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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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52
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Trivedi P, Abbas A, Lehmann C, Rupasinghe HPV. Antiviral and Anti-Inflammatory Plant-Derived Bioactive Compounds and Their Potential Use in the Treatment of COVID-19-Related Pathologies. J Xenobiot 2022; 12:289-306. [PMID: 36278757 PMCID: PMC9589987 DOI: 10.3390/jox12040020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
The highly contagious coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic and public health emergency as it has taken the lives of over 5.7 million in more than 180 different countries. This disease is characterized by respiratory tract symptoms, such as dry cough and shortness of breath, as well as other symptoms, including fever, chills, and fatigue. COVID-19 is also characterized by the excessive release of cytokines causing inflammatory injury to the lungs and other organs. It is advised to undergo precautionary measures, such as vaccination, social distancing, use of masks, hygiene, and a healthy diet. This review is aimed at summarizing the pathophysiology of COVID-19 and potential biologically active compounds (bioactive) found in plants and plant food. We conclude that many plant food bioactive compounds exhibit antiviral and anti-inflammatory properties and support in attenuating organ damage due to reduced cytokine release and improving the recovery process from COVID-19 infection.
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Affiliation(s)
- Purvi Trivedi
- Department of Anesthesia, Pain Management and Perioperative Medicine, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 3E2, Canada
| | - Amna Abbas
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Christian Lehmann
- Department of Anesthesia, Pain Management and Perioperative Medicine, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 3E2, Canada
| | - H. P. Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 3E2, Canada
- Correspondence:
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53
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Prameswari HS, Putra ICS, Raffaello WM, Nathaniel M, Suhendro AS, Khalid AF, Pranata R. Managing Covid-19 in patients with heart failure: current status and future prospects. Expert Rev Cardiovasc Ther 2022; 20:807-828. [PMID: 36185009 DOI: 10.1080/14779072.2022.2132230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
INTRODUCTION COVID-19 may contribute to decompensation of previously stable chronic HF or cause a de-novo heart failure, which may come from the hyperinflammatory response and subsequent increase in metabolic demand. AREAS COVERED Two independent investigators searched MEDLINE (via PubMed), Europe PMC, and ScienceDirect databases with the following search terms: COVID-19, heart failure, COVID-19 drugs, heart failure drugs, and device therapy. All of the included full-text articles were rigorously evaluated by both authors in case there was disagreement about whether research should be included or not. In total, 157 studies were included and underwent extensive reading by the authors. EXPERT OPINION The World Health Organization (WHO) and the National Institute of Health (NIH) have published COVID-19 drug recommendations, although recommendations for HF-specific drug choices in COVID-19 are still lacking. We hope that this review can answer the void of comprehensive research data regarding the management options of HF in the COVID-19 condition so that clinicians can at least choose a more beneficial therapy or avoid combination therapies that have a high burden of side effects on HF; thus, morbidity and mortality in COVID-19 patients with HF may be reduced.
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Affiliation(s)
- Hawani Sasmaya Prameswari
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Iwan Cahyo Santosa Putra
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | | | - Michael Nathaniel
- School of Medicine and Health Sciences Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Adrian Sebastian Suhendro
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Achmad Fitrah Khalid
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Raymond Pranata
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
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54
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Ozdemir ES, Ranganathan SV, Nussinov R. How has artificial intelligence impacted COVID-19 drug repurposing and what lessons have we learned? Expert Opin Drug Discov 2022; 17:1061-1065. [PMID: 36154343 DOI: 10.1080/17460441.2022.2128333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- E Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Srivathsan V Ranganathan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Ruth Nussinov
- Cancer Innovation Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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55
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Yuan B, Peng Q, Cheng J, Wang M, Zhong J, Qi J, Gao GF, Shi Y. Structure of the Ebola virus polymerase complex. Nature 2022; 610:394-401. [PMID: 36171293 PMCID: PMC9517992 DOI: 10.1038/s41586-022-05271-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022]
Abstract
Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal antibodies have been approved to treat the Ebola virus disease1,2, there are no approved broadly reactive drugs to control diverse filovirus infection. Filovirus has a large polymerase (L) protein and the cofactor viral protein 35 (VP35), which constitute the basic functional unit responsible for virus genome RNA synthesis3. Owing to its conservation, the L-VP35 polymerase complex is a promising target for broadly reactive antiviral drugs. Here we determined the structure of Ebola virus L protein in complex with tetrameric VP35 using cryo-electron microscopy (state 1). Structural analysis revealed that Ebola virus L possesses a filovirus-specific insertion element that is essential for RNA synthesis, and that VP35 interacts extensively with the N-terminal region of L by three protomers of the VP35 tetramer. Notably, we captured the complex structure in a second conformation with the unambiguous priming loop and supporting helix away from polymerase active site (state 2). Moreover, we demonstrated that the century-old drug suramin could inhibit the activity of the Ebola virus polymerase in an enzymatic assay. The structure of the L-VP35-suramin complex reveals that suramin can bind at the highly conserved NTP entry channel to prevent substrates from entering the active site. These findings reveal the mechanism of Ebola virus replication and may guide the development of more powerful anti-filovirus drugs.
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Affiliation(s)
- Bin Yuan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinlong Cheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jin Zhong
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
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56
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Zang Y, Su M, Wang Q, Cheng X, Zhang W, Zhao Y, Chen T, Jiang Y, Shen Q, Du J, Tan Q, Wang P, Gao L, Jin Z, Zhang M, Li C, Zhu Y, Feng B, Tang B, Xie H, Wang MW, Zheng M, Pan X, Yang H, Xu Y, Wu B, Zhang L, Rao Z, Yang X, Jiang H, Xiao G, Zhao Q, Li J. High-throughput screening of SARS-CoV-2 main and papain-like protease inhibitors. Protein Cell 2022; 14:17-27. [PMID: 36726755 PMCID: PMC9871955 DOI: 10.1093/procel/pwac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
The global COVID-19 coronavirus pandemic has infected over 109 million people, leading to over 2 million deaths up to date and still lacking of effective drugs for patient treatment. Here, we screened about 1.8 million small molecules against the main protease (Mpro) and papain like protease (PLpro), two major proteases in severe acute respiratory syndrome-coronavirus 2 genome, and identified 1851Mpro inhibitors and 205 PLpro inhibitors with low nmol/l activity of the best hits. Among these inhibitors, eight small molecules showed dual inhibition effects on both Mpro and PLpro, exhibiting potential as better candidates for COVID-19 treatment. The best inhibitors of each protease were tested in antiviral assay, with over 40% of Mpro inhibitors and over 20% of PLpro inhibitors showing high potency in viral inhibition with low cytotoxicity. The X-ray crystal structure of SARS-CoV-2 Mpro in complex with its potent inhibitor 4a was determined at 1.8 Å resolution. Together with docking assays, our results provide a comprehensive resource for future research on anti-SARS-CoV-2 drug development.
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Affiliation(s)
| | | | | | | | | | | | - Tong Chen
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingyan Jiang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiang Shen
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Juan Du
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Qiuxiang Tan
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peipei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lixin Gao
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhenming Jin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengmeng Zhang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cong Li
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ya Zhu
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bo Feng
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bixi Tang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Han Xie
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yechun Xu
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beili Wu
- State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China,University of Chinese Academy of Sciences, Beijing 100049, China,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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57
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Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication-Transcription Complex of SARS-CoV-2. Biochemistry 2022; 61:1966-1973. [PMID: 36044776 PMCID: PMC9469760 DOI: 10.1021/acs.biochem.2c00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/18/2022] [Indexed: 01/18/2023]
Abstract
Remdesivir is an adenosine analogue that has a cyano substitution in the C1' position of the ribosyl moiety and a modified base structure to stabilize the linkage of the base to the C1' atom with its strong electron-withdrawing cyano group. Within the replication-transcription complex (RTC) of SARS-CoV-2, the RNA-dependent RNA polymerase nsp12 selects remdesivir monophosphate (RMP) over adenosine monophosphate (AMP) for nucleotide incorporation but noticeably slows primer extension after the added RMP of the RNA duplex product is translocated by three base pairs. Cryo-EM structures have been determined for the RTC with RMP at the nucleotide-insertion (i) site or at the i + 1, i + 2, or i + 3 sites after product translocation to provide a structural basis for a delayed-inhibition mechanism by remdesivir. In this study, we applied molecular dynamics (MD) simulations to extend the resolution of structures to the measurable maximum that is intrinsically limited by MD properties of these complexes. Our MD simulations provide (i) a structural basis for nucleotide selectivity of the incoming substrates of remdesivir triphosphate over adenosine triphosphate and of ribonucleotide over deoxyribonucleotide, (ii) new detailed information on hydrogen atoms involved in H-bonding interactions between the enzyme and remdesivir, and (iii) direct information on the catalytically active complex that is not easily captured by experimental methods. Our improved resolution of interatomic interactions at the nucleotide-binding pocket between remedesivir and the polymerase could help to design a new class of anti-SARS-CoV-2 inhibitors.
