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Sibille G, Mannino G, Frasson I, Pavan M, Luganini A, Salata C, Maffei ME, Gribaudo G. The Novel A-Type Proanthocyanidin-Rich Phytocomplex SP4™ Acts as a Broad-Spectrum Antiviral Agent against Human Respiratory Viruses. Int J Mol Sci 2024; 25:7370. [PMID: 39000477 PMCID: PMC11242173 DOI: 10.3390/ijms25137370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
The appearance of new respiratory virus infections in humans with epidemic or pandemic potential has underscored the urgent need for effective broad-spectrum antivirals (BSAs). Bioactive compounds derived from plants may provide a natural source of new BSA candidates. Here, we investigated the novel phytocomplex formulation SP4™ as a candidate direct-acting BSA against major current human respiratory viruses, including coronaviruses and influenza viruses. SP4™ inhibited the in vitro replication of SARS-CoV-2, hCoV-OC43, hCoV-229E, Influenza A and B viruses, and respiratory syncytial virus in the low-microgram range. Using hCoV-OC43 as a representative respiratory virus, most of the antiviral activity of SP4™ was observed to stem primarily from its dimeric A-type proanthocyanidin (PAC-A) component. Further investigations of the mechanistic mode of action showed SP4™ and its PAC-A-rich fraction to prevent hCoV-OC43 from attaching to target cells and exert virucidal activity. This occurred through their interaction with the spike protein of hCoV-OC43 and SARS-CoV-2, thereby interfering with spike functions and leading to the loss of virion infectivity. Overall, these findings support the further development of SP4™ as a candidate BSA of a natural origin for the prevention of human respiratory virus infections.
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Affiliation(s)
- Giulia Sibille
- Microbiology and Virology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Turin, Italy; (G.S.); (M.P.); (A.L.)
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Quarello 15/a, 10135 Torino, Italy; (G.M.); (M.E.M.)
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (I.F.); (C.S.)
| | - Marta Pavan
- Microbiology and Virology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Turin, Italy; (G.S.); (M.P.); (A.L.)
| | - Anna Luganini
- Microbiology and Virology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Turin, Italy; (G.S.); (M.P.); (A.L.)
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (I.F.); (C.S.)
| | - Massimo E. Maffei
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Quarello 15/a, 10135 Torino, Italy; (G.M.); (M.E.M.)
| | - Giorgio Gribaudo
- Microbiology and Virology Unit, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Turin, Italy; (G.S.); (M.P.); (A.L.)
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2
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Zhang X, Luo F, Zhang H, Guo H, Zhou J, Li T, Chen S, Song S, Shen M, Wu Y, Gao Y, Han X, Wang Y, Hu C, Zhao X, Guo H, Zhang D, Lu Y, Wang W, Wang K, Tang N, Jin T, Ding M, Luo S, Lin C, Lu T, Lu B, Tian Y, Yang C, Cheng G, Yang H, Jin A, Ji X, Gong R, Chiu S, Huang A. Prophylactic efficacy of an intranasal spray with 2 synergetic antibodies neutralizing Omicron. JCI Insight 2024; 9:e171034. [PMID: 38587080 PMCID: PMC11128199 DOI: 10.1172/jci.insight.171034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDAs Omicron is prompted to replicate in the upper airway, neutralizing antibodies (NAbs) delivered through inhalation might inhibit early-stage infection in the respiratory tract. Thus, elucidating the prophylactic efficacy of NAbs via nasal spray addresses an important clinical need.METHODSThe applicable potential of a nasal spray cocktail containing 2 NAbs was characterized by testing its neutralizing potency, synergetic neutralizing mechanism, emergency protective and therapeutic efficacy in a hamster model, and pharmacokinetics/pharmacodynamic (PK/PD) in human nasal cavity.RESULTSThe 2 NAbs displayed broad neutralizing efficacy against Omicron, and they could structurally compensate each other in blocking the Spike-ACE2 interaction. When administrated through the intranasal mucosal route, this cocktail demonstrated profound efficacy in the emergency prevention in hamsters challenged with authentic Omicron BA.1. The investigator-initiated trial in healthy volunteers confirmed the safety and the PK/PD of the NAb cocktail delivered via nasal spray. Nasal samples from the participants receiving 4 administrations over a course of 16 hours demonstrated potent neutralization against Omicron BA.5 in an ex vivo pseudovirus neutralization assay.CONCLUSIONThese results demonstrate that the NAb cocktail nasal spray provides a good basis for clinical prophylactic efficacy against Omicron infections.TRIAL REGISTRATIONwww.chictr.org.cn, ChiCTR2200066525.FUNDINGThe National Science and Technology Major Project (2017ZX10202203), the National Key Research and Development Program of China (2018YFA0507100), Guangzhou National Laboratory (SRPG22-015), Lingang Laboratory (LG202101-01-07), Science and Technology Commission of Shanghai Municipality (YDZX20213100001556), and the Emergency Project from the Science & Technology Commission of Chongqing (cstc2021jscx-fyzxX0001).
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Affiliation(s)
- Xinghai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Feiyang Luo
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Huajun Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Junhui Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Li
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Shaohong Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Song
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Meiying Shen
- Department of Endocrine Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiaojian Han
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Yingming Wang
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Chao Hu
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | | | | | | | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | | | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ni Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Tengchuan Jin
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | | | - Shuhui Luo
- Mindao Haoyue Co., Ltd., Chongqing, China
| | - Cuicui Lin
- Mindao Haoyue Co., Ltd., Chongqing, China
| | | | - Bingxia Lu
- Mindao Haoyue Co., Ltd., Chongqing, China
| | - Yang Tian
- Mindao Haoyue Co., Ltd., Chongqing, China
| | | | | | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, and
- Chongqing Key Laboratory of Basic and Translational Research of Tumor Immunology, Chongqing Medical University, Chongqing, China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
- Institute of Life Sciences, and
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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3
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Tasneem A, Sultan A, Singh P, Bairagya HR, Almasoudi HH, Alhazmi AYM, Binshaya AS, Hakami MA, Alotaibi BS, Abdulaziz Eisa A, Alolaiqy ASI, Hasan MR, Dev K, Dohare R. Identification of potential therapeutic targets for COVID-19 through a structural-based similarity approach between SARS-CoV-2 and its human host proteins. Front Genet 2024; 15:1292280. [PMID: 38370514 PMCID: PMC10869566 DOI: 10.3389/fgene.2024.1292280] [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: 09/11/2023] [Accepted: 01/08/2024] [Indexed: 02/20/2024] Open
Abstract
Background: The COVID-19 pandemic caused by SARS-CoV-2 has led to millions of deaths worldwide, and vaccination efficacy has been decreasing with each lineage, necessitating the need for alternative antiviral therapies. Predicting host-virus protein-protein interactions (HV-PPIs) is essential for identifying potential host-targeting drug targets against SARS-CoV-2 infection. Objective: This study aims to identify therapeutic target proteins in humans that could act as virus-host-targeting drug targets against SARS-CoV-2 and study their interaction against antiviral inhibitors. Methods: A structure-based similarity approach was used to predict human proteins similar to SARS-CoV-2 ("hCoV-2"), followed by identifying PPIs between hCoV-2 and its target human proteins. Overlapping genes were identified between the protein-coding genes of the target and COVID-19-infected patient's mRNA expression data. Pathway and Gene Ontology (GO) term analyses, the construction of PPI networks, and the detection of hub gene modules were performed. Structure-based virtual screening with antiviral compounds was performed to identify potential hits against target gene-encoded protein. Results: This study predicted 19,051 unique target human proteins that interact with hCoV-2, and compared to the microarray dataset, 1,120 target and infected group differentially expressed genes (TIG-DEGs) were identified. The significant pathway and GO enrichment analyses revealed the involvement of these genes in several biological processes and molecular functions. PPI network analysis identified a significant hub gene with maximum neighboring partners. Virtual screening analysis identified three potential antiviral compounds against the target gene-encoded protein. Conclusion: This study provides potential targets for host-targeting drug development against SARS-CoV-2 infection, and further experimental validation of the target protein is required for pharmaceutical intervention.
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Affiliation(s)
- Alvea Tasneem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Armiya Sultan
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Hridoy R. Bairagya
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Hassan Hussain Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | | | - Abdulkarim S. Binshaya
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Bader S. Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Alaa Abdulaziz Eisa
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | | | - Mohammad Raghibul Hasan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Kapil Dev
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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4
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Zhang H, Li B, Yang H, Tan Y, Tan X, Tang Y. Total Synthesis of Carolacton and Demethylcarolactons with Potent Antiviral Activity. Org Lett 2024; 26:370-375. [PMID: 38170945 DOI: 10.1021/acs.orglett.3c04038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Carolacton, a naturally occurring MTHFD1 inhibitor, exhibits potent inhibitory activity against various RNA viruses including SARS-CoV-2. Herein, we present a concise total synthesis of carolacton, featuring the Krische allylation, Marshall coupling, NHK coupling, and RCM reaction as key elements. Additionally, we have synthesized three simplified carolacton analogues, one of which, namely, 14-demethyl-carolacton, exhibited notable antiviral activity. The present work paves the way for further exploration of the therapeutic potential of carolacton and its analogues.
