template binding motifs F and G showed negatively correlated motions. K551, R553, and R555, a part of motif F appear to form strong interactions with the ligand molecules. R836, a primer binding residue was observed to strongly bind to the analogues. MSM analysis helped to extract statistically distinct conformations explored by the RdRP. Ensemble docking of the ligands on the Markov states also suggested the involvement of the above residues in ligand interactions. Markov states obtained clearly demarcated the open/closed conformations of the template entry site. These observations on residues from the conserved motifs involved in binding to the ligands may provide an insight into designing new inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Vinod Jani
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Mallikarjunachari Uppuladinne V N
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
| | - Rajendra Joshi
- High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchawati, Pashan, Pune, India
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46
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Villa TG, Abril AG, Sánchez S, de Miguel T, Sánchez-Pérez A. Animal and human RNA viruses: genetic variability and ability to overcome vaccines. Arch Microbiol 2021; 203:443-464. [PMID: 32989475 PMCID: PMC7521576 DOI: 10.1007/s00203-020-02040-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/29/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023]
Abstract
RNA viruses, in general, exhibit high mutation rates; this is mainly due to the low fidelity displayed by the RNA-dependent polymerases required for their replication that lack the proofreading machinery to correct misincorporated nucleotides and produce high mutation rates. This lack of replication fidelity, together with the fact that RNA viruses can undergo spontaneous mutations, results in genetic variants displaying different viral morphogenesis, as well as variation on their surface glycoproteins that affect viral antigenicity. This diverse viral population, routinely containing a variety of mutants, is known as a viral 'quasispecies'. The mutability of their virions allows for fast evolution of RNA viruses that develop antiviral resistance and overcome vaccines much more rapidly than DNA viruses. This also translates into the fact that pathogenic RNA viruses, that cause many diseases and deaths in humans, represent the major viral group involved in zoonotic disease transmission, and are responsible for worldwide pandemics.
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Affiliation(s)
- T G Villa
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain.
| | - Ana G Abril
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - S Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - T de Miguel
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - A Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
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47
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Woodby B, Arnold MM, Valacchi G. SARS-CoV-2 infection, COVID-19 pathogenesis, and exposure to air pollution: What is the connection? Ann N Y Acad Sci 2021; 1486:15-38. [PMID: 33022781 PMCID: PMC7675684 DOI: 10.1111/nyas.14512] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022]
Abstract
Exposure to air pollutants has been previously associated with respiratory viral infections, including influenza, measles, mumps, rhinovirus, and respiratory syncytial virus. Epidemiological studies have also suggested that air pollution exposure is associated with increased cases of SARS-CoV-2 infection and COVID-19-associated mortality, although the molecular mechanisms by which pollutant exposure affects viral infection and pathogenesis of COVID-19 remain unknown. In this review, we suggest potential molecular mechanisms that could account for this association. We have focused on the potential effect of exposure to nitrogen dioxide (NO2 ), ozone (O3 ), and particulate matter (PM) since there are studies investigating how exposure to these pollutants affects the life cycle of other viruses. We have concluded that pollutant exposure may affect different stages of the viral life cycle, including inhibition of mucociliary clearance, alteration of viral receptors and proteases required for entry, changes to antiviral interferon production and viral replication, changes in viral assembly mediated by autophagy, prevention of uptake by macrophages, and promotion of viral spread by increasing epithelial permeability. We believe that exposure to pollutants skews adaptive immune responses toward bacterial/allergic immune responses, as opposed to antiviral responses. Exposure to air pollutants could also predispose exposed populations toward developing COIVD-19-associated immunopathology, enhancing virus-induced tissue inflammation and damage.
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Affiliation(s)
- Brittany Woodby
- Animal Science DepartmentPlants for Human Health Institute, N.C. Research Campus, North Carolina State UniversityKannapolisNorth Carolina
| | - Michelle M. Arnold
- Department of Microbiology and ImmunologyCenter for Molecular and Tumor VirologyLouisiana State University Health Sciences CenterShreveportLouisiana
| | - Giuseppe Valacchi
- Animal Science DepartmentPlants for Human Health Institute, N.C. Research Campus, North Carolina State UniversityKannapolisNorth Carolina
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
- Department of Food and NutritionKyung Hee UniversitySeoulSouth Korea
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48
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Eweas AF, Alhossary AA, Abdel-Moneim AS. Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2. Front Microbiol 2021; 11:592908. [PMID: 33746908 PMCID: PMC7976659 DOI: 10.3389/fmicb.2020.592908] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/24/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 is a newly emerged coronavirus that causes a respiratory disease with variable severity and fatal consequences. It was first reported in Wuhan and subsequently caused a global pandemic. The viral spike protein binds with the ACE-2 cell surface receptor for entry, while TMPRSS2 triggers its membrane fusion. In addition, RNA dependent RNA polymerase (RdRp), 3'-5' exoribonuclease (nsp14), viral proteases, N, and M proteins are important in different stages of viral replication. Accordingly, they are attractive targets for different antiviral therapeutic agents. Although many antiviral agents have been used in different clinical trials and included in different treatment protocols, the mode of action against SARS-CoV-2 is still not fully understood. Different potential repurposed drugs, including, chloroquine, hydroxychloroquine, ivermectin, remdesivir, and favipiravir, were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target proteins, including spike and membrane proteins, RdRp, nucleoproteins, viral proteases, and nsp14, was performed. Moreover, the binding affinities of the human ACE-2 receptor and TMPRSS2 to the different drugs were evaluated. Molecular dynamics simulation and MM-PBSA calculation were also conducted. Ivermectin and remdesivir were found to be the most promising drugs. Our results suggest that both these drugs utilize different mechanisms at the entry and post-entry stages and could be considered potential inhibitors of SARS-CoV-2 replication.