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Affiliation(s)
- Jimin Wang
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Yuanjun Shi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Krystle Reiss
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Federica Maschietto
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
| | - Elias Lolis
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06520-8066, United States
| | - William H. Konigsberg
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - George P. Lisi
- Department
of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8499, United States
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58
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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59
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Kayabolen A, Akcan U, Özturan D, Ulbegi‐Polat H, Sahin GN, Pinarbasi‐Degirmenci N, Bayraktar C, Soyler G, Sarayloo E, Nurtop E, Ozer B, Guney‐Esken G, Barlas T, Yildirim IS, Dogan O, Karahuseyinoglu S, Lack NA, Kaya M, Albayrak C, Can F, Solaroglu I, Bagci‐Onder T. Protein Scaffold-Based Multimerization of Soluble ACE2 Efficiently Blocks SARS-CoV-2 Infection In Vitro and In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201294. [PMID: 35896894 PMCID: PMC9353362 DOI: 10.1002/advs.202201294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Soluble ACE2 (sACE2) decoys are promising agents to inhibit SARS-CoV-2, as their efficiency is unlikely to be affected by escape mutations. However, their success is limited by their relatively poor potency. To address this challenge, multimeric sACE2 consisting of SunTag or MoonTag systems is developed. These systems are extremely effective in neutralizing SARS-CoV-2 in pseudoviral systems and in clinical isolates, perform better than the dimeric or trimeric sACE2, and exhibit greater than 100-fold neutralization efficiency, compared to monomeric sACE2. SunTag or MoonTag fused to a more potent sACE2 (v1) achieves a sub-nanomolar IC50 , comparable with clinical monoclonal antibodies. Pseudoviruses bearing mutations for variants of concern, including delta and omicron, are also neutralized efficiently with multimeric sACE2. Finally, therapeutic treatment of sACE2(v1)-MoonTag provides protection against SARS-CoV-2 infection in an in vivo mouse model. Therefore, highly potent multimeric sACE2 may offer a promising treatment approach against SARS-CoV-2 infections.
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Affiliation(s)
- Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Ugur Akcan
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Doğancan Özturan
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Hivda Ulbegi‐Polat
- Genetic Engineering and Biotechnology InstituteTUBITAK Marmara Research CenterKocaeli41470Turkey
| | - Gizem Nur Sahin
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | | | - Canan Bayraktar
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Gizem Soyler
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Ehsan Sarayloo
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of BiotechnologyBeykoz Institute of Life Sciences and Biotechnology (BILSAB)Bezmialem Vakif UniversityIstanbul34820Turkey
| | - Elif Nurtop
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Berna Ozer
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Gulen Guney‐Esken
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Tayfun Barlas
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Ismail Selim Yildirim
- Genetic Engineering and Biotechnology InstituteTUBITAK Marmara Research CenterKocaeli41470Turkey
| | - Ozlem Dogan
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
- Koç University School of MedicineDepartment of Medical MicrobiologyIstanbul34010Turkey
| | - Sercin Karahuseyinoglu
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Koç University School of Medicine, Department of Histology and EmbryologyIstanbul34450Türkiye
| | - Nathan A. Lack
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Vancouver Prostate CentreUniversity of British ColumbiaVancouverBC V6H 3Z6Canada
| | - Mehmet Kaya
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Cem Albayrak
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of BiotechnologyBeykoz Institute of Life Sciences and Biotechnology (BILSAB)Bezmialem Vakif UniversityIstanbul34820Turkey
| | - Fusun Can
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
- Koç University School of MedicineDepartment of Medical MicrobiologyIstanbul34010Turkey
| | - Ihsan Solaroglu
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of Basic SciencesLoma Linda UniversityLoma LindaCA92354USA
| | - Tugba Bagci‐Onder
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
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60
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Yi J, Miao J, Zuo Q, Owusu F, Dong Q, Lin P, Wang Q, Gao R, Kong X, Yang L. COVID-19 pandemic: A multidisciplinary perspective on the pathogenesis of a novel coronavirus from infection, immunity and pathological responses. Front Immunol 2022; 13:978619. [PMID: 36091053 PMCID: PMC9459044 DOI: 10.3389/fimmu.2022.978619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus2 (SARS-CoV-2), has spread to more than 200 countries and regions, having a huge impact on human health, hygiene, and economic activities. The epidemiological and clinical phenotypes of COVID-19 have increased since the onset of the epidemic era, and studies into its pathogenic mechanisms have played an essential role in clinical treatment, drug development, and prognosis prevention. This paper reviews the research progress on the pathogenesis of the novel coronavirus (SARS-CoV-2), focusing on the pathogenic characteristics, loci of action, and pathogenic mechanisms leading to immune response malfunction of SARS-CoV-2, as well as summarizing the pathological damage and pathological manifestations it causes. This will update researchers on the latest SARS-CoV-2 research and provide directions for future therapeutic drug development.
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Affiliation(s)
- Jia Yi
- College of Traditional Chinese medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jiameng Miao
- College of Traditional Chinese medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qingwei Zuo
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Felix Owusu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qiutong Dong
- College of Traditional Chinese medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Peizhe Lin
- College of Traditional Chinese medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qilong Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rui Gao
- Institute of Clinical Pharmacology of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xianbin Kong
- College of Traditional Chinese medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Long Yang
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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61
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Prediction of Potential Commercially Available Inhibitors against SARS-CoV-2 by Multi-Task Deep Learning Model. Biomolecules 2022; 12:biom12081156. [PMID: 36009050 PMCID: PMC9405964 DOI: 10.3390/biom12081156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms, or even death for those infected. Fortunately, many efforts have been made and several effective drugs have been identified. The rapidly increasing amount of data is of great help for training an effective and specific deep learning model. In this study, we propose a multi-task deep learning model for the purpose of screening commercially available and effective inhibitors against SARS-CoV-2. First, we pretrained a model on several heterogenous protein-ligand interaction datasets. The model achieved competitive results on some benchmark datasets. Next, a coronavirus-specific dataset was collected and used to fine-tune the model. Then, the fine-tuned model was used to select commercially available drugs against SARS-CoV-2 protein targets. Overall, twenty compounds were listed as potential inhibitors. We further explored the model interpretability and exhibited the predicted important binding sites. Based on this prediction, molecular docking was also performed to visualize the binding modes of the selected inhibitors.
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62
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Hu F, Jiang J, Yin P. Prediction of Potential Commercially Available Inhibitors against SARS-CoV-2 by Multi-Task Deep Learning Model. Biomolecules 2022. [PMID: 36009050 DOI: 10.48550/arxiv.2003.00728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms, or even death for those infected. Fortunately, many efforts have been made and several effective drugs have been identified. The rapidly increasing amount of data is of great help for training an effective and specific deep learning model. In this study, we propose a multi-task deep learning model for the purpose of screening commercially available and effective inhibitors against SARS-CoV-2. First, we pretrained a model on several heterogenous protein-ligand interaction datasets. The model achieved competitive results on some benchmark datasets. Next, a coronavirus-specific dataset was collected and used to fine-tune the model. Then, the fine-tuned model was used to select commercially available drugs against SARS-CoV-2 protein targets. Overall, twenty compounds were listed as potential inhibitors. We further explored the model interpretability and exhibited the predicted important binding sites. Based on this prediction, molecular docking was also performed to visualize the binding modes of the selected inhibitors.
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Affiliation(s)
- Fan Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiaxin Jiang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Peng Yin
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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63
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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64
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Ouyang J, Zaongo SD, Harypursat V, Li X, Routy JP, Chen Y. SARS-CoV-2 pre-exposure prophylaxis: A potential COVID-19 preventive strategy for high-risk populations, including healthcare workers, immunodeficient individuals, and poor vaccine responders. Front Public Health 2022; 10:945448. [PMID: 36003629 PMCID: PMC9393547 DOI: 10.3389/fpubh.2022.945448] [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: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023] Open
Abstract
The unprecedented worldwide spread of SARS-CoV-2 has imposed severe challenges on global health care systems. The roll-out and widespread administration of COVID-19 vaccines has been deemed a major milestone in the race to restrict the severity of the infection. Vaccines have as yet not entirely suppressed the relentless progression of the pandemic, due mainly to the emergence of new virus variants, and also secondary to the waning of protective antibody titers over time. Encouragingly, an increasing number of antiviral drugs, such as remdesivir and the newly developed drug combination, Paxlovid® (nirmatrelvir/ritonavir), as well as molnupiravir, have shown significant benefits for COVID-19 patient outcomes. Pre-exposure prophylaxis (PrEP) has been proven to be an effective preventive strategy in high-risk uninfected people exposed to HIV. Building on knowledge from what is already known about the use of PrEP for HIV disease, and from recently gleaned knowledge of antivirals used against COVID-19, we propose that SARS-CoV-2 PrEP, using specific antiviral and adjuvant drugs against SARS-CoV-2, may represent a novel preventive strategy for high-risk populations, including healthcare workers, immunodeficient individuals, and poor vaccine responders. Herein, we critically review the risk factors for severe COVID-19 and discuss PrEP strategies against SARS-CoV-2. In addition, we outline details of candidate anti-SARS-CoV-2 PrEP drugs, thus creating a framework with respect to the development of alternative and/or complementary strategies to prevent COVID-19, and contributing to the global armamentarium that has been developed to limit SARS-CoV-2 infection, severity, and transmission.