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Affiliation(s)
- Haoyu Zhang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Bingsong Li
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Hongzhi Yang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Ya Tan
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xu Tan
- Chinese Institutes for Medical Research, Beijing 100069, China
| | - Yefeng Tang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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5
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Arman BY, Brun J, Hill ML, Zitzmann N, von Delft A. An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic. Int J Mol Sci 2023; 25:354. [PMID: 38203525 PMCID: PMC10779148 DOI: 10.3390/ijms25010354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.
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Affiliation(s)
- Benediktus Yohan Arman
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Juliane Brun
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Michelle L. Hill
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Nicole Zitzmann
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Annette von Delft
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
- Centre for Medicine Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
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6
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Dahal S, Clayton K, Cabral T, Cheng R, Jahanshahi S, Ahmed C, Koirala A, Villasmil Ocando A, Malty R, Been T, Hernandez J, Mangos M, Shen D, Babu M, Calarco J, Chabot B, Attisano L, Houry WA, Cochrane A. On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine. J Virol 2023; 97:e0039623. [PMID: 37706687 PMCID: PMC10617549 DOI: 10.1128/jvi.00396-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4+ T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.
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Affiliation(s)
- Subha Dahal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kiera Clayton
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tyler Cabral
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahrzad Jahanshahi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Choudhary Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amrit Koirala
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ramy Malty
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Terek Been
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Javier Hernandez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Mangos
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Shen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mohan Babu
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - John Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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7
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Yu X, Kong Q. Potential value of neuroimmunotherapy for COVID-19: efficacies and mechanisms of vagus nerve stimulation, electroacupuncture, and cholinergic drugs. Front Immunol 2023; 14:1197467. [PMID: 37475861 PMCID: PMC10355152 DOI: 10.3389/fimmu.2023.1197467] [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: 03/31/2023] [Accepted: 05/23/2023] [Indexed: 07/22/2023] Open
Abstract
COVID-19 is an inflammatory disease with multiple organs involved, mainly respiratory symptoms. Although the majority of patients with COVID-19 present with a mild to moderate self-limited course of illness, about 5-10% of patients with inflammatory disorders in severe COVID-19 have life-threatening progression. With the exception of a few drugs that have shown outstanding anti-COVID-19 effects, the efficacy of most drugs remains controversial. An increasing number of animal and clinical studies have shown that neuromodulation has a significant effect on reducing inflammatory markers of COVID-19, thus exerting an effective neuroimmunotherapeutic value. Currently, the main neuroimmunomodulatory measures effective against COVID-19 include vagus nerve stimulation, electroacupuncture, and cholinergic drugs. In this review, we will summarize the research progress of potential value of this neuroimmunotherapy measures for COVID-19 and elaborate its efficacies and mechanisms, in order to provide reliable evidence for clinical intervention.
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Affiliation(s)
- Xianqiang Yu
- Women and Children's Hospital Affiliated to Qingdao University, Heart center, Qingdao, China
- University of California, Los Angeles, Department of Cardiology, Los Angeles, CA, United States
| | - Qingming Kong
- School of Laboratory Medicine and Bioengineering, Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang province, Key Laboratory of Bio-tech Vaccine of Zhejiang Province, Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou, China
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8
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Milan Bonotto R, Mitrović A, Sosič I, Martinez-Orellana P, Dattola F, Gobec S, Kos J, Marcello A. Cathepsin inhibitors nitroxoline and its derivatives inhibit SARS-CoV-2 infection. Antiviral Res 2023:105655. [PMID: 37355023 PMCID: PMC10287183 DOI: 10.1016/j.antiviral.2023.105655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The severity of the SARS-CoV-2 pandemic and the recurring (re)emergence of viruses prompted the development of new therapeutic approaches that target viral and host factors crucial for viral infection. Among them, host peptidases cathepsins B and L have been described as essential enzymes during SARS-CoV-2 entry. In this study, we evaluated the effect of potent selective cathepsin inhibitors as antiviral agents. We demonstrated that selective cathepsin B inhibitors, such as the antimicrobial agent nitroxoline and its derivatives, impair SARS-CoV-2 infection in vitro. Antiviral activity observed at early stage of virus entry was cell-type dependent and correlated well with the intracellular content and enzymatic function of cathepsins B or L. Furthermore, tested inhibitors were effective against the ancestral SARS-CoV-2 D614 as well as against the more recent BA.1_4 (Omicron). Taken together, our results highlight the important role of host cysteine cathepsin B in SARS-CoV-2 virus entry and show that cathepsin-specific inhibitors, such as nitroxoline and its derivatives, could be used to treat COVID-19. Finally, these results also suggest that nitroxoline has potential to be further explored as repurposed drug in antiviral therapy.
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Affiliation(s)
- Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Pamela Martinez-Orellana
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Federica Dattola
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy.
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9
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Santos-Mendoza T. The Envelope (E) Protein of SARS-CoV-2 as a Pharmacological Target. Viruses 2023; 15:v15041000. [PMID: 37112980 PMCID: PMC10143767 DOI: 10.3390/v15041000] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus is still a global health concern. Several spike (S) protein-based vaccines have been developed that efficiently protect the human population against severe forms of COVID-19. However, some SARS-CoV-2 variants of concern (VOCs) have emerged that evade the protective effect of vaccine-induced antibodies. Therefore, efficient and specific antiviral treatments to control COVID-19 are indispensable. To date, two drugs have been approved for mild COVID-19 treatment; nevertheless, more drugs, preferably broad-spectrum and ready-to-use therapeutic agents for new pandemics, are needed. Here, I discuss the PDZ-dependent protein-protein interactions of the viral E protein with host proteins as attractive alternatives for the development of antivirals against coronavirus.
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Affiliation(s)
- Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
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10
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Svilenov HL, Delhommel F, Siebenmorgen T, Rührnößl F, Popowicz GM, Reiter A, Sattler M, Brockmeyer C, Buchner J. Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2. Commun Biol 2023; 6:386. [PMID: 37031320 PMCID: PMC10082628 DOI: 10.1038/s42003-023-04762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.
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Affiliation(s)
- Hristo L Svilenov
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Johannes Buchner
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
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11
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Glusac KD, Saicic RN. Are science and technology friends or foes? Nat Chem 2023; 15:439-442. [PMID: 36997699 DOI: 10.1038/s41557-023-01171-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Ksenija D Glusac
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Chemical Sciences and Engineering, Argonne National Laboratory, Lemont, IL, USA.
| | - Radomir N Saicic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia.
- Serbian Academy of Sciences and Arts, Belgrade, Serbia.
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12
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Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023; 63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
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Affiliation(s)
- Rajendra P. Joshi
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Katherine J. Schultz
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Jesse William Wilson
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Agustin Kruel
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Rohith Anand Varikoti
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Chathuri J. Kombala
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Process Research and Development,
Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New
Jersey 07065, United States
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Leighton Coates
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Second Target Station, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Ying Kong
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Austin Clyde
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Colleen B. Jonsson
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
- Institute for the Study of Host-Pathogen Systems,
University of Tennessee Health Science Center, Memphis,
Tennessee 38103, United States
- Department of Microbiology, Immunology and
Biochemistry, University of Tennessee Health Science Center,
Memphis, Tennessee 38103, United States
| | - Kristoffer R. Brandvold
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Martha S. Head
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- Center for Research Acceleration by Digital
Innovation, Amgen Research, Thousand Oaks, California 91320,
United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
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13
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Earth-friendly-assessed silver-nanoparticles spectrophotometric method for rapid and sensitive analysis of Molnupiravir, an FDA-approved candidate for COVID-19: application on pharmaceutical formulation and dissolution test. BMC Chem 2023; 17:13. [PMID: 36899439 PMCID: PMC9999326 DOI: 10.1186/s13065-023-00933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Molnupiravir is the first oral direct-acting antiviral prodrug recently approved for the COVID-19 pandemic. Here and for the first time, we present a novel, sensitive, robust, and simple silver-nanoparticles spectrophotometric technique for molnupiravir analysis in its capsules and dissolution media. This spectrophotometric technique involved silver-nanoparticles synthesis through a redox reaction between the reducing agent (molnupiravir) and the oxidizing agent (silver nitrate) in presence of polyvinylpyrrolidone as a stabilizing agent. The produced silver-nanoparticles have an intense surface plasmon resonance peak at 416 nm where the measured absorbance values were utilized for the quantitative analysis of molnupiravir. The produced silver-nanoparticles were recognized by using the transmission electron microscope. Under optimal conditions, a good linear rapport was accomplished between molnupiravir concentrations and the corresponding absorbance values in a range of (100-2000) ng/mL with a detection limit of 30 ng/mL. Greenness assessment was implemented using eco-scale scoring and GAPI disclosing the excellent greenness of the suggested technique. The suggested silver-nanoparticles technique was authenticated according to recommendations of the ICH and statistically assessed with the reported liquid chromatographic method without significant differences regarding accuracy or precision. Accordingly, the suggested technique is deemed a green and cheap alternative for assaying molnupiravir due to its reliance primarily on water. Furthermore, the suggested technique's high sensitivity can be employed for investigating molnupiravir bioequivalence in future studies.