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Affiliation(s)
- Ahmad F. Eweas
- Department of Pharmaceutical and Medicinal Chemistry, National Research Centre, Cairo, Egypt
- Department of Science, University of Technology and Applied Sciences Rustaq, Rustaq, Oman
| | - Amr A. Alhossary
- Rehabilitation Research Institute of Singapore, Nanyang Technological University, Singapore, Singapore
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Taif, Saudi Arabia
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49
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Wu Y, Li Z, Zhao YS, Huang YY, Jiang MY, Luo HB. Therapeutic targets and potential agents for the treatment of COVID-19. Med Res Rev 2021; 41:1775-1797. [PMID: 33393116 DOI: 10.1002/med.21776] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 01/18/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has become a global crisis. As of November 9, COVID-19 has already spread to more than 190 countries with 50,000,000 infections and 1,250,000 deaths. Effective therapeutics and drugs are in high demand. The structure of SARS-CoV-2 is highly conserved with those of SARS-CoV and Middle East respiratory syndrome-CoV. Enzymes, including RdRp, Mpro /3CLpro , and PLpro , which play important roles in viral transcription and replication, have been regarded as key targets for therapies against coronaviruses, including SARS-CoV-2. The identification of readily available drugs for repositioning in COVID-19 therapy is a relatively rapid approach for clinical treatment, and a series of approved or candidate drugs have been proven to be efficient against COVID-19 in preclinical or clinical studies. This review summarizes recent progress in the development of drugs against SARS-CoV-2 and the targets involved.
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Affiliation(s)
- Yinuo Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yun-Song Zhao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yi-You Huang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mei-Yan Jiang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, China
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50
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Singh SP, Pritam M, Pandey B, Yadav TP. Microstructure, pathophysiology, and potential therapeutics of COVID-19: A comprehensive review. J Med Virol 2021; 93:275-299. [PMID: 32617987 PMCID: PMC7361355 DOI: 10.1002/jmv.26254] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/14/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
There have been over seven million cases and almost 413 372 deaths globally due to the novel coronavirus (2019-nCoV) associated disease COVID-19, as of 11 June 2020. Phylogenetic analysis suggests that there is a common source for these infections. The overall sequence similarities between the spike protein of 2019-nCoV and that of SARS-CoV are known to be around 76% to 78% and 73% to 76% for the whole protein and receptor-binding domain (RBD), respectively. Thus, they have the potential to serve as the drug and/or vaccine candidate. However, the individual response against 2019-nCoV differs due to genetic variations in the human population. Understanding the variations in angiotensin-converting enzyme 2 (ACE2) and human leukocyte antigen (HLA) that may affect the severity of 2019-nCoV infection could help in identifying individuals at a higher risk from the COVID-19. A number of potential drugs/vaccines as well as antibody/cytokine-based therapeutics are in various developmental stages of preclinical/clinical trials against SARS-CoV, MERS-CoV, and 2019-nCoV with substantial cross-reactivity, and may be used against COVID-19. For diagnosis, the reverse-transcription polymerase chain reaction is the gold standard test for initial diagnosis of COVID-19. A kit based on serological tests are also recommended for investigating the spread of COVID-19 but this is challenging due to the antibodies cross-reactivity. This review comprehensively summarizes the recent reports available regarding the host-pathogen interaction, morphological and genomic structure of the virus, and the diagnostic techniques as well as the available potential therapeutics against COVID-19.
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Affiliation(s)
| | - Manisha Pritam
- Amity Institute of BiotechnologyAmity University Uttar PradeshLucknowIndia
| | - Brijesh Pandey
- Department of BiotechnologyMahatma Gandhi Central UniversityMotihariIndia
| | - Thakur Prasad Yadav
- Department of Physics, Institute of ScienceBanaras Hindu UniversityVaranasiIndia
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