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Affiliation(s)
- Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Silvere D. Zaongo
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Xiaofang Li
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada
- Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC, Canada
- Division of Hematology, McGill University Health Centre, Montréal, QC, Canada
| | - Yaokai Chen
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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Mukherjee MD, Kumar A, Solanki PR, Verma D, Yadav AK, Chaudhary N, Kumar P. Recent Advances in Understanding SARS-CoV-2 Infection and Updates on
Potential Diagnostic and Therapeutics for COVID-19. CORONAVIRUSES 2022; 3. [DOI: 10.2174/2666796703666220302143102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/09/2021] [Accepted: 12/13/2021] [Indexed: 09/25/2023]
Abstract
Abstract:
A more focused approach is needed to understand the SARS-CoV-2 virulence, structure, and
genomics to devise more effective diagnostic and treatment interventions as this virus can evade the immune
attack and causes life-threatening complications such as cytokine storm. The spread of the virus is
still amplifying and causing thousands of new cases worldwide. It is essential to review current diagnostics
and treatment approaches to pave the way to correct or modify our current practices to make more
effective interventions against COVID-19. COVID-19 vaccine development has moved at a breakneck
pace since the outbreak began, utilizing practically all possible platforms or tactics to ensure the success
of vaccines. A total of 42 vaccine candidates have already entered clinical trials, including promising
results from numerous vaccine candidates in phase 1 or phase 2 trials. Further, many existing drugs are
being explored on broad-spectrum antiviral medications for their use in clinical recovery against COVID-
19. The present review attempts to re-examine the SARS-CoV-2 structure, its viral life cycle, clinical
symptoms and pathogenesis, mode of transmission, diagnostics, and treatment strategies that may be useful
for resorting to more effective approaches for controlling COVID-19. Various antiviral drugs and
vaccination strategies with their strengths and weaknesses are also discussed in the paper to augment our
understanding of COVID-19 management.
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Affiliation(s)
- Maumita D. Mukherjee
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh-201313, India
| | - Anil Kumar
- National Institute of Immunology, New Delhi-110067, India
| | - Pratima R. Solanki
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
| | - Damini Verma
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh-201313, India
| | - Amit K. Yadav
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi-110067, India
| | - Navneet Chaudhary
- Department of Biotechnology,
Delhi Technological University, Delhi-110042, India
| | - Pramod Kumar
- Sri Aurobindo College, Delhi University, New Delhi-110017,
India
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66
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Vatandaslar H. A Systematic Study on the Optimal Nucleotide Analogue Concentration and Rate Limiting Nucleotide of the SARS-CoV-2 RNA-Dependent RNA Polymerase. Int J Mol Sci 2022; 23:ijms23158302. [PMID: 35955442 PMCID: PMC9369030 DOI: 10.3390/ijms23158302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 02/01/2023] Open
Abstract
The current COVID-19 pandemic has highlighted the necessity of more efficient antiviral compounds. The antiviral efficacy of adenosine-based analogs, the main repurposed drugs for SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition, is mainly assessed through in vitro or cell-free polymerization assays, under arbitrary conditions that do not reflect the physiological environment. We show that SARS-CoV-2 RdRp inhibition efficiency of remdesivir and cordycepin, two common adenosine analogs, is influenced by endogenous adenosine level, and that the current clinically approved concentrations for COVID-19 treatment are suboptimal for effective RdRp inhibition. Furthermore, we identified GTP as the rate-limiting nucleotide of SARS-CoV-2 replication. Our results demonstrate that nucleotide sensitivity of the RdRp complex and competition of nucleoside analog drugs against endogenous concentrations of nucleotides are crucial elements to be considered when designing new SARS-CoV-2 antiviral compounds.
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Affiliation(s)
- Hasan Vatandaslar
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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67
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Ogunsakin RE, Ebenezer O, Jordaan MA, Shapi M, Ginindza TG. Mapping Scientific Productivity Trends and Hotspots in Remdesivir Research Publications: A Bibliometric Study from 2016 to 2021. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148845. [PMID: 35886696 PMCID: PMC9318242 DOI: 10.3390/ijerph19148845] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023]
Abstract
In response to global efforts to control and exterminate infectious diseases, this study aims to provide insight into the productivity of remdesivir research and highlight future directions. To achieve this, there is a need to summarize and curate evidence from the literature. As a result, this study carried out comprehensive scientific research to detect trends in published articles related to remdesivir using a bibliometric analysis. Keywords associated with remdesivir were used to access pertinent published articles using the Scopus database. A total of 5321 research documents were retrieved, primarily as novel research articles (n = 2440; 46%). The number of publications increased exponentially from 2020 up to the present. The papers published by the top 12 institutions focusing on remdesivir accounted for 25.69% of the overall number of articles. The USA ranked as the most productive country, with 906 documents (37.1%), equivalent to one-third of the global publications in this field. The most productive institution was Icahn School of Medicine, Mount Sinai, in the USA (103 publications). The New England Journal of Medicine was the most cited, with an h-index of 13. The publication of research on remdesivir has gained momentum in the past year. The importance of remdesivir suggests that it needs continued research to help global health organizations detect areas requiring instant action to implement suitable measures. Furthermore, this study offers evolving hotspots and valuable insights into the scientific advances in this field and provides scaling-up analysis and evidence diffusion on remdesivir.
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Affiliation(s)
- Ropo E. Ogunsakin
- Discipline of Public Health Medicine, School of Nursing & Public Health, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
- Correspondence:
| | - Oluwakemi Ebenezer
- Department of Chemistry, Faculty of Natural Sciences, Mangosuthu University of Technology, Umlazi 4031, South Africa; (O.E.); (M.A.J.); (M.S.)
| | - Maryam A. Jordaan
- Department of Chemistry, Faculty of Natural Sciences, Mangosuthu University of Technology, Umlazi 4031, South Africa; (O.E.); (M.A.J.); (M.S.)
| | - Michael Shapi
- Department of Chemistry, Faculty of Natural Sciences, Mangosuthu University of Technology, Umlazi 4031, South Africa; (O.E.); (M.A.J.); (M.S.)
| | - Themba G. Ginindza
- Discipline of Public Health Medicine, School of Nursing & Public Health, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
- Cancer & Infectious Diseases Epidemiology Research Unit (CIDERU), College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
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68
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Arba M, Paradis N, Wahyudi ST, Brunt DJ, Hausman KR, Lakernick PM, Singh M, Wu C. Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations. Chem Phys Lett 2022; 799:139638. [PMID: 35475235 PMCID: PMC9020840 DOI: 10.1016/j.cplett.2022.139638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 01/18/2023]
Abstract
The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy. This suggest that these analogues might be able to covalently link to the primer strand as RTP, but their 3' modification would terminate the primer strand growth.
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Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia
| | - Nicholas Paradis
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Setyanto T Wahyudi
- Department of Physics, Faculty of Mathematic and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Dylan J Brunt
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Katherine R Hausman
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Phillip M Lakernick
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Mursalin Singh
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Chun Wu
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
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Bandaru R, Rout SR, Kamble OS, Samal SK, Gorain B, Sahebkar A, Ahmed FJ, Kesharwani P, Dandela R. Clinical progress of therapeutics and vaccines: Rising hope against COVID-19 treatment. Process Biochem 2022; 118:154-170. [PMID: 35437418 PMCID: PMC9008982 DOI: 10.1016/j.procbio.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
Cases of deaths due to COVID-19 (COrona VIrus Disease-19) infection are increasing gradually worldwide. Immense research is ongoing to control this pandemic condition. Continual research outcomes are indicating that therapeutic and prophylactic agents are the possible hope to prevent the pandemic from spreading and to combat this increasing death count. Experience gained from previous coronavirus infections (eg., SARS (Severe Acute Respiratory Syndrome), MERS (Middle Ease Respiratory Syndrome), accumulated clinical knowledge during this pandemic, and research helped to identify a few therapeutic agents for emergency treatment of COVID-19. Thereby, monoclonal antibodies, antivirals, broad-spectrum antimicrobials, immunomodulators, and supplements are being suggested for treatment depending on the stage of the disease. These recommended treatments are authorized under medical supervision in emergency conditions only. Urgent need to control the pandemic condition had resulted in various approaches of repurposing the existing drugs, However, poorly designed clinical trials and associated outcomes do not provide enough evidence to fully approve treatments against COVID-19. So far, World Health Organization (WHO) authorized three vaccines as prophylactic against SARS-CoV-2. Here, we discussed about various therapeutic agents, their clinical trials, and limitations of trials for the management of COVID-19. Further, we have also spotlighted different vaccines in research in combating COVID-19.
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Affiliation(s)
- Ravi Bandaru
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Smruti Rekha Rout
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Omkar S Kamble
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Sangram K Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, Indian Council of Medical Research-Regional Medical Research Center, Bhubaneswar 751023, India
| | - Bapi Gorain
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farhan J Ahmed
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard 110062, New Delhi, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard 110062, New Delhi, India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
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70
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Kato Y, Nishiyama K, Nishimura A, Noda T, Okabe K, Kusakabe T, Kanda Y, Nishida M. Drug repurposing for the treatment of COVID-19. J Pharmacol Sci 2022; 149:108-114. [PMID: 35641023 PMCID: PMC9040495 DOI: 10.1016/j.jphs.2022.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains prevalent worldwide since its onset was confirmed in Wuhan, China in 2019. Vaccines against the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have shown a preventive effect against the onset and severity of COVID-19, and social and economic activities are gradually recovering. However, the presence of vaccine-resistant variants has been reported, and the development of therapeutic agents for patients with severe COVID-19 and related sequelae remains urgent. Drug repurposing, also called drug repositioning or eco-pharma, is the strategy of using previously approved and safe drugs for a therapeutic indication that is different from their original indication. The risk of severe COVID-19 and mortality increases with advancing age, cardiovascular disease, hypertension, diabetes, and cancer. We have reported three protein-protein interactions that are related to heart failure, and recently identified that one mechanism increases the risk of SARS-CoV-2 infection in mammalian cells. This review outlines the global efforts and outcomes of drug repurposing research for the treatment of severe COVID-19. It also discusses our recent finding of a new protein-protein interaction that is common to COVID-19 aggravation and heart failure.