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14
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Treating COVID-19: Targeting the Host Response, Not the Virus. Life (Basel) 2023; 13:life13030712. [PMID: 36983871 PMCID: PMC10054780 DOI: 10.3390/life13030712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 03/09/2023] Open
Abstract
In low- and middle-income countries (LMICs), inexpensive generic drugs like statins, ACE inhibitors, and ARBs, especially if used in combination, might be the only practical way to save the lives of patients with severe COVID-19. These drugs will already be available in all countries on the first pandemic day. Because they target the host response to infection instead of the virus, they could be used to save lives during any pandemic. Observational studies show that inpatient statin treatment reduces 28–30-day mortality but randomized controlled trials have failed to show this benefit. Combination treatment has been tested for antivirals and dexamethasone but, with the exception of one observational study in Belgium, not for inexpensive generic drugs. Future pandemic research must include testing combination generic drug treatments that could be used in LMICs.
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15
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Gao H, Dai R, Su R. Computer-aided drug design for the pain-like protease (PL pro) inhibitors against SARS-CoV-2. Biomed Pharmacother 2023; 159:114247. [PMID: 36689835 PMCID: PMC9841087 DOI: 10.1016/j.biopha.2023.114247] [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: 11/25/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A new coronavirus, known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is a highly contagious virus and has caused a massive worldwide health crisis. While large-scale vaccination efforts are underway, the management of population health, economic impact and asof-yet unknown long-term effects on physical and mental health will be a key challenge for the next decade. The papain-like protease (PLpro) of SARS-CoV-2 is a promising target for antiviral drugs. This report used pharmacophore-based drug design technology to identify potential compounds as PLpro inhibitors against SARS-CoV-2. The optimal pharmacophore model was fully validated using different strategies and then was employed to virtually screen out 10 compounds with inhibitory. Molecular docking and non-bonding interactions between the targeted protein PLpro and compounds showed that UKR1129266 was the best compound. These results provided a theoretical foundation for future studies of PLpro inhibitors against SARS-CoV-2.
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Affiliation(s)
- Hongwei Gao
- School of Life Science, Ludong University, Yantai, Shandong 264025, China.
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16
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Firouzi R, Ashouri M. Identification of Potential Anti‐COVID‐19 Drug Leads from Medicinal Plants through Virtual High‐Throughput Screening. ChemistrySelect 2023. [DOI: 10.1002/slct.202203865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry Chemistry and Chemical Engineering Research Center of Iran Tehran Iran
| | - Mitra Ashouri
- Department of Physical Chemistry School of Chemistry College of Science University of Tehran Tehran Iran
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17
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Zhang J, He M, Xie Q, Su A, Yang K, Liu L, Liang J, Li Z, Huang X, Hu J, Liu Q, Song B, Hu C, Chen L, Wang Y. Predicting In Vitro and In Vivo Anti-SARS-CoV-2 Activities of Antivirals by Intracellular Bioavailability and Biochemical Activity. ACS OMEGA 2022; 7:45023-45035. [PMID: 36530252 PMCID: PMC9753181 DOI: 10.1021/acsomega.2c05376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Cellular drug response (concentration required for obtaining 50% of a maximum cellular effect, EC50) can be predicted by the intracellular bioavailability (F ic) and biochemical activity (half-maximal inhibitory concentration, IC50) of drugs. In an ideal model, the cellular negative log of EC50 (pEC50) equals the sum of log F ic and the negative log of IC50 (pIC50). Here, we measured F ic's of remdesivir, favipiravir, and hydroxychloroquine in various cells and calculated their anti-SARS-CoV-2 EC50's. The predicted EC50's are close to the observed EC50's in vitro. When the lung concentrations of antiviral drugs are higher than the predicted EC50's in alveolar type 2 cells, the antiviral drugs inhibit virus replication in vivo, and vice versa. Overall, our results indicate that both in vitro and in vivo antiviral activities of drugs can be predicted by their intracellular bioavailability and biochemical activity without using virus. This virus-free strategy can help medicinal chemists and pharmacologists to screen antivirals during early drug discovery, especially for researchers who are not able to work in the high-level biosafety lab.
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Affiliation(s)
- Jinwen Zhang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Mingfeng He
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Qian Xie
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ailing Su
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Kuangyang Yang
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Lichu Liu
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Jianhui Liang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ziqi Li
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Xiuxin Huang
- The
First Clinical College of Changsha Medical College, Changsha410219, China
| | - Jianshu Hu
- Department
of Pharmacology, University of Oxford, OxfordOX1 3QT, UK
| | - Qian Liu
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Bing Song
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Chun Hu
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Lei Chen
- School of
Life Science and Technology, Key Laboratory of Developmental Genes
and Human Disease, Southeast University, Nanjing210096, China
| | - Yan Wang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
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18
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Tackling the Future Pandemics: Broad-Spectrum Antiviral Agents (BSAAs) Based on A-Type Proanthocyanidins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238353. [PMID: 36500445 PMCID: PMC9736452 DOI: 10.3390/molecules27238353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
A-type proanthocyanidins (PAC-As) are plant-derived natural polyphenols that occur as oligomers or polymers of flavan-3-ol monomers, such as (+)-catechin and (-)-epicatechin, connected through an unusual double A linkage. PAC-As are present in leaves, seeds, flowers, bark, and fruits of many plants, and are thought to exert protective natural roles against microbial pathogens, insects, and herbivores. Consequently, when tested in isolation, PAC-As have shown several biological effects, through antioxidant, antibacterial, immunomodulatory, and antiviral activities. PAC-As have been observed in fact to inhibit replication of many different human viruses, and both enveloped and non-enveloped DNA and RNA viruses proved sensible to their inhibitory effect. Mechanistic studies revealed that PAC-As cause reduction of infectivity of viral particles they come in contact with, as a result of their propensity to interact with virion surface capsid proteins or envelope glycoproteins essential for viral attachment and entry. As viral infections and new virus outbreaks are a major public health concern, development of effective Broad-Spectrum Antiviral Agents (BSAAs) that can be rapidly deployable even against future emerging viruses is an urgent priority. This review summarizes the antiviral activities and mechanism of action of PAC-As, and their potential to be deployed as BSAAs against present and future viral infections.
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19
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Reaching the Final Endgame for Constant Waves of COVID-19. Viruses 2022; 14:v14122637. [PMID: 36560641 PMCID: PMC9783511 DOI: 10.3390/v14122637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Despite intramuscular vaccines saving millions of lives, constant devastating waves of SARS-CoV-2 infections continue. The elimination of COVID-19 is challenging, but necessary in order to avoid millions more people who would suffer from long COVID if we fail. Our paper describes rapidly advancing and innovative therapeutic strategies for the early stage of infection with COVID-19 so that tolerating continuing cycles of infection should be unnecessary in the future. These therapies include new vaccines with broader specificities, nasal therapies and antiviral drugs some targeting COVID-19 at the first stage of infection and preventing the virus entering the body in the first place. Our article describes the advantages and disadvantages of each of these therapeutic options which in various combinations could eventually prevent renewed waves of infection. Finally, important consideration is given to political, social and economic barriers that since 2020 hindered vaccine application and are likely to interfere again with any COVID-19 endgame.
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20
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Tyrkalska SD, Candel S, Pedoto A, García-Moreno D, Alcaraz-Pérez F, Sánchez-Ferrer Á, Cayuela ML, Mulero V. Zebrafish models of COVID-19. FEMS Microbiol Rev 2022; 47:6794271. [PMID: 36323404 PMCID: PMC9841970 DOI: 10.1093/femsre/fuac042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Although COVID-19 has only recently appeared, research studies have already developed and implemented many animal models for deciphering the secrets of the disease and provided insights into the biology of SARS-CoV-2. However, there are several major factors that complicate the study of this virus in model organisms, such as the poor infectivity of clinical isolates of SARS-CoV-2 in some model species, and the absence of persistent infection, immunopathology, severe acute respiratory distress syndrome, and, in general, all the systemic complications which characterize COVID-19 clinically. Another important limitation is that SARS-CoV-2 mainly causes severe COVID-19 in older people with comorbidities, which represents a serious problem when attempting to use young and immunologically naïve laboratory animals in COVID-19 testing. We review here the main animal models developed so far to study COVID-19 and the unique advantages of the zebrafish model that may help to contribute to understand this disease, in particular to the identification and repurposing of drugs to treat COVID-19, to reveal the mechanism of action and side-effects of Spike-based vaccines, and to decipher the high susceptibility of aged people to COVID-19.
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Affiliation(s)
| | | | - Annamaria Pedoto
- Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Diana García-Moreno
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisca Alcaraz-Pérez
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain,Grupo de Telomerasa, Cáncer y Envejecimiento (TCAG), Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Álvaro Sánchez-Ferrer
- Instituto Murciano de Investigación Biosanitaria (IMIB)-Arrixaca, 30120 Murcia, Spain,Departmento de Bioloquímica y Biología Molecular A, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | | | - Victoriano Mulero
- Corresponding author: Departmento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain. E-mail:
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21
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Sainas S, Giorgis M, Circosta P, Poli G, Alberti M, Passoni A, Gaidano V, Pippione AC, Vitale N, Bonanni D, Rolando B, Cignetti A, Ramondetti C, Lanno A, Ferraris DM, Canepa B, Buccinnà B, Piccinini M, Rizzi M, Saglio G, Al-Karadaghi S, Boschi D, Miggiano R, Tuccinardi T, Lolli ML. Targeting Acute Myelogenous Leukemia Using Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on the 2-Hydroxypyrazolo[1,5- a]pyridine Scaffold: SAR of the Aryloxyaryl Moiety. J Med Chem 2022; 65:12701-12724. [PMID: 36162075 PMCID: PMC9574863 DOI: 10.1021/acs.jmedchem.2c00496] [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: 03/30/2022] [Indexed: 11/28/2022]
Abstract
In recent years, human dihydroorotate dehydrogenase inhibitors have been associated with acute myelogenous leukemia as well as studied as potent host targeting antivirals. Starting from MEDS433 (IC50 1.2 nM), we kept improving the structure-activity relationship of this class of compounds characterized by 2-hydroxypyrazolo[1,5-a]pyridine scaffold. Using an in silico/crystallography supported design, we identified compound 4 (IC50 7.2 nM), characterized by the presence of a decorated aryloxyaryl moiety that replaced the biphenyl scaffold, with potent inhibition and pro-differentiating abilities on AML THP1 cells (EC50 74 nM), superior to those of brequinar (EC50 249 nM) and boosted when in combination with dipyridamole. Finally, compound 4 has an extremely low cytotoxicity on non-AML cells as well as MEDS433; it has shown a significant antileukemic activity in vivo in a xenograft mouse model of AML.
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Affiliation(s)
- Stefano Sainas
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
| | - Marta Giorgis
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
| | - Paola Circosta
- Department
of Clinical and Biological Sciences, University
of Turin, Regione Gonzole 10, Orbassano, Turin 10043, Italy
- Molecular
Biotechnology Center, University of Turin, Via Nizza 52, Turin 10126, Italy
| | - Giulio Poli
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Marta Alberti
- Department
of Pharmaceutical Sciences, University of
Piemonte Orientale, Via
G. Bovio 6, Novara 28100, Italy
| | - Alice Passoni
- Laboratory
of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milan 20156, Italy
| | - Valentina Gaidano
- Division
of Hematology and Cell Therapy, AO Ordine
Mauriziano, Largo Filippo
Turati, 62, Turin 10128, Italy
| | - Agnese C. Pippione
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
| | - Nicoletta Vitale
- Department
of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, Turin 10126, Italy
| | - Davide Bonanni
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
- Life
Science Department, University of Modena, Via Università 4, Modena 41121, Italy
| | - Barbara Rolando
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
| | - Alessandro Cignetti
- Division
of Hematology and Cell Therapy, AO Ordine
Mauriziano, Largo Filippo
Turati, 62, Turin 10128, Italy
| | - Cristina Ramondetti
- Department
of Oncology, University of Turin, Via Michelangelo 27/B, Turin 10125, Italy
| | - Alessia Lanno
- Laboratory
of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, Milan 20156, Italy
| | - Davide M. Ferraris
- Department
of Pharmaceutical Sciences, University of
Piemonte Orientale, Via
G. Bovio 6, Novara 28100, Italy
| | - Barbara Canepa
- GEM FORLAB, Via Ing.
Comotto 36, Caluso, Turin, 10014, Italy
| | - Barbara Buccinnà
- Department
of Oncology, University of Turin, Via Michelangelo 27/B, Turin 10125, Italy
| | - Marco Piccinini
- Department
of Oncology, University of Turin, Via Michelangelo 27/B, Turin 10125, Italy
| | - Menico Rizzi
- Department
of Pharmaceutical Sciences, University of
Piemonte Orientale, Via
G. Bovio 6, Novara 28100, Italy
| | - Giuseppe Saglio
- Department
of Clinical and Biological Sciences, University
of Turin, Regione Gonzole 10, Orbassano, Turin 10043, Italy
- Division
of Hematology and Cell Therapy, AO Ordine
Mauriziano, Largo Filippo
Turati, 62, Turin 10128, Italy
| | - Salam Al-Karadaghi
- Department
of Biochemistry and Structural Biology, Lund University, Naturvetarvägen
14, Box 124, Lund 221 00, Sweden
| | - Donatella Boschi
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
| | - Riccardo Miggiano
- Department
of Pharmaceutical Sciences, University of
Piemonte Orientale, Via
G. Bovio 6, Novara 28100, Italy
| | - Tiziano Tuccinardi
- Molecular
Biotechnology Center, University of Turin, Via Nizza 52, Turin 10126, Italy
| | - Marco L. Lolli
- Department
of Drug Science and Technology, University
of Turin, Via P. Giuria 9, Turin 10125, Italy
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22
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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23
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Apostolopoulos V, Bojarska J, Feehan J, Matsoukas J, Wolf W. Smart therapies against global pandemics: A potential of short peptides. Front Pharmacol 2022; 13:914467. [PMID: 36046832 PMCID: PMC9420997 DOI: 10.3389/fphar.2022.914467] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/01/2022] [Indexed: 12/20/2022] Open
Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC, Australia
| | - Joanna Bojarska
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
- *Correspondence: Joanna Bojarska,
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - John Matsoukas
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- NewDrug, Patras Science Park, Patras, Greece
| | - Wojciech Wolf
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
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24
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Soriano V, Edagwa B, Mendoza CD, Barreiro P, Corral O, Treviño A, Gendelman HE. Ultra-long-acting antivirals as chemical vaccines to prevent viral diseases. Future Microbiol 2022; 17:887-897. [PMID: 35658545 DOI: 10.2217/fmb-2021-0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
For two centuries, vaccines have been successful in the fight against viruses, triggering immune protection. Indeed, the elimination of smallpox, the only infectious disease eradicated to date, was made possible through vaccination. For measles, polio and hepatitis B, vaccines are available but significant challenges exist for universal coverage. For other viruses, such as HIV and hepatitis C, vaccines have remained elusive. Recent advances in medicinal chemistry have resulted in the production of antivirals that can extend activity for months. We envision the use of ultra-long-acting antivirals for the prevention of certain viral illnesses, halting either contagions or reactivations under immunosuppression. Such 'chemical vaccines' would fill an immediate need in providing protection when classic vaccines do not exist, responses are suboptimal, escape mutants emerge or immunity wanes.
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Affiliation(s)
| | - Benson Edagwa
- Department of Pharmacology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carmen de Mendoza
- Internal Medicine Research Laboratory, Puerta de Hierro University Hospital, Majadahonda, Madrid 28222, Spain
| | - Pablo Barreiro
- Research Laboratory, Isabel Zendal Emergency Hospital, Madrid 28055, Spain
| | | | - Ana Treviño
- UNIR Health Sciences School, Madrid 28035, Spain
| | - Howard E Gendelman
- Department of Pharmacology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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25
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Remdesivir: an overview of patenting trends, clinical evidence on COVID-19 treatment, pharmacology and chemistry. Pharm Pat Anal 2022; 11:57-73. [DOI: 10.4155/ppa-2021-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
By December 2021, the COVID-19 caused approximately 6.1 million deaths around the world. Several vaccines have been approved, but there is still a need for non-prophylactic treatments for COVID-19. Remdesivir is an antiviral drug approved for emergency use against COVID-19 in several countries, but one of the first clinical trials was inconclusive about the mortality reduction, although the drug showed a reduction in the recovery time of hospitalized patients. Thus, the present investigation revisits the clinical evidence of using remdesivir for COVID-19 treatment, patent status, pharmacology and chemistry. We found 184 families of patents in the Cortellis database, and concerning the clinical evidence, we retrieved 14 systematic reviews with meta-analysis involving remdesivir as a treatment for COVID-19, discussing the reduction of adverse events, hospitalization days, mortality rate and the mechanical ventilation period.
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26
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Virucidal Activity of the Pyridobenzothiazolone Derivative HeE1-17Y against Enveloped RNA Viruses. Viruses 2022; 14:v14061157. [PMID: 35746629 PMCID: PMC9228864 DOI: 10.3390/v14061157] [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: 04/12/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Pyridobenzothiazolone derivatives are a promising class of broad-spectrum antivirals. However, the mode of action of these compounds remains poorly understood. The HeE1-17Y derivative has already been shown to be a potent compound against a variety of flaviviruses of global relevance. In this work, the mode of action of HeE1-17Y has been studied for West Nile virus taking advantage of reporter replication particles (RRPs). Viral infectivity was drastically reduced by incubating the compound with the virus before infection, thus suggesting a direct interaction with the viral particles. Indeed, RRPs incubated with the inhibitor appeared to be severely compromised in electron microscopy analysis. HeE1-17Y is active against other enveloped viruses, including SARS-CoV-2, but not against two non-enveloped viruses, suggesting a virucidal mechanism that involves the alteration of the viral membrane.
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27
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Niemeyer BF, Benam KH. Untapping host-targeting cross-protective efficacy of anticoagulants against SARS-CoV-2. Pharmacol Ther 2022; 233:108027. [PMID: 34718070 PMCID: PMC8552695 DOI: 10.1016/j.pharmthera.2021.108027] [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: 07/27/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
Responding quickly to emerging respiratory viruses, such as SARS-CoV-2 the causative agent of coronavirus disease 2019 (COVID-19) pandemic, is essential to stop uncontrolled spread of these pathogens and mitigate their socio-economic impact globally. This can be achieved through drug repurposing, which tackles inherent time- and resource-consuming processes associated with conventional drug discovery and development. In this review, we examine key preclinical and clinical therapeutic and prophylactic approaches that have been applied for treatment of SARS-CoV-2 infection. We break these strategies down into virus- versus host-targeting and discuss their reported efficacy, advantages, and disadvantages. Importantly, we highlight emerging evidence on application of host serine protease-inhibiting anticoagulants, such as nafamostat mesylate, as a potentially powerful therapy to inhibit virus activation and offer cross-protection against multiple strains of coronavirus, lower inflammatory response independent of its antiviral effect, and modulate clotting problems seen in COVID-19 pneumonia.