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Affiliation(s)
- Yuri Kato
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Kazuhiro Nishiyama
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Akiyuki Nishimura
- Division of Cardiocirculatory Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, SOKENDAI, Okazaki, Aichi, Japan
| | - Takamasa Noda
- Department of Psychiatry, National Center of Neurology and Psychiatry, Tokyo, Japan; Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neuropsychopharmacology, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Brain Bioregulatory Science, The Jikei University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Okabe
- Department of Psychiatry, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Japan
| | - Motohiro Nishida
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan; Division of Cardiocirculatory Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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Barman RK, Mukhopadhyay A, Maulik U, Das S. A network biology approach to identify crucial host targets for COVID-19. Methods 2022; 203:108-115. [PMID: 35364279 PMCID: PMC8960288 DOI: 10.1016/j.ymeth.2022.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/09/2022] [Accepted: 03/27/2022] [Indexed: 12/23/2022] Open
Abstract
The ongoing global pandemic of COVID-19, caused by SARS-CoV-2 has killed more than 5.9 million individuals out of ∼43 million confirmed infections. At present, several parts of the world are encountering the 3rd wave. Mass vaccination has been started in several countries but they are less likely to be broadly available for the current pandemic, repurposing of the existing drugs has drawn highest attention for an immediate solution. A recent publication has mapped the physical interactions of SARS-CoV-2 and human proteins by affinity-purification mass spectrometry (AP-MS) and identified 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Here, we taken a network biology approach and constructed a human protein-protein interaction network (PPIN) with the above SARS-CoV-2 targeted proteins. We utilized a combination of essential network centrality measures and functional properties of the human proteins to identify the critical human targets of SARS-CoV-2. Four human proteins, namely PRKACA, RHOA, CDK5RAP2, and CEP250 have emerged as the best therapeutic targets, of which PRKACA and CEP250 were also found by another group as potential candidates for drug targets in COVID-19. We further found candidate drugs/compounds, such as guanosine triphosphate, remdesivir, adenosine monophosphate, MgATP, and H-89 dihydrochloride that bind the target human proteins. The urgency to prevent the spread of infection and the death of diseased individuals has prompted the search for agents from the pool of approved drugs to repurpose them for COVID-19. Our results indicate that host targeting therapy with the repurposed drugs may be a useful strategy for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Ranjan Kumar Barman
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India; Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Anirban Mukhopadhyay
- Department of Computer Science and Engineering, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Santasabuj Das
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India; ICMR-National Institute of Occupational Health, Ahmedabad 380016, India.
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72
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Bao Q, Yang T, Yang M, Mao C. Detection, prevention and treatment of COVID-19 and opportunities for nanobiotechnology. VIEW 2022; 3:20200181. [PMID: 35600668 PMCID: PMC9111118 DOI: 10.1002/viw.20200181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/12/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Since the outbreak of COVID-19, the number of confirmed cases and deaths has increased globally at a dramatic speed. In view of the serious health threat to humans, this review discusses the state-of-the-art studies about fighting this disease. It summarizes the current strategies and recent advances in detecting, preventing, and treating COVID-19 and interprets the underlying mechanisms in detail. Detection of COVID-19 can be successfully achieved by multiple techniques such as polymerase chain reaction, computed tomography imaging, and nano-biosensing. Inactivated virus vaccine, nucleic acid vaccine, and different nanoparticles have been employed to effectively prevent COVID-19. A variety of agents such as antiviral agents, neutralizing antibodies, and nanotherapeutics have been developed to treat COVID-19 with exciting efficacy. Although nanobiotechnology has shown great potential in the diagnosis, prevention, and treatment of COVID-19, efforts should be made to explore new biocompatible nano-biomaterials to advance this field to clinical applications. Hence, nanobiotechnology paves a new way to detect, prevent, and treat COVID-19 effectively.
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Affiliation(s)
- Qing Bao
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiangChina
| | - Tao Yang
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiangChina
| | - Mingying Yang
- College of Animal ScienceInstitute of Applied Bioresource ResearchZhejiang UniversityHangzhouZhejiangChina
| | - Chuanbin Mao
- School of Materials Science and EngineeringZhejiang UniversityHangzhouZhejiangChina
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
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The Nucleoside/Nucleotide Analogs Tenofovir and Emtricitabine Are Inactive against SARS-CoV-2. Molecules 2022; 27:molecules27134212. [PMID: 35807457 PMCID: PMC9267940 DOI: 10.3390/molecules27134212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
The urgent response to the COVID-19 pandemic required accelerated evaluation of many approved drugs as potential antiviral agents against the causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using cell-based, biochemical, and modeling approaches, we studied the approved HIV-1 nucleoside/tide reverse transcriptase inhibitors (NRTIs) tenofovir (TFV) and emtricitabine (FTC), as well as prodrugs tenofovir alafenamide (TAF) and tenofovir disoproxilfumarate (TDF) for their antiviral effect against SARS-CoV-2. A comprehensive set of in vitro data indicates that TFV, TAF, TDF, and FTC are inactive against SARS-CoV-2. None of the NRTIs showed antiviral activity in SARS-CoV-2 infected A549-hACE2 cells or in primary normal human lung bronchial epithelial (NHBE) cells at concentrations up to 50 µM TAF, TDF, FTC, or 500 µM TFV. These results are corroborated by the low incorporation efficiency of respective NTP analogs by the SARS-CoV-2 RNA-dependent-RNA polymerase (RdRp), and lack of the RdRp inhibition. Structural modeling further demonstrated poor fitting of these NRTI active metabolites at the SARS-CoV-2 RdRp active site. Our data indicate that the HIV-1 NRTIs are unlikely direct-antivirals against SARS-CoV-2, and clinicians and researchers should exercise caution when exploring ideas of using these and other NRTIs to treat or prevent COVID-19.
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Chen CC, Zhuang ZJ, Wu CW, Tan YL, Huang CH, Hsu CY, Tsai EM, Hsieh TH. Venetoclax Decreases the Expression of the Spike Protein through Amino Acids Q493 and S494 in SARS-CoV-2. Cells 2022; 11:cells11121924. [PMID: 35741053 PMCID: PMC9221610 DOI: 10.3390/cells11121924] [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: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
The new coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has been reported and spread globally. There is an urgent need to take urgent measures to treat and prevent further infection of this virus. Here, we use virtual drug screening to establish pharmacophore groups and analyze the ACE2 binding site of the spike protein with the ZINC drug database and DrugBank database by molecular docking and molecular dynamics simulations. Screening results showed that Venetoclax, a treatment drug for chronic lymphocytic leukemia, has a potential ability to bind to the spike protein of SARS-CoV-2. In addition, our in vitro study found that Venetoclax degraded the expression of the spike protein of SARS-CoV-2 through amino acids Q493 and S494 and blocked the interaction with the ACE2 receptor. Our results suggest that Venetoclax is a candidate for clinical prevention and treatment and deserves further research.
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Affiliation(s)
- Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Zhi-Jie Zhuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chia-Wei Wu
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Yi-Ling Tan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chen-Hsiu Huang
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Chia-Yi Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
| | - Eing-Mei Tsai
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Tsung-Hua Hsieh
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
- Correspondence: ; Tel.: +886-7615-1100 (ext. 5072)
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Valipour M. Different Aspects of Emetine's Capabilities as a Highly Potent SARS-CoV-2 Inhibitor against COVID-19. ACS Pharmacol Transl Sci 2022; 5:387-399. [PMID: 35702393 PMCID: PMC9159504 DOI: 10.1021/acsptsci.2c00045] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 01/18/2023]
Abstract
In the global movement to find the appropriate agents to fight the coronavirus disease of 2019 (COVID-19), emetine is one of the strongest anti-SARS-CoV-2 compounds with sub-micromolar EC50 values, identified in several studies and high-throughput screening efforts. The reported anti-SARS-CoV-2 mechanisms indicate the effect of this compound on both virus-based and host-based targets. In addition to having excellent antiviral effects, emetine can relieve COVID-19 patients by reducing inflammation through inhibitory activity against NF-κB by the mechanism of IκBα phosphorylation inhibition; it can also limit the lipopolysaccharide-induced expression of pro-inflammatory cytokines TNFα, IL-1β, and IL-6. Emetine also can well reduce pulmonary arterial hypertension as an important COVID-19 complication by modulating a variety of cellular processes such as the Rho-kinase/CyPA/Bsg signaling pathway. The therapeutic value of emetine for combating COVID-19 was highlighted when in vivo pharmacokinetic studies showed that the concentration of this compound in the lungs increases significantly higher than the EC50 of the drug. Despite its valuable therapeutic effects, emetine has some cardiotoxic effects that limit its use in high doses. However, high therapeutic capabilities make emetine a valuable lead compound that can be used for the design and development of less toxic anti-COVID-19 agents in the future. This Review provides a collection of information on the capabilities of emetine and its potential for the treatment of COVID-19, along with structural analysis which could be used for further research in the future.