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Affiliation(s)
- Brian F Niemeyer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kambez H Benam
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15219, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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28
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Wang LG, Wang L. Current Strategies in Treating Cytokine Release Syndrome Triggered by Coronavirus SARS-CoV-2. Immunotargets Ther 2022; 11:23-35. [PMID: 35611161 PMCID: PMC9124488 DOI: 10.2147/itt.s360151] [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: 01/27/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022] Open
Abstract
Since the beginning of the SARS-CoV-2 pandemic, the treatments and management of the deadly COVID-19 disease have made great progress. The strategies for developing novel treatments against COVID-19 include antiviral small molecule drugs, cell and gene therapies, immunomodulators, neutralizing antibodies, and combination therapies. Among them, immunomodulators are the most studied treatments. The small molecule antiviral drugs and immunoregulators are expected to be effective against viral variants of SARS-CoV-2 as these drugs target either conservative parts of the virus or common pathways of inflammation. Although the immunoregulators have shown benefits in reducing mortality of cytokine release syndrome (CRS) triggered by SARS-CoV-2 infections, extensive investigations on this class of treatment to launch novel therapies that substantially improve efficacy and reduce side effects are still warranted. Moreover, great challenges have emerged as the SARS-CoV-2 virus quickly, frequently, and continuously evolved. This review provides an update and summarizes the recent advances in the treatment of COVID-19 and in particular emphasized the strategies in managing CRS triggered by SARS-CoV-2. A brief perspective in the battle against the deadly disease was also provided.
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Affiliation(s)
- Long G Wang
- Department of Research and Development, Natrogen Therapeutics International, Inc., Valhalla, NY, USA
- Correspondence: Long G Wang, Department of Research and Development, Natrogen Therapeutics International, Inc., Vosburgh 213, NYMC Campus, Valhalla, NY, 10595, USA, Tel +1 646 229-7583, Email
| | - Luxi Wang
- Department of Clinical Research, Clinipace Clinical Research, Morrisville, NC, USA
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29
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Yang K, Wang C, White KI, Pfuetzner RA, Esquivies L, Brunger AT. Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle. Proc Natl Acad Sci U S A 2022; 119:e2119467119. [PMID: 35363556 PMCID: PMC9169775 DOI: 10.1073/pnas.2119467119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/22/2022] [Indexed: 01/10/2023] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
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Affiliation(s)
- Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - K. Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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30
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Calleja DJ, Kuchel N, Lu BGC, Birkinshaw RW, Klemm T, Doerflinger M, Cooney JP, Mackiewicz L, Au AE, Yap YQ, Blackmore TR, Katneni K, Crighton E, Newman J, Jarman KE, Call MJ, Lechtenberg BC, Czabotar PE, Pellegrini M, Charman SA, Lowes KN, Mitchell JP, Nachbur U, Lessene G, Komander D. Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors. Front Chem 2022; 10:861209. [PMID: 35494659 PMCID: PMC9039177 DOI: 10.3389/fchem.2022.861209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic continues unabated, emphasizing the need for additional antiviral treatment options to prevent hospitalization and death of patients infected with SARS-CoV-2. The papain-like protease (PLpro) domain is part of the SARS-CoV-2 non-structural protein (nsp)-3, and represents an essential protease and validated drug target for preventing viral replication. PLpro moonlights as a deubiquitinating (DUB) and deISGylating enzyme, enabling adaptation of a DUB high throughput (HTS) screen to identify PLpro inhibitors. Drug repurposing has been a major focus through the COVID-19 pandemic as it may provide a fast and efficient route for identifying clinic-ready, safe-in-human antivirals. We here report our effort to identify PLpro inhibitors by screening the ReFRAME library of 11,804 compounds, showing that none inhibit PLpro with any reasonable activity or specificity to justify further progression towards the clinic. We also report our latest efforts to improve piperidine-scaffold inhibitors, 5c and 3k, originally developed for SARS-CoV PLpro. We report molecular details of binding and selectivity, as well as in vitro absorption, distribution, metabolism and excretion (ADME) studies of this scaffold. A co-crystal structure of SARS-CoV-2 PLpro bound to inhibitor 3k guides medicinal chemistry efforts to improve binding and ADME characteristics. We arrive at compounds with improved and favorable solubility and stability characteristics that are tested for inhibiting viral replication. Whilst still requiring significant improvement, our optimized small molecule inhibitors of PLpro display decent antiviral activity in an in vitro SARS-CoV-2 infection model, justifying further optimization.
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Affiliation(s)
- Dale J. Calleja
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Nathan Kuchel
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernadine G. C. Lu
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Richard W. Birkinshaw
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Theresa Klemm
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marcel Doerflinger
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - James P. Cooney
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Liana Mackiewicz
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda E. Au
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Yu Q. Yap
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy R Blackmore
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, VIC, Australia
| | - Kate E. Jarman
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa J. Call
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernhard C. Lechtenberg
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Peter E. Czabotar
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marc Pellegrini
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Kym N. Lowes
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jeffrey P. Mitchell
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Ueli Nachbur
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
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31
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Lang T. Enabling evidence to tackle everyday diseases to mitigate another pandemic. Gates Open Res 2022; 6:45. [PMID: 35923865 PMCID: PMC9296833 DOI: 10.12688/gatesopenres.13497.1] [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] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The next emergent novel pathogen is likely to occur where the ability to undertake health research and collect life-saving data is lacking. Without embedded and ongoing research activities in place spotting and stopping a new threat is not possible, thereby enabling undetected infection and unchecked transmission within a community. Without local existing capabilities to collect such data delay is catastrophic. Fundamental goals in pandemic preparedness should be to stop an outbreak before it becomes a pandemic. This requires immediate action from teams already in place with the right skills, this could be readily achieved if we shift our thinking and enable research capabilities to be present in every healthcare setting. Addressing fundamental gaps in health research capacity and equity could tackle this and then we would be better prepared, globally.
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Affiliation(s)
- Trudie Lang
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
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32
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Recent Advances in Influenza, HIV and SARS-CoV-2 Infection Prevention and Drug Treatment—The Need for Precision Medicine. CHEMISTRY 2022. [DOI: 10.3390/chemistry4020019] [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] Open
Abstract
Viruses, and in particular, RNA viruses, dominate the WHO’s current list of ten global health threats. Of these, we review the widespread and most common HIV, influenza virus, and SARS-CoV-2 infections, as well as their possible prevention by vaccination and treatments by pharmacotherapeutic approaches. Beyond the vaccination, we discuss the virus-targeting and host-targeting drugs approved in the last five years, in the case of SARS-CoV-2 in the last one year, as well as new drug candidates and lead molecules that have been published in the same periods. We share our views on vaccination and pharmacotherapy, their mutually reinforcing strategic significance in combating pandemics, and the pros and cons of host and virus-targeted drug therapy. The COVID-19 pandemic has provided evidence of our limited armamentarium to fight emerging viral diseases. Novel broad-spectrum vaccines as well as drugs that could even be applied as prophylactic treatments or in early phases of the viremia, possibly through oral administration, are needed in all three areas. To meet these needs, the use of multi-data-based precision medicine in the practice and innovation of vaccination and drug therapy is inevitable.
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Khan A, Rao TS, Joshi HM. Phage therapy in the Covid-19 era: Advantages over antibiotics. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100115. [PMID: 35187507 PMCID: PMC8847111 DOI: 10.1016/j.crmicr.2022.100115] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Excessive use of antibiotics during the COVID-19 pandemic may accelerate the emergence of AMR. Antibiotic-mediated dysbiosis significantly impacts immune-homoeostasis and thereby negatively impacting the recovery from COVID-19. Antibiotic-induced dysbiosis will also negatively impacts the pulmonary functioning of the COVID-19 patient via the Gut-Lung Axis. Bacteriophages or “phage therapy” can be an ideal alternative for antibiotics having desired specificity and availability. Phage therapy can also act as an anti-inflammatory agent to avoid cytokine storm in COVID19.
Today, the entire world is battling to contain the spread of COVID-19. Massive efforts are being made to find a therapeutic solution in the shortest possible time. However, the research community is becoming increasingly concerned about taking a shortsighted strategy without contemplating the long-term consequences. For example, It has been reported that only 8.4% of total COVID-19 patients develop a secondary bacterial infection. In comparison, 74.6% of them are administered with antibiotics as prophylactic treatment. We contend that overuse of broad-spectrum antibiotics increases the likelihood of AMR development and negatively affects the patient's recovery due to the prevalence of the "gut-lung axis.". Consequently, the use of antibiotics to treat COVID-19 patients must be rationalized, or an alternative treatment must be sought that does not risk contributing to AMR development and positively impacts the treatment outcomes. Phage therapy, a century-old concept, is one of the most promising approaches that can be adapted to serve this purpose. This review emphasizes the negative impact of excessive antibiotic use in COVID-19 treatment and provides an overview of how phage therapy can be used as an alternative treatment option. We have argued that targeted killing (narrow spectrum) and anti-inflammatory (which can target the primary cause of mortality in COVID-19) properties of phages can be an effective alternative to antibiotics.
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Affiliation(s)
- Atif Khan
- Water & Steam Chemistry Division, BARC Facilities, Kalpakkam, Tamil Nadu, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - T Subba Rao
- Water & Steam Chemistry Division, BARC Facilities, Kalpakkam, Tamil Nadu, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Hiren M Joshi
- Water & Steam Chemistry Division, BARC Facilities, Kalpakkam, Tamil Nadu, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
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34
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Negahdaripour M, Rahbar MR, Mosalanejad Z, Gholami A. Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9735626. [PMID: 35154362 PMCID: PMC8829439 DOI: 10.1155/2022/9735626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/28/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was characterized as a pandemic by the World Health Organization (WHO) in Dec. 2019. SARS-CoV-2 binds to the cell membrane through spike proteins on its surface and infects the cell. Furin, a host-cell enzyme, possesses a binding site for the spike protein. Thus, molecules that block furin could potentially be a therapeutic solution. Defensins are antimicrobial peptides that can hypothetically inhibit furin because of their arginine-rich structure. Theta-defensins, a subclass of defensins, have attracted attention as drug candidates due to their small size, unique structure, and involvement in several defense mechanisms. Theta-defensins could be a potential treatment for COVID-19 through furin inhibition and an anti-inflammatory mechanism. Note that inflammatory events are a significant and deadly condition that could happen at the later stages of COVID-19 infection. Here, the potential of theta-defensins against SARS-CoV-2 infection was investigated through in silico approaches. Based on docking analysis results, theta-defensins can function as furin inhibitors. Additionally, a novel candidate peptide against COVID-19 with optimal properties regarding antigenicity, stability, electrostatic potential, and binding strength was proposed. Further in vitro/in vivo investigations could verify the efficiency of the designed novel peptide.
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Affiliation(s)
- Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mosalanejad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Gholami
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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35
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Chang KP, Reynolds JM, Liu Y, He JJ. Leishmaniac Quest for Developing a Novel Vaccine Platform. Is a Roadmap for Its Advances Provided by the Mad Dash to Produce Vaccines for COVID-19? Vaccines (Basel) 2022; 10:vaccines10020248. [PMID: 35214706 PMCID: PMC8874365 DOI: 10.3390/vaccines10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
“Bugs as drugs” in medicine encompasses the use of microbes to enhance the efficacy of vaccination, such as the delivery of vaccines by Leishmania—the protozoan etiological agent of leishmaniasis. This novel approach is appraised in light of the successful development of vaccines for Covid-19. All relevant aspects of this pandemic are summarized to provide the necessary framework in contrast to leishmaniasis. The presentation is in a side-by-side matching format with particular emphasis on vaccines. The comparative approach makes it possible to highlight the timeframe of the vaccine workflows condensed by the caveats of pandemic urgency and, at the same time, provides the background of Leishmania behind its use as a vaccine carrier. Previous studies in support of the latter are summarized as follows. Leishmaniasis confers life-long immunity on patients after cure, suggesting the effective vaccination is achievable with whole-cell Leishmania. A new strategy was developed to inactivate these cells in vitro, rendering them non-viable, hence non-disease causing, albeit retaining their immunogenicity and adjuvanticity. This was achieved by installing a dual suicidal mechanism in Leishmania for singlet oxygen (1O2)-initiated inactivation. In vitro cultured Leishmania were genetically engineered for cytosolic accumulation of UV-sensitive uroporphyrin I and further loaded endosomally with a red light-sensitive cationic phthalocyanine. Exposing these doubly dye-loaded Leishmania to light triggers intracellular production of highly reactive but extremely short-lived 1O2, resulting in their rapid and complete inactivation. Immunization of susceptible animals with such inactivated Leishmania elicited immunity to protect them against experimental leishmaniasis. Significantly, the inactivated Leishmania was shown to effectively deliver transgenically add-on ovalbumin (OVA) to antigen-presenting cells (APC), wherein OVA epitopes were processed appropriately for presentation with MHC molecules to activate epitope-specific CD8+ T cells. Application of this approach to deliver cancer vaccine candidates, e.g., enolase-1, was shown to suppress tumor development in mouse models. A similar approach is predicted to elicit lasting immunity against infectious diseases, including complementation of the spike protein-based vaccines in use for COVID-19. This pandemic is devastating, but brings to light the necessity of considering many facets of the disease in developing vaccination programs. Closer collaboration is essential among those in diverse disciplinary areas to provide the roadmap toward greater success in the future. Highlighted herein are several specific issues of vaccinology and new approaches worthy of consideration due to the pandemic.
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Martinez MA. Efficacy of repurposed antiviral drugs: lessons from COVID-19. Drug Discov Today 2022; 27:1954-1960. [PMID: 35192924 PMCID: PMC8857759 DOI: 10.1016/j.drudis.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 12/15/2022]
Abstract
The clinical, social, and economic impacts of the coronavirus disease 2019 (COVID-19) pandemic, originated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have motivated a massive search and investment to find treatments for this new disease. Repurposing drugs has been an appealing strategy for the rapid translation of in vitro and ex vivo drug discovery to the clinic. Several repurposed drugs have been assessed clinically, but no effective repurposed antiviral has been identified so far. Of note, no effective treatments for COVID-19 or for any other viral disease have been found by repurposing drugs identified through hypothesis-free screens. Here, I discuss whether drug repurposing is the best strategy for developing effective therapies to eradicate COVID-19 and other viral human infections.
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Affiliation(s)
- Miguel Angel Martinez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
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37
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Ngo ST, Nguyen TH, Tung NT, Mai BK. Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M pro. RSC Adv 2022; 12:3729-3737. [PMID: 35425393 PMCID: PMC8979274 DOI: 10.1039/d1ra08752e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 μs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. The successfully generated bound state between the two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of the thioimidate product from SARS-CoV-2 Mpro and the PF-07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for a better understanding of the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro. The catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam .,Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam .,Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology Hanoi 11307 Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 11307 Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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38
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Song Y, Deng Y, Wang H, Bei Z, Gu H, Zhao H, Wang H, Zhang D, Xu L, Wang B, Li Y, Wang H. Naphthoquine: A Potent Broad-Spectrum Anti-Coronavirus Drug In Vitro. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030712. [PMID: 35163977 PMCID: PMC8840560 DOI: 10.3390/molecules27030712] [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] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
COVID-19 has spread around the world and caused serious public health and social problems. Although several vaccines have been authorized for emergency use, new effective antiviral drugs are still needed. Some repurposed drugs including Chloroquine, Hydroxychloroquine and Remdesivir were immediately used to treat COVID-19 after the pandemic. However, the therapeutic effects of these drugs have not been fully demonstrated in clinical studies. In this paper, we found an antimalarial drug, Naphthoquine, showed good broad-spectrum anti-coronavirus activity. Naphthoquineinhibited HCoV-229E, HCoV-OC43 and SARS-CoV-2 replication in vitro, with IC50 = 2.05 ± 1.44 μM, 5.83 ± 0.74 μM, and 2.01 ± 0.38 µM, respectively. Time-of-addition assay was also performed to explore at which stage Naphthoquine functions during SARS-CoV-2 replication. The results suggested that Naphthoquine may influence virus entry and post-entry replication. Considering the safety of Naphthoquine was even better than that of Chloroquine, we think Naphthoquine has the potential to be used as a broad-spectrum drug for coronavirus infection.
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Affiliation(s)
- Yabin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Yongqiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Huiqiang Wang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China;
| | - Zhuchun Bei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Hongjing Gu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Hui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Hong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Dongna Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Likun Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Baogang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China;
- Correspondence: (Y.L.); (H.W.)
| | - Hongquan Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (Y.S.); (Y.D.); (Z.B.); (H.G.); (H.Z.); (H.W.); (D.Z.); (L.X.); (B.W.)
- Correspondence: (Y.L.); (H.W.)
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Santos SDS, Torres M, Galeano D, Sánchez MDM, Cernuzzi L, Paccanaro A. Machine learning and network medicine approaches for drug repositioning for COVID-19. PATTERNS (NEW YORK, N.Y.) 2022; 3:100396. [PMID: 34778851 PMCID: PMC8576113 DOI: 10.1016/j.patter.2021.100396] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022]
Abstract
We present two machine learning approaches for drug repurposing. While we have developed them for COVID-19, they are disease-agnostic. The two methodologies are complementary, targeting SARS-CoV-2 and host factors, respectively. Our first approach consists of a matrix factorization algorithm to rank broad-spectrum antivirals. Our second approach, based on network medicine, uses graph kernels to rank drugs according to the perturbation they induce on a subnetwork of the human interactome that is crucial for SARS-CoV-2 infection/replication. Our experiments show that our top predicted broad-spectrum antivirals include drugs indicated for compassionate use in COVID-19 patients; and that the ranking obtained by our kernel-based approach aligns with experimental data. Finally, we present the COVID-19 repositioning explorer (CoREx), an interactive online tool to explore the interplay between drugs and SARS-CoV-2 host proteins in the context of biological networks, protein function, drug clinical use, and Connectivity Map. CoREx is freely available at: https://paccanarolab.org/corex/.