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Affiliation(s)
- Mehdi Valipour
- Department of Medicinal Chemistry,
Faculty of Pharmacy, Mazandaran University
of Medical Sciences, 48175-866 Sari, Iran
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76
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Su S, Chen R, Zhang S, Shu H, Luo J. Immune system changes in those with hypertension when infected with SARS-CoV-2. Cell Immunol 2022; 378:104562. [PMID: 35901625 PMCID: PMC9183242 DOI: 10.1016/j.cellimm.2022.104562] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) outbreak has become an evolving global health crisis. With an increasing incidence of primary hypertension, there is greater awareness of the relationship between primary hypertension and the immune system [including CD4+, CD8+ T cells, interleukin-17 (IL-17)/T regulatory cells (Treg) balance, macrophages, natural killer (NK) cells, neutrophils, B cells, and cytokines]. Hypertension is associated with an increased risk of various infections, post-infection complications, and increased mortality from severe infections. Despite ongoing reports on the epidemiological and clinical features of COVID-19, no articles have systematically addressed the role of primary hypertension in COVID-19 or how COVID-19 affects hypertension or specific treatment in these high-risk groups. Here, we synthesize recent advances in understanding the relationship between primary hypertension and COVID-19 and its underlying mechanisms and provide specific treatment guidelines for these high-risk groups.
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77
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Goyal A, Duke ER, Cardozo-Ojeda EF, Schiffer JT. Modeling explains prolonged SARS-CoV-2 nasal shedding relative to lung shedding in remdesivir treated rhesus macaques. iScience 2022; 25:104448. [PMID: 35634576 PMCID: PMC9130309 DOI: 10.1016/j.isci.2022.104448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 12/12/2022] Open
Abstract
In clinical trials, remdesivir decreased recovery time in hospitalized patients with SARS- CoV-2 and prevented hospitalization when given early during infection, despite not reducing nasal viral loads. In rhesus macaques, early remdesivir prevented pneumonia and lowered lung viral loads, but viral loads increased in nasal passages after five days. We developed mathematical models to explain these results. Our model raises the hypotheses that: 1) in contrast to nasal passages viral load monotonically decreases in lungs during therapy because of infection-dependent generation of refractory cells, 2) slight reduction in lung viral loads with an imperfect agent may result in a substantial decrease in lung damage, and 3) increases in nasal viral load may occur due to a blunting of peak viral load which decreases the intensity of the innate immune response. We demonstrate that a higher potency drug could lower viral loads in nasal passages and lung.
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Affiliation(s)
- Ashish Goyal
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Elizabeth R Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Medicine, University of Washington, Seattle
| | | | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Medicine, University of Washington, Seattle.,Clinical Research Division, Fred Hutchinson Cancer Research Center
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78
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Cross RW, Bornholdt ZA, Prasad AN, Woolsey C, Borisevich V, Agans KN, Deer DJ, Abelson DM, Kim DH, Shestowsky WS, Campbell LA, Bunyan E, Geisbert JB, Dobias NS, Fenton KA, Porter DP, Zeitlin L, Geisbert TW. Combination therapy with remdesivir and monoclonal antibodies protects nonhuman primates against advanced Sudan virus disease. JCI Insight 2022; 7:e159090. [PMID: 35413016 PMCID: PMC9220838 DOI: 10.1172/jci.insight.159090] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/06/2022] [Indexed: 12/02/2022] Open
Abstract
A major challenge in managing acute viral infections is ameliorating disease when treatment is delayed. Previously, we reported the success of a 2-pronged mAb and antiviral remdesivir therapeutic approach to treat advanced illness in rhesus monkeys infected with Marburg virus (MARV). Here, we explored the benefit of a similar combination therapy for Sudan ebolavirus (Sudan virus; SUDV) infection. Importantly, no licensed anti-SUDV therapeutics currently exist, and infection of rhesus macaques with SUDV results in a rapid disease course similar to MARV with a mean time to death of 8.3 days. When initiation of therapy with either remdesivir or a pan-ebolavirus mAb cocktail (MBP431) was delayed until 6 days after inoculation, only 20% of macaques survived. In contrast, when remdesivir and MBP431 treatment were combined beginning 6 days after inoculation, significant protection (80%) was achieved. Our results suggest that combination therapy may be a viable treatment for patients with advanced filovirus disease that warrants further clinical testing in future outbreaks.
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Affiliation(s)
- Robert W. Cross
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Abhishek N. Prasad
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Courtney Woolsey
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Krystle N. Agans
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Daniel J. Deer
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Do H. Kim
- Mapp Biopharmaceutical, Inc., San Diego, California, USA
| | | | | | | | - Joan B. Geisbert
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Natalie S. Dobias
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Karla A. Fenton
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, California, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory and
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
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79
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Solís A, Cano A, Martínez-Casares RM, Solís-Oba M, Castro-Rivera R, Velázquez Flores O. Preparation of optically active cyanohydrins from 2-substituted benzaldehydes using a hydroxynitrile lyase from Pouteria sapota seeds immobilized on celite. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2070430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Aida Solís
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de México, México
| | - Abraham Cano
- Universidad Autónoma Metropolitana, Unidad Xochimilco, Maestría en Ciencias Farmacéuticas, Ciudad de México, México
| | - R. Marlen Martínez-Casares
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de México, México
| | - Myrna Solís-Oba
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
| | - Rigoberto Castro-Rivera
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Tlaxcala, México
| | - Oscar Velázquez Flores
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco, Ciudad de México, México
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Thadathil DA, Varghese A, Ahamed CVS, Krishnakumar K, Varma SS, Lankalapalli RS, Radhakrishnan KV. Enzyme based bioelectrocatalysis over laccase immobilized poly-thiophene supported carbon fiber paper for the oxidation of D-ribofuranose to D-ribonolactone. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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81
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Shah MK, Parikh M, Prajapati D, Kute VB, Bhende P, Prajapati A, Chhajwani SH, Yajnik K, Ganjiwale J, Mannari JG, Vaishnav B. Safety and Tolerability of Remdesivir in Patients with End-stage Renal Disease on Maintenance Hemodialysis. Indian J Crit Care Med 2022; 26:619-625. [PMID: 35719430 PMCID: PMC9160629 DOI: 10.5005/jp-journals-10071-24168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Introduction The use of remdesivir is not recommended in patients with end-stage renal disease (ESRD) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection unless potential advantage offset disadvantage due to limited safety data. Our objective was to assess the safety of remdesivir in patients with end-stage renal failure and evaluate the outcome of this vulnerable group. Methodology We carried out a retrospective observational study in dialysis-dependent ESRD patients with SARS-CoV-2 infection who received a standard 5-day course of remdesivir (powder form) from June 2020 to December 2020. Oxygen requirement, hemogram, inflammatory markers, and liver function tests before and after remdesivir treatment were compared. Result We found thirty-nine such patients with mean age of patients 58.79 ± 12.13 years. Diabetes mellitus, hypertension, and cardiac diseases were present in 58.97, 87.17, and 23.07% of patients, respectively. Mean oxygen saturation on admission was 85.41% (±7.73). There were no events of hepatotoxicity, altered behavior, or infusion reaction. There was statistically significant improvement in total leukocyte count, absolute lymphocyte counts, and C-reactive protein (p value <0.001, 0.01, and 0.02, respectively) post remdesivir treatment. A total of 60% of patients had improved oxygenation while 13% of patients had no change in oxygen requirement after completion of remdesivir course. Mortality in our study was 28.21%. We did not find any significant benefit of early remdesivir administration (3-6 days of illness) on mortality or days of hospitalization. Conclusion The use of remdesivir in end-stage kidney disease is safe. Improvement in oxygenation was significant when baseline oxygen requirement was less. It requires prospective controlled trials with larger population to assess its impact on mortality. How to cite this article Shah MK, Parikh M, Prajapati D, Kute VB, Bhende P, Prajapati A, et al. Safety and Tolerability of Remdesivir in Patients with End-stage Renal Disease on Maintenance Hemodialysis. Indian J Crit Care Med 2022;26(5):619-625.
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Affiliation(s)
- Maulin K Shah
- Division of Nephrology, Department of Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Mital Parikh
- Department of Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Dhavalkumar Prajapati
- Department of Critical Care Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Vivek B Kute
- Department of Nephrology, IKDRC-ITS, Ahmedabad, Gujarat, India
| | - Punam Bhende
- Department of Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Abhishek Prajapati
- Department of Critical Care Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Sunil H Chhajwani
- Department of Anaesthesiology and Critical Care, Pramukh Swami Medical College, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Bhaikaka University, Karamsad, Gujarat, India
| | - Krushan Yajnik
- Department of Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Jaishree Ganjiwale
- Department of Community Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
| | - Jyoti G Mannari
- Department of Medicine, Pramukh Swami Medical College, Vadodara, Gujarat, India
| | - Bhalendu Vaishnav
- Department of Medicine, Shree Krishna Hospital, HM Patel Centre for Medical Care and Education, Anand, Gujarat, India
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Ho WS, Zhang R, Tan YL, Chai CLL. COVID-19 and the promise of small molecule therapeutics: Are there lessons to be learnt? Pharmacol Res 2022; 179:106201. [PMID: 35367622 PMCID: PMC8970615 DOI: 10.1016/j.phrs.2022.106201] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic had grounded the world to a standstill. As the disease continues to rage two years on, it is apparent that effective therapeutics are critical for a successful endemic living with COVID-19. A dearth in suitable antivirals has prompted researchers and healthcare professionals to investigate existing and developmental drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although some of these drugs initially appeared to be promising for the treatment of COVID-19, they were ultimately found to be ineffective. In this review, we provide a retrospective analysis on the merits and limitations of some of these drugs that were tested against SARS-CoV-2 as well as those used for adjuvant therapy. While many of these drugs are no longer part of our arsenal for the treatment of COVID-19, important lessons can be learnt. The recent inclusion of molnupiravir and Paxlovid™ as treatment options for COVID-19 represent our best hope to date for endemic living with COVID-19. Our viewpoints on these two drugs and their prospects as current and future antiviral agents will also be provided.