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Affiliation(s)
- Suzana de Siqueira Santos
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- COVID-19 International Research Team
| | - Mateo Torres
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- COVID-19 International Research Team
| | - Diego Galeano
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- Facultad de Ingenieria, Universidad Nacional de Asunción, Luque 110948, Paraguay
- COVID-19 International Research Team
| | | | - Luca Cernuzzi
- Universidad Católica “Nuestra Señora de la Asunción”, Asunción C.C. 1683, Paraguay
| | - Alberto Paccanaro
- Escola de Matemática Aplicada, Fundação Getulio Vargas, Rio de Janeiro 22250-900, Brazil
- Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
- COVID-19 International Research Team
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40
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Kaore S, Atal S. Molnupiravir in COVID-19: A Scoping Review. Curr Drug Res Rev 2022; 14:203-214. [PMID: 35638286 DOI: 10.2174/2589977514666220527105158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND COVID-19, first detected in Wuhan, China, has evolved into a lifethreatening pandemic spread across six continents, with the global case count being more than 243 million, and mortality over 4.95 million, along with causing significant morbidity. It has initiated an era of research on repurposed drugs such as hydroxychloroquine, lopinavir/ritonavir, corticosteroids, remedesivir, ivermectin, alongside selective antivirals to treat or prevent COVID- 19. Molnupiravir is an orally available emerging antiviral drug considered highly promising for COVID-19. METHODS AND RESULTS We have performed a scoping review for the use of molnupiravir against SARS-CoV-2 and COVID-19. It acts by inhibiting RNA-dependent RNA polymerase (RdRp), and exhibits broad-spectrum antiviral activity. Preclinical studies have evaluated the therapeutic efficacy as well as prophylactic activity of molnupiravir against SARS CoV-2 in various animal models that include ferrets, hamsters, mice, immunodeficient mice implanted with human lung tissue and cell cultures, in various doses ranging from 5-300 mg/kg, and results have been encouraging. Initial evidence of safety and efficacy from early phase clinical studies has been encouraging too, and recent results from a large phase 3 global trial have shown significant benefits among symptomatic outpatients. Other late-phase clinical trials are still underway with the aim of establishing molnulpiravir as a therapeutic option for COVID-19, particularly for non-hospitalized patients. CONCLUSION AND RELEVANCE On the basis of the limited evidence available as of now, molnupiravir could prove to be a promising oral therapy, worthy of further exploration of its utility for both treatment and prevention of COVID-19 in humans. Elaborate clinical evaluation is further warranted to confirm whether the results are replicable to the clinical scenario among outpatients to reduce the chance of progression to more severe disease.
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Affiliation(s)
- Shilpa Kaore
- Department of Pharmacology, All India Institute of Medical Sciences, Bhopal, India
| | - Shubham Atal
- Department of Pharmacology, All India Institute of Medical Sciences, Bhopal, India
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Feng T, Nie C, Peng P, Lu H, Wang T, Li P, Huang W. Nanoagent-based theranostic strategies against human coronaviruses. NANO RESEARCH 2022; 15:3323-3337. [PMID: 35003529 PMCID: PMC8727479 DOI: 10.1007/s12274-021-3949-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 05/08/2023]
Abstract
The emergence of human coronaviruses (HCoVs), especially the current pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), engender severe threats to public health globally. Despite the outstanding breakthrough of new vaccines and therapeutic medicines in the past years, HCoVs still undergo unpredictable mutations, thus demanding more effective diagnostic and therapeutic strategies. Benefitting from the unique physicochemical properties and multiple nano-bio interactions, nanomaterials hold promising potential to fight against various HCoVs, either by providing sensitive and economic nanosensors for rapid viral detection, or by developing translatable nanovaccines and broad-spectrum nanomedicines for HCoV treatment. Herein, we systemically summarized the recent applications of nanoagents in diagnostics and therapeutics for HCoV-induced diseases, as well as their limitations and perspectives against HCoV variants. We believe this review will promote the design of innovative theranostic nanoagents for the current and future HCoV-caused pandemics.
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Affiliation(s)
- Tao Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Chaofan Nie
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Pandi Peng
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Hui Lu
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Tengjiao Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi’an Institute of Flexible Electronics (IFE), Xi’an Institute of Biomedical Materials and Engineering (IBME), Ningbo Institute & Chongqing Technology Innovation Center, Northwestern Polytechnical University (NPU), Xi’an, 710072 China
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing, 211816 China
- State Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023 China
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White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ. Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses. mBio 2021; 12:e0334721. [PMID: 34933447 PMCID: PMC8689562 DOI: 10.1128/mbio.03347-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The world was unprepared for coronavirus disease 2019 (COVID-19) and remains ill-equipped for future pandemics. While unprecedented strides have been made developing vaccines and treatments for COVID-19, there remains a need for highly effective and widely available regimens for ambulatory use for novel coronaviruses and other viral pathogens. We posit that a priority is to develop pan-family drug cocktails to enhance potency, limit toxicity, and avoid drug resistance. We urge cocktail development for all viruses with pandemic potential both in the short term (<1 to 2 years) and longer term with pairs of drugs in advanced clinical testing or repurposed agents approved for other indications. While significant efforts were launched against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in vitro and in the clinic, many studies employed solo drugs and had disappointing results. Here, we review drug combination studies against SARS-CoV-2 and other viruses and introduce a model-driven approach to assess drug pairs with the highest likelihood of clinical efficacy. Where component agents lack sufficient potency, we advocate for synergistic combinations to achieve therapeutic levels. We also discuss issues that stymied therapeutic progress against COVID-19, including testing of agents with low likelihood of efficacy late in clinical disease and lack of focus on developing virologic surrogate endpoints. There is a need to expedite efficient clinical trials testing drug combinations that could be taken at home by recently infected individuals and exposed contacts as early as possible during the next pandemic, whether caused by a coronavirus or another viral pathogen. The approach herein represents a proactive plan for global viral pandemic preparedness.
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Affiliation(s)
- Judith M. White
- University of Virginia, Department of Cell Biology, Charlottesville, Virginia, USA
- University of Virginia, Department of Microbiology, Charlottesville, Virginia, USA
| | - Joshua T. Schiffer
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Rachel A. Bender Ignacio
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shuang Xu
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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43
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John L, Soujanya Y, Mahanta HJ, Narahari Sastry G. Chemoinformatics and Machine Learning Approaches for Identifying Antiviral Compounds. Mol Inform 2021; 41:e2100190. [PMID: 34811938 DOI: 10.1002/minf.202100190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Current pandemics propelled research efforts in unprecedented fashion, primarily triggering computational efforts towards new vaccine and drug development as well as drug repurposing. There is an urgent need to design novel drugs with targeted biological activity and minimum adverse reactions that may be useful to manage viral outbreaks. Hence an attempt has been made to develop Machine Learning based predictive models that can be used to assess whether a compound has the potency to be antiviral or not. To this end, a set of 2358 antiviral compounds were compiled from the CAS COVID-19 antiviral SAR dataset whose activity was reported based on IC50 value. A total 1157 two-dimensional molecular descriptors were computed among which, the most highly correlated descriptors were selected using Tree-based, Correlation-based and Mutual information-based feature selection methods. Seven Machine Learning algorithms i. e., Random Forest, XGBoost, Support Vector Machine, KNN, Decision Tree, MLP Classifier and Logistic Regression were benchmarked. The best performance was achieved by the models developed using Random Forest and XGBoost algorithms in all the feature selection methods. The maximum predictive accuracy of both these models was 88 % with internal validation. Whereas, with an external dataset, a maximum accuracy of 93.10 % for XGBoost and 100 % for Random Forest based model was achievable. Furthermore, the study demonstrated scaffold analysis of the molecules as a pragmatic approach to explore the importance of structurally diverse compounds in data driven studies.
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Affiliation(s)
- Lijo John
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Yarasi Soujanya
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500 007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat, 785006, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR- North East Institute of Science and Technology, Jorhat, 785006, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
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44
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Spanakis M, Patelarou A, Patelarou E, Tzanakis N. Drug Interactions for Patients with Respiratory Diseases Receiving COVID-19 Emerged Treatments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11711. [PMID: 34770225 PMCID: PMC8583457 DOI: 10.3390/ijerph182111711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022]
Abstract
Pandemic of coronavirus disease (COVID-19) is still pressing the healthcare systems worldwide. Thus far, the lack of available COVID-19-targeted treatments has led scientists to look through drug repositioning practices and exploitation of available scientific evidence for potential efficient drugs that may block biological pathways of SARS-CoV-2. Till today, several molecules have emerged as promising pharmacological agents, and more than a few medication protocols are applied during hospitalization. On the other hand, given the criticality of the disease, it is important for healthcare providers, especially those in COVID-19 clinics (i.e., nursing personnel and treating physicians), to recognize potential drug interactions that may lead to adverse drug reactions that may negatively impact the therapeutic outcome. In this review, focusing on patients with respiratory diseases (i.e., asthma or chronic obstructive pulmonary disease) that are treated also for COVID-19, we discuss possible drug interactions, their underlying pharmacological mechanisms, and possible clinical signs that healthcare providers in COVID-19 clinics may need to acknowledge as adverse drug reactions due to drug-drug interactions.
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Affiliation(s)
- Marios Spanakis
- Department of Nursing, School of Health Sciences, Hellenic Mediterranean University, GR-71004 Heraklion, Crete, Greece; (A.P.); (E.P.)