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Affiliation(s)
- Wei Shen Ho
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Ruirui Zhang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Yeong Lan Tan
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - Christina Li Lin Chai
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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Cooreman A, Caufriez A, Tabernilla A, Van Campenhout R, Leroy K, Kadam P, Sanz Serrano J, dos Santos Rodrigues B, Annaert P, Vinken M. Effects of Drugs Formerly Proposed for COVID-19 Treatment on Connexin43 Hemichannels. Int J Mol Sci 2022; 23:5018. [PMID: 35563409 PMCID: PMC9103705 DOI: 10.3390/ijms23095018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 02/07/2023] Open
Abstract
Connexin43 (Cx43) hemichannels form a pathway for cellular communication between the cell and its extracellular environment. Under pathological conditions, Cx43 hemichannels release adenosine triphosphate (ATP), which triggers inflammation. Over the past two years, azithromycin, chloroquine, dexamethasone, favipiravir, hydroxychloroquine, lopinavir, remdesivir, ribavirin, and ritonavir have been proposed as drugs for the treatment of the coronavirus disease 2019 (COVID-19), which is associated with prominent systemic inflammation. The current study aimed to investigate if Cx43 hemichannels, being key players in inflammation, could be affected by these drugs which were formerly designated as COVID-19 drugs. For this purpose, Cx43-transduced cells were exposed to these drugs. The effects on Cx43 hemichannel activity were assessed by measuring extracellular ATP release, while the effects at the transcriptional and translational levels were monitored by means of real-time quantitative reverse transcriptase polymerase chain reaction analysis and immunoblot analysis, respectively. Exposure to lopinavir and ritonavir combined (4:1 ratio), as well as to remdesivir, reduced Cx43 mRNA levels. None of the tested drugs affected Cx43 protein expression.
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Affiliation(s)
- Axelle Cooreman
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Anne Caufriez
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Andrés Tabernilla
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Raf Van Campenhout
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Kaat Leroy
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Prashant Kadam
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Julen Sanz Serrano
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Bruna dos Santos Rodrigues
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
| | - Pieter Annaert
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium;
| | - Mathieu Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (A.C.); (A.C.); (A.T.); (R.V.C.); (K.L.); (P.K.); (J.S.S.); (B.d.S.R.)
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84
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Calleja DJ, Lessene G, Komander D. Inhibitors of SARS-CoV-2 PLpro. Front Chem 2022; 10:876212. [PMID: 35559224 PMCID: PMC9086436 DOI: 10.3389/fchem.2022.876212] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The emergence of SARS-CoV-2 causing the COVID-19 pandemic, has highlighted how a combination of urgency, collaboration and building on existing research can enable rapid vaccine development to fight disease outbreaks. However, even countries with high vaccination rates still see surges in case numbers and high numbers of hospitalized patients. The development of antiviral treatments hence remains a top priority in preventing hospitalization and death of COVID-19 patients, and eventually bringing an end to the SARS-CoV-2 pandemic. The SARS-CoV-2 proteome contains several essential enzymatic activities embedded within its non-structural proteins (nsps). We here focus on nsp3, that harbours an essential papain-like protease (PLpro) domain responsible for cleaving the viral polyprotein as part of viral processing. Moreover, nsp3/PLpro also cleaves ubiquitin and ISG15 modifications within the host cell, derailing innate immune responses. Small molecule inhibition of the PLpro protease domain significantly reduces viral loads in SARS-CoV-2 infection models, suggesting that PLpro is an excellent drug target for next generation antivirals. In this review we discuss the conserved structure and function of PLpro and the ongoing efforts to design small molecule PLpro inhibitors that exploit this knowledge. We first discuss the many drug repurposing attempts, concluding that it is unlikely that PLpro-targeting drugs already exist. We next discuss the wealth of structural information on SARS-CoV-2 PLpro inhibition, for which there are now ∼30 distinct crystal structures with small molecule inhibitors bound in a surprising number of distinct crystallographic settings. We focus on optimisation of an existing compound class, based on SARS-CoV PLpro inhibitor GRL-0617, and recapitulate how new GRL-0617 derivatives exploit different features of PLpro, to overcome some compound liabilities.
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Affiliation(s)
- Dale J. Calleja
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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85
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Boglione L, Dodaro V, Meli G, Rostagno R, Poletti F, Moglia R, Bianchi B, Esposito M, Borrè S. Remdesivir treatment in hospitalized patients affected by COVID-19 pneumonia: a case-control study. J Med Virol 2022; 94:3653-3660. [PMID: 35411627 PMCID: PMC9088403 DOI: 10.1002/jmv.27768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022]
Abstract
To date the optimal antiviral treatment against severe coronavirus disease 2019 (COVID‐19) has not been proven; remdesivir is a promising drug with in vitro activity against several viruses, but in COVID‐19 the clinical results are currently not definitive. In this retrospective observational study, we analyzed the clinical outcomes (survival analysis, efficacy, and safety) in a group of hospitalized patients with COVID‐19 treated with remdesivir in comparison with a control group of patients treated with other antiviral or supportive therapies. We included 163 patients treated with remdesivir and 403 subjects in the control group; the baseline characteristics were similar in the two groups; the mortality rate was higher in the control group (24.8% vs. 2.4%, p < 0.001), the risk of intensive care unit (ICU) admission was higher in the control group (17.8% vs. 9.8%, p = 0.008); hospitalization time was significantly lower in patients treated with remdesivir (9.5 vs. 12.5 days, p < 0.001). The safety of remdesivir was good and no significant adverse events were reported. In multivariate analysis, the remdesivir treatment was independently associated with a 34% lower mortality rate (odds ratio = 0.669; p = 0.014). In this analysis, the treatment with remdesivir was associated with lower mortality, lower rate of ICU admission, and shorter time of hospitalization. No adverse events were observed. This promising antiviral treatment should also be confirmed by other studies.
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Affiliation(s)
- Lucio Boglione
- University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | | | - Giulia Meli
- University of Eastern Piedmont, Department of Translational Medicine, Novara, Italy
| | - Roberto Rostagno
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
| | - Federica Poletti
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
| | - Roberta Moglia
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
| | - Bianca Bianchi
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
| | - Maria Esposito
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
| | - Silvio Borrè
- Saint Andrea Hospital, Unit of Infectious Diseases, Vercelli, Italy
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86
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Schultz DC, Johnson RM, Ayyanathan K, Miller J, Whig K, Kamalia B, Dittmar M, Weston S, Hammond HL, Dillen C, Ardanuy J, Taylor L, Lee JS, Li M, Lee E, Shoffler C, Petucci C, Constant S, Ferrer M, Thaiss CA, Frieman MB, Cherry S. Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2. Nature 2022; 604:134-140. [PMID: 35130559 PMCID: PMC10377386 DOI: 10.1038/s41586-022-04482-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
The SARS-CoV-2 virus has infected more than 261 million people and has led to more than 5 million deaths in the past year and a half1 ( https://www.who.org/ ). Individuals with SARS-CoV-2 infection typically develop mild-to-severe flu-like symptoms, whereas infection of a subset of individuals leads to severe-to-fatal clinical outcomes2. Although vaccines have been rapidly developed to combat SARS-CoV-2, there has been a dearth of antiviral therapeutics. There is an urgent need for therapeutics, which has been amplified by the emerging threats of variants that may evade vaccines. Large-scale efforts are underway to identify antiviral drugs. Here we screened approximately 18,000 drugs for antiviral activity using live virus infection in human respiratory cells and validated 122 drugs with antiviral activity and selectivity against SARS-CoV-2. Among these candidates are 16 nucleoside analogues, the largest category of clinically used antivirals. This included the antivirals remdesivir and molnupiravir, which have been approved for use in COVID-19. RNA viruses rely on a high supply of nucleoside triphosphates from the host to efficiently replicate, and we identified a panel of host nucleoside biosynthesis inhibitors as antiviral. Moreover, we found that combining pyrimidine biosynthesis inhibitors with antiviral nucleoside analogues synergistically inhibits SARS-CoV-2 infection in vitro and in vivo against emerging strains of SARS-CoV-2, suggesting a clinical path forward.
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Affiliation(s)
- David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Johnson
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kasirajan Ayyanathan
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesse Miller
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanupriya Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Brinda Kamalia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Holly L Hammond
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carly Dillen
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeremy Ardanuy
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Louis Taylor
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jae Seung Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minghua Li
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Clarissa Shoffler
- Metabolomics Core, Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Petucci
- Metabolomics Core, Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Christoph A Thaiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Sara Cherry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.