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research & Technology-Hellas (FORTH), GR-70013 Heraklion, Crete, Greece
| | - Athina Patelarou
- Department of Nursing, School of Health Sciences, Hellenic Mediterranean University, GR-71004 Heraklion, Crete, Greece; (A.P.); (E.P.)
| | - Evridiki Patelarou
- Department of Nursing, School of Health Sciences, Hellenic Mediterranean University, GR-71004 Heraklion, Crete, Greece; (A.P.); (E.P.)
| | - Nikolaos Tzanakis
- Department of Respiratory Medicine, University Hospital of Heraklion, Medical School, University of Crete, GR-71303 Heraklion, Crete, Greece;
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45
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Brüssow H. Clinical trials with antiviral drugs against COVID-19: some progress and many shattered hopes. Environ Microbiol 2021; 23:6364-6376. [PMID: 34519154 PMCID: PMC8652531 DOI: 10.1111/1462-2920.15769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/27/2022]
Abstract
Vaccines and drugs are the cornerstones in the fight against the SARS-CoV-2 pandemic. While vaccines were a success story, the development of antiviral drugs against SARS-CoV-2 turned out to be difficult. For an accelerated use of antivirals in the clinic, most SARS-CoV-2 antivirals represented repurposed drugs. The present article summarizes the outcomes of clinical trials with antiviral drugs in COVID-19 patients. Many antiviral drugs failed to demonstrate beneficial effects or showed mixed results. One reason for the low success rate of clinical trials was shortcomings of antiviral tests in cell culture systems and another reason was the abundance of ill-coordinated and underpowered clinical trials. However, large pragmatic clinical trials particularly of the British RECOVERY trial series demonstrated that even under emergency situation drug trials can be conducted in a timely way such that the therapy of COVID-19 patients can be based on evidence basis instead on expert opinion or even worse on political pressure.
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Affiliation(s)
- Harald Brüssow
- Department of Biosystems, Laboratory of Gene TechnologyKU LeuvenLeuvenBelgium
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46
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Yoo JH. Antivirals for Coexistence with COVID-19: Brief Review for General Physicians. J Korean Med Sci 2021; 36:e298. [PMID: 34725982 PMCID: PMC8560319 DOI: 10.3346/jkms.2021.36.e298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022] Open
Abstract
In order to end the coronavirus disease 2019 (COVID-19) pandemic that has lasted for nearly two years, it is most necessary to introduce antiviral drugs specific to COVID-19 along with the establishment of herd immunity by vaccination. Candidates currently being studied include nucleoside analogues that inhibit replication, protease inhibitors, and entry blockers. Not only the virus itself, but also the host protein that the virus uses in its pathogenesis is the target of treatment. Although the severe acute respiratory syndrome coronavirus 2 will not be completely eradicated, if the use of antiviral drugs is established, the COVID-19 pandemic will end through coexistence with the virus.
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Affiliation(s)
- Jin-Hong Yoo
- Division of Infectious Diseases, Department of Internal Medicine, Bucheon St. Mary's Hospital, Bucheon, Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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47
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Kamat A, Sah A. Early Detection of COVID-19 Waves From Cases in a Neighboring Country With an Open Border. Front Public Health 2021; 9:739738. [PMID: 34778174 PMCID: PMC8585937 DOI: 10.3389/fpubh.2021.739738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022] Open
Abstract
Border closure or travel restriction is a critical issue as closing the border early can badly affect the economy of the country, whereas substantial delay can put human lives at stake. While many papers discuss closing the border early in the pandemic, the question of when to close the border has not been addressed well. We have tried to estimate a date of closing the border by taking the reference of a neighboring country with a high correlation in Covid-19 incidence. Here we have used non-linear methods to probe the landscape of correlation between temporal COVID-19 incidences and deaths. We have tested our method on two neighboring countries, Nepal and India, with open borders, where closing the borders are among the top priorities to reduce the spread and spill-out of variants. We have selected these countries as they have close connectivity and intertwined socio-economic network with thousands of people crossing the border every day. We found the distance correlation for COVID-19 incidence between these countries to be statistically significant (p < 0.001) and there is a lag of 6 days for maximum correlation. In addition, we analyzed the correlation for each wave and found the distance correlation for the first phase is 0.8145 (p < 0.001) with a lag of 2 days, and the distance correlation for the second wave is 0.9685 (p < 0.001) without any lag. This study can be a critical planning tool for policymakers and public health practitioners to make an informed decision on border closure in the early days as it is critically associated with the legal and diplomatic agreements and regulations between two countries.
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Affiliation(s)
- Anil Kamat
- Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Amrita Sah
- Nepalgunj Medical College, Nepalgunj, Nepal
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48
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Bai B, Arutyunova E, Khan MB, Lu J, Joyce MA, Saffran HA, Shields JA, Kandadai AS, Belovodskiy A, Hena M, Vuong W, Lamer T, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors. RSC Med Chem 2021; 12:1722-1730. [PMID: 34778773 PMCID: PMC8529539 DOI: 10.1039/d1md00247c] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Tragically, the death toll from the COVID-19 pandemic continues to rise, and with variants being observed around the globe new therapeutics, particularly direct-acting antivirals that are easily administered, are desperately needed. Studies targeting the SARS-CoV-2 3CL protease, which is critical for viral replication, with different peptidomimetics and warheads is an active area of research for development of potential drugs. To date, however, only a few publications have evaluated the nitrile warhead as a viral 3CL protease inhibitor, with only modest activity reported. This article describes our investigation of P3 4-methoxyindole peptidomimetic analogs with select P1 and P2 groups with a nitrile warhead that are potent inhibitors of SARS-CoV-2 3CL protease and demonstrate in vitro SARS-CoV-2 antiviral activity. A selectivity for SARS-CoV-2 3CL protease over human cathepsins B, S and L was also observed with the nitrile warhead, which was superior to that with the aldehyde warhead. A co-crystal structure with SARS-CoV-2 3CL protease and a reversibility study indicate that a reversible, thioimidate adduct is formed when the catalytic sulfur forms a covalent bond with the carbon of the nitrile. This effort also identified efflux as a property limiting antiviral activity of these compounds, and together with the positive attributes described these results provide insight for further drug development of novel nitrile peptidomimetics targeting SARS-CoV-2 3CL protease.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Elena Arutyunova
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
| | - Jimmy Lu
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - Wayne Vuong
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Howard S Young
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - D Lorne Tyrrell
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - M Joanne Lemieux
- Department of Biochemistry, University of Alberta Edmonton Alberta T6G 2H7 Canada
- Li Ka Shing Institute of Virology, University of Alberta Edmonton Alberta T6G 2E1 Canada
| | - James A Nieman
- Li Ka Shing Applied Virology Institute, University of Alberta Edmonton Alberta T6G 2E1 Canada
- Department of Medical Microbiology and Immunology, University of Alberta Edmonton Alberta T6G 2E1 Canada
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49
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Doxycycline Inhibition of a Pseudotyped Virus Transduction Does Not Translate to Inhibition of SARS-CoV-2 Infectivity. Viruses 2021; 13:v13091745. [PMID: 34578326 PMCID: PMC8473150 DOI: 10.3390/v13091745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/20/2022] Open
Abstract
The rapid spread of the pandemic caused by the SARS-CoV-2 virus has created an unusual situation, with rapid searches for compounds to interfere with the biological processes exploited by the virus. Doxycycline, with its pleiotropic effects, including anti-viral activity, has been proposed as a therapeutic candidate for COVID-19 and about twenty clinical trials have started since the beginning of the pandemic. To gain information on the activity of doxycycline against SARS-CoV-2 infection and clarify some of the conflicting clinical data published, we designed in vitro binding tests and infection studies with a pseudotyped virus expressing the spike protein, as well as a clinically isolated SARS-CoV-2 strain. Doxycycline inhibited the transduction of the pseudotyped virus in Vero E6 and HEK-293 T cells stably expressing human receptor angiotensin-converting enzyme 2 but did not affect the entry and replication of SARS-CoV-2. Although this conclusion is apparently disappointing, it is paradigmatic of an experimental approach aimed at developing an integrated multidisciplinary platform which can shed light on the mechanisms of action of potential anti-COVID-19 compounds. To avoid wasting precious time and resources, we believe very stringent experimental criteria are needed in the preclinical phase, including infectivity studies with clinically isolated SARS-CoV-2, before moving on to (futile) clinical trials.
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50
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Kabinger F, Stiller C, Schmitzová J, Dienemann C, Kokic G, Hillen HS, Höbartner C, Cramer P. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nat Struct Mol Biol 2021; 28:740-746. [PMID: 34381216 DOI: 10.1101/2021.05.11.443555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/28/2021] [Indexed: 05/20/2023]
Abstract
Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp). Biochemical assays show that the RdRp uses the active form of molnupiravir, β-D-N4-hydroxycytidine (NHC) triphosphate, as a substrate instead of cytidine triphosphate or uridine triphosphate. When the RdRp uses the resulting RNA as a template, NHC directs incorporation of either G or A, leading to mutated RNA products. Structural analysis of RdRp-RNA complexes that contain mutagenesis products shows that NHC can form stable base pairs with either G or A in the RdRp active center, explaining how the polymerase escapes proofreading and synthesizes mutated RNA. This two-step mutagenesis mechanism probably applies to various viral polymerases and can explain the broad-spectrum antiviral activity of molnupiravir.
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Affiliation(s)
- Florian Kabinger
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Carina Stiller
- Universität Würzburg, Lehrstuhl für Organische Chemie I, Würzburg, Germany
| | - Jana Schmitzová
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Goran Kokic
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Hauke S Hillen
- University Medical Center Göttingen, Department of Cellular Biochemistry, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Research Group Structure and Function of Molecular Machines, Göttingen, Germany
| | - Claudia Höbartner
- Universität Würzburg, Lehrstuhl für Organische Chemie I, Würzburg, Germany.
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
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