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87
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Hassanein SS, Sharaby MR, Tawfik NM, Rashed SA, Adel M, Fayez A, Mansour H, Amer HM. Latest Insights on the Diagnostic Approaches and Treatment Strategies of COVID-19. Intervirology 2022; 65:167-180. [PMID: 35249006 PMCID: PMC9148896 DOI: 10.1159/000522336] [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: 05/28/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND COVID-19 has emerged as the most serious pandemic in the 21st century to date. COVID-19 patients may develop various disease symptoms that hinder the accurate clinical diagnosis. SUMMARY Routine diagnosis of COVID-19 requires complementary investigations, including computed tomography, immunological assays, and molecular assays like real-time RT-PCR, loop-mediated isothermal amplification, metagenomic next-generation sequencing, and clusters of regularly interspaced short palindromic repeats-based assays. Clinically approved antiviral drugs available for the COVID-19 treatment are very limited. The most common measurements that enhance health condition and patients' viability are conservation fluid management, oxygen therapy, and antibiotics. Several therapeutic options have been developed or repurposed to prevent virus replication and/or modulate the immune response against virus infection. These options include various drugs that affect virus entry and membrane fusion, inhibit polymerase and protease activity, suppress the host pro-inflammatory cytokines, and utilize cell therapy approaches. KEY MESSAGES In this review, we aimed to provide an up-to-date discussion on the current diagnostic options and therapeutic strategies used to control and manage COVID-19 in clinical and point-of-care settings.
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Affiliation(s)
- Sarah S. Hassanein
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Muhammed R. Sharaby
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Noran M. Tawfik
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Suzan A. Rashed
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed Adel
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo, Egypt
| | - Ayat Fayez
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
| | - Heba Mansour
- Basic and Applied Sciences (BAS) Institute, Biotechnology Program, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt
- Polymeric Materials Research Department, Advanced Technology and New Materials Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Haitham M. Amer
- Virology Department, Faculty of Medicine Veterinary, Cairo University, Giza, Egypt
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88
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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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89
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Hickman MR, Saunders DL, Bigger CA, Kane CD, Iversen PL. The development of broad-spectrum antiviral medical countermeasures to treat viral hemorrhagic fevers caused by natural or weaponized virus infections. PLoS Negl Trop Dis 2022; 16:e0010220. [PMID: 35259154 PMCID: PMC8903284 DOI: 10.1371/journal.pntd.0010220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND) began development of a broad-spectrum antiviral countermeasure against deliberate use of high-consequence viral hemorrhagic fevers (VHFs) in 2016. The effort featured comprehensive preclinical research, including laboratory testing and rapid advancement of lead molecules into nonhuman primate (NHP) models of Ebola virus disease (EVD). Remdesivir (GS-5734, Veklury, Gilead Sciences) was the first small molecule therapeutic to successfully emerge from this effort. Remdesivir is an inhibitor of RNA-dependent RNA polymerase, a viral enzyme that is essential for viral replication. Its robust potency and broad-spectrum antiviral activity against certain RNA viruses including Ebola virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to its clinical evaluation in randomized, controlled trials (RCTs) in human patients during the 2018 EVD outbreak in the Democratic Republic of the Congo (DRC) and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic today. Remdesivir was recently approved by the US Food and Drug Administration (FDA) for the treatment of COVID-19 requiring hospitalization. Substantial gaps remain in improving the outcomes of acute viral infections for patients afflicted with both EVD and COVID-19, including how to increase therapeutic breadth and strategies for the prevention and treatment of severe disease. Combination therapy that joins therapeutics with complimentary mechanisms of action appear promising, both preclinically and in RCTs. Importantly, significant programmatic challenges endure pertaining to a clear drug and biological product development pathway for therapeutics targeting biodefense and emerging pathogens when human efficacy studies are not ethical or feasible. For example, remdesivir's clinical development was facilitated by outbreaks of Ebola and SARS-CoV-2; as such, the development pathway employed for remdesivir is likely to be the exception rather than the rule. The current regulatory licensure pathway for therapeutics targeting rare, weaponizable VHF agents is likely to require use of FDA's established Animal Rule (21 CFR 314.600-650 for drugs; 21 CFR 601.90-95 for biologics). The FDA may grant marketing approval based on adequate and well-controlled animal efficacy studies when the results of those studies establish that the drug is safe and likely to produce clinical benefit in humans. In practical terms, this is anticipated to include a series of rigorous, well-documented, animal challenge studies, to include aerosol challenge, combined with human safety data. While small clinical studies against naturally occurring, high-consequence pathogens are typically performed where possible, approval for the therapeutics currently under development against biodefense pathogens will likely require the Animal Rule pathway utilizing studies in NHPs. We review the development of remdesivir as illustrative of the effort that will be needed to field future therapeutics against highly lethal, infectious agents.
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Affiliation(s)
- Mark R. Hickman
- Joint Project Manager for Chemical, Biological, Radiological, and Nuclear Medical (JPM CBRN Medical), Fort Detrick, Maryland, United States of America
| | - David L. Saunders
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Catherine A. Bigger
- Logistics Management International Inc, Tysons Corner, Virginia, United States of America
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90
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Wang Q, Cao R, Li L, Liu J, Yang J, Li W, Yan L, Wang Y, Yan Y, Li J, Deng F, Zhou Y, Wang M, Zhong W, Hu Z. In vitro and in vivo efficacy of a novel nucleoside analog H44 against Crimean–Congo hemorrhagic fever virus. Antiviral Res 2022; 199:105273. [DOI: 10.1016/j.antiviral.2022.105273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/02/2022]
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91
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Cihlar T, Mackman RL. Journey of remdesivir from the inhibition of hepatitis C virus to the treatment of COVID-19. Antivir Ther 2022; 27:13596535221082773. [DOI: 10.1177/13596535221082773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
If a planned path reaches a dead-end, one can simply stop. Or one can turn around, walk back to the last intersection and take another path, or one can consider taking few paths in parallel. The last scenario is reflective of the journey of remdesivir, the first antiviral for the treatment of COVID-19, that was approved by FDA less than 10 months after the isolation of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. As of January 2022, 10 million COVID-19 patients have been treated with remdesivir worldwide, but the journey of this molecule started more than a decade earlier with the search for a cure of hepatitis C virus. The development path of remdesivir before the emergence of COVID-19 represents a valuable example of a preemptive pandemic preparedness, but the pursuit of this path would not have been possible without sustaining support of John C. Martin, whom we will sorely miss for his piercing vision, uncompromising leadership, and genuine compassion for patients suffering around the world.
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Significance of Immune Status of SARS-CoV-2 Infected Patients in Determining the Efficacy of Therapeutic Interventions. J Pers Med 2022; 12:jpm12030349. [PMID: 35330349 PMCID: PMC8955701 DOI: 10.3390/jpm12030349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is now being investigated for its distinctive patterns in the course of disease development which can be indicated with miscellaneous immune responses in infected individuals. Besides this series of investigations on the pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), significant fundamental immunological and physiological processes are indispensable to address clinical markers of COVID-19 disease and essential to identify or design effective therapeutics. Recent developments in the literature suggest that deficiency of type I interferon (IFN) in serum samples can be used to represent a severe progression of COVID-19 disease and can be used as the basis to develop combined immunotherapeutic strategies. Precise control over inflammatory response is a significant aspect of targeting viral infections. This account presents a brief review of the pathophysiological characteristics of the SARS-CoV-2 virus and the understanding of the immune status of infected patients. We further discuss the immune system’s interaction with the SARS-CoV-2 virus and their subsequent involvement of dysfunctional immune responses during the progression of the disease. Finally, we highlight some of the implications of the different approaches applicable in developing promising therapeutic interventions that redirect immunoregulation and viral infection.
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93
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022; 65:2716-2746. [PMID: 33186044 PMCID: PMC7688049 DOI: 10.1021/acs.jmedchem.0c01140] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Francesco Saverio Di Leva
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
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94
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022. [PMID: 33186044 DOI: 10.1021/acs.jmedchem.0c01140/suppl_file/jm0c01140_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
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95
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Nagamine T, Randhawa S, Nishimura Y, Huang R, Leesutipornchai T, Benavente K, Yoshimura S, Zhang J, Kanitsorphan C. Characteristics of bradyarrhythmia in patients with COVID-19: Systematic scoping review. Pacing Clin Electrophysiol 2022; 45:556-566. [PMID: 35182433 PMCID: PMC9115401 DOI: 10.1111/pace.14466] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/16/2022] [Accepted: 01/30/2022] [Indexed: 11/26/2022]
Abstract
COVID‐19 has recently been associated with the development of bradyarrhythmias, although its mechanism is still unclear. We aim to summarize the existing evidence regarding bradyarrhythmia in COVID‐19 and provide future directions for research. Following the PRISMA Extension for Scoping Reviews, we searched MEDLINE and EMBASE for all peer‐reviewed articles using keywords including“Bradycardia,” “atrioventricular block,” and “COVID‐19″ from their inception to October 13, 2021. Forty‐three articles, including 11 observational studies and 59 cases from case reports and series, were included in the systematic review. Although some observational studies reported increased mortality in those with bradyarrhythmia and COVID‐19, the lack of comparative groups and small sample sizes hinder the ability to draw definitive conclusions. Among 59 COVID‐19 patients with bradycardia from case reports and series, bradycardia most often occurred in those with severe or critical COVID‐19, and complete heart block occurred in the majority of cases despite preserved LVEF (55.9%). Pacemaker insertion was required in 76.3% of the patients, most of which were permanent implants (45.8%). This systematic review summarizes the current evidence and characteristics of bradyarrhythmia in patients with COVID‐19. Further studies are critical to assess the reversibility of bradyarrhythmia in COVID‐19 patients and to clarify potential therapeutic targets including the need for permanent pacing.
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Affiliation(s)
- Todd Nagamine
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Sandeep Randhawa
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Yoshito Nishimura
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Ricky Huang
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Thiratest Leesutipornchai
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Kevin Benavente
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - Stephanie Yoshimura
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
| | - James Zhang
- Queen's Heart Institute, The Queen's Medical Center, Honolulu, HI, 96813, USA
| | - Chanavuth Kanitsorphan
- Department of Medicine, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96813, USA
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96
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Teixeira JP, Barone S, Zahedi K, Soleimani M. Kidney Injury in COVID-19: Epidemiology, Molecular Mechanisms and Potential Therapeutic Targets. Int J Mol Sci 2022; 23:2242. [PMID: 35216358 PMCID: PMC8877127 DOI: 10.3390/ijms23042242] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/08/2023] Open
Abstract
As of December 2021, SARS-CoV-2 had caused over 250 million infections and 5 million deaths worldwide. Furthermore, despite the development of highly effective vaccines, novel variants of SARS-CoV-2 continue to sustain the pandemic, and the search for effective therapies for COVID-19 remains as urgent as ever. Though the primary manifestation of COVID-19 is pneumonia, the disease can affect multiple organs, including the kidneys, with acute kidney injury (AKI) being among the most common extrapulmonary manifestations of severe COVID-19. In this article, we start by reflecting on the epidemiology of kidney disease in COVID-19, which overwhelmingly demonstrates that AKI is common in COVID-19 and is strongly associated with poor outcomes. We also present emerging data showing that COVID-19 may result in long-term renal impairment and delve into the ongoing debate about whether AKI in COVID-19 is mediated by direct viral injury. Next, we focus on the molecular pathogenesis of SARS-CoV-2 infection by both reviewing previously published data and presenting some novel data on the mechanisms of cellular viral entry. Finally, we relate these molecular mechanisms to a series of therapies currently under investigation and propose additional novel therapeutic targets for COVID-19.
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Affiliation(s)
- J. Pedro Teixeira
- Department of Internal Medicine, Division of Nephrology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.B.); (K.Z.)
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Sharon Barone
- Department of Internal Medicine, Division of Nephrology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.B.); (K.Z.)
- Research/Medicine Services, New Mexico Veterans Healthcare Medical Center, Albuquerque, NM 87108, USA
| | - Kamyar Zahedi
- Department of Internal Medicine, Division of Nephrology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.B.); (K.Z.)
- Research/Medicine Services, New Mexico Veterans Healthcare Medical Center, Albuquerque, NM 87108, USA
| | - Manoocher Soleimani
- Department of Internal Medicine, Division of Nephrology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; (S.B.); (K.Z.)
- Research/Medicine Services, New Mexico Veterans Healthcare Medical Center, Albuquerque, NM 87108, USA
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97
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Nappi F, Iervolino A, Avtaar Singh SS. Molecular Insights of SARS-CoV-2 Antivirals Administration: A Balance between Safety Profiles and Impact on Cardiovascular Phenotypes. Biomedicines 2022; 10:437. [PMID: 35203646 PMCID: PMC8962379 DOI: 10.3390/biomedicines10020437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic has resulted in a complex clinical challenge, caused by a novel coronavirus, partially similar to previously known coronaviruses but with a different pattern of contagiousness, complications, and mortality. Since its global spread, several therapeutic agents have been developed to address the heterogeneous disease treatment, in terms of severity, hospital or outpatient management, and pre-existing clinical conditions. To better understand the rationale of new or old repurposed medications, the structure and host-virus interaction molecular bases are presented. The recommended agents by EDSA guidelines comprise of corticosteroids, JAK-targeting monoclonal antibodies, IL-6 inhibitors, and antivirals, some of them showing narrow indications due to the lack of large population trials and statistical power. The aim of this review is to present FDA-approved or authorized for emergency use antivirals, namely remdesivir, molnupinavir, and the combination nirmatrelvir-ritonavir and their impact on the cardiovascular system. We reviewed the literature for metanalyses, randomized clinical trials, and case reports and found positive associations between remdesivir and ritonavir administration at therapeutic doses and changes in cardiac conduction, relatable to their previously known pro-arrhythmogenic effects and important ritonavir interactions with cardioactive medications including antiplatelets, anti-arrhythmic agents, and lipid-lowering drugs, possibly interfering with pre-existing therapeutic regimens. Nonetheless, safety profiles of antivirals are largely questioned and addressed by health agencies, in consideration of COVID-19 cardiac and pro-thrombotic complications generally experienced by predisposed subjects. Our advice is to continuously adhere to the strict indications of FDA documents, monitor the possible side effects of antivirals, and increase physicians' awareness on the co-administration of antivirals and cardiovascular-relevant medications. This review dissects the global and local tendency to structure patient-based treatment plans, for a glance towards practical application of precision medicine.
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Affiliation(s)
- Francesco Nappi
- Department of Cardiac Surgery, Centre Cardiologique du Nord de Saint-Denis, 93200 Saint-Denis, France
| | - Adelaide Iervolino
- Department of Internal Medicine, University Policlinic Federico II, 80131 Naples, Italy;
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98
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Ribaudo G, Ongaro A, Oselladore E, Zagotto G, Memo M, Gianoncelli A. A computational approach to drug repurposing against SARS-CoV-2 RNA dependent RNA polymerase (RdRp). J Biomol Struct Dyn 2022; 40:1101-1108. [PMID: 32948103 PMCID: PMC7544925 DOI: 10.1080/07391102.2020.1822209] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/06/2020] [Indexed: 01/18/2023]
Abstract
The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused a worldwide outbreak of coronavirus disease 19 (COVID-19), which rapidly evolved as a global concern. The efforts of the scientific community are pointed towards the identification of promptly available therapeutic options. RNA-dependent RNA polymerase (RdRp) is a promising target for developing small molecules to contrast SARS-CoV-2 replication. Modern computational tools can boost identification and repurposing of known drugs targeting RdRp. We here report the results regarding the screening of a database containing more than 8800 molecules, including approved, experimental, nutraceutical, illicit, withdrawn and investigational compounds. The molecules were docked against the cryo-electron microscopy structure of SARS-CoV-2 RdRp, optimized by means of molecular dynamics (MD) simulations. The adopted three-stage ensemble docking study underline that compounds formerly developed as kinase inhibitors may interact with RdRp.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Erika Oselladore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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99
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Finn A, Jindal A, Andrea SB, Selvaraj V, Dapaah-Afriyie K. Association of Treatment with Remdesivir and 30-day Hospital Readmissions in Patients Hospitalized with COVID-19. Am J Med Sci 2022; 363:403-410. [PMID: 35151637 PMCID: PMC8830144 DOI: 10.1016/j.amjms.2022.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/25/2022]
Abstract
Background Since the beginning of COVID-19 pandemic, there has been a widespread use of remdesivir in adults and children. There is little known information about remdesivir's role in reducing 30-day readmissions after hospitalization with COVID-19. This study aimed to determine whether treatment with remdesivir was associated with reduced risk of 30-day readmission after index hospitalization with COVID-19. Methods The study was a multi-center cohort study in Rhode Island, USA. Patients included all adults that were discharged after hospital treatment for COVID-19 between April 1st and December 31st, 2020. The main study outcomes were length of hospital stay, 30-day readmission, and post-discharge 30 days mortality. Results A total of 2,062 patients (2,279 hospitalizations) were included in the analytic sample. Patients were less likely to be readmitted within 30 days if they received remdesivir relative to not receiving remdesivir; associations were strongest for those with mild disease (RR: 0.31; 95% CI: 0.13,0.75). Remdesivir treatment was associated with reduction in all-cause mortality (HR: 0.65; 95% CI: 0.49,0.85) and an increase in length of stay (estimated average increase of 3.27 days; 95% CI: 2.11,4.44). Limitation: Unmeasured factors such as time-to-treatment and severity of disease prior to initiation of remdesivir. Conclusions Remdesivir may be an effective strategy for reducing progression to severe COVID-19 disease and limiting morbidity associated with readmission to hospital. Larger prospective studies are justified to study the role of remdesivir in mild or early COVID-19 with high risk of disease progression and readmission to hospital within 30 days.
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Affiliation(s)
- Arkadiy Finn
- Division of Hospital Medicine, The Miriam Hospital, Providence, RI, USA; Department of Medicine, Warren Alpert School of Medicine at Brown University, Providence, RI, USA.
| | - Atin Jindal
- Division of Hospital Medicine, The Miriam Hospital, Providence, RI, USA; Department of Medicine, Warren Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Sarah B Andrea
- Lifespan Biostatistics Epidemiology and Research Design Core, Providence, RI, USA
| | - Vijairam Selvaraj
- Division of Hospital Medicine, The Miriam Hospital, Providence, RI, USA; Department of Medicine, Warren Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Kwame Dapaah-Afriyie
- Division of Hospital Medicine, The Miriam Hospital, Providence, RI, USA; Department of Medicine, Warren Alpert School of Medicine at Brown University, Providence, RI, USA
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100
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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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