Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the...
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| Published in: | Journal of biomolecular structure & dynamics Vol. 39; no. 9; pp. 3099 - 3114 |
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| Main Authors: | , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Taylor & Francis
13-06-2021
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| Online Access: | Get full text |
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| Abstract | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (M
Pro
) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of M
Pro
, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae M
Pro
in five clusters specific to viral hosts. This clustering was corroborated with the comparison of M
Pro
structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 M
Pro
. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 M
Pro
as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 M
Pro
. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.
Communicated by Ramaswamy H. Sarma |
|---|---|
| AbstractList | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (M
Pro
) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of M
Pro
, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae M
Pro
in five clusters specific to viral hosts. This clustering was corroborated with the comparison of M
Pro
structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 M
Pro
. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 M
Pro
as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 M
Pro
. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.
Communicated by Ramaswamy H. Sarma Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was corroborated with the comparison of MPro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 MPro. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 MPro as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 MPro. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was corroborated with the comparison of MPro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 MPro. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 MPro as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 MPro. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (M ) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of M , we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae M in five clusters specific to viral hosts. This clustering was corroborated with the comparison of M structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 M . In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 M as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 M . Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma. |
| Author | Joshi, Rakesh S. Shankar, S. Shiva Pandya, Vaibhav Kumar Kulkarni, Mahesh J. Tellis, Meenakshi B. Chugh, Anita Jagdale, Shounak S. Giri, Ashok P. Bansode, Sneha B. |
| Author_xml | – sequence: 1 givenname: Rakesh S. surname: Joshi fullname: Joshi, Rakesh S. email: rs.joshi@ncl.res.in, mj.kulkarni@ncl.res.in, ap.giri@ncl.res.in organization: Academy of Scientific and Innovative Research (AcSIR) – sequence: 2 givenname: Shounak S. surname: Jagdale fullname: Jagdale, Shounak S. organization: Biochemical Sciences Division, CSIR-National Chemical Laboratory – sequence: 3 givenname: Sneha B. surname: Bansode fullname: Bansode, Sneha B. organization: Biochemical Sciences Division, CSIR-National Chemical Laboratory – sequence: 4 givenname: S. Shiva surname: Shankar fullname: Shankar, S. Shiva organization: Academy of Scientific and Innovative Research (AcSIR) – sequence: 5 givenname: Meenakshi B. surname: Tellis fullname: Tellis, Meenakshi B. organization: Department of Botany, Savitribai Phule Pune University – sequence: 6 givenname: Vaibhav Kumar surname: Pandya fullname: Pandya, Vaibhav Kumar organization: Biochemical Sciences Division, CSIR-National Chemical Laboratory – sequence: 7 givenname: Anita surname: Chugh fullname: Chugh, Anita organization: INTOX Private Limited – sequence: 8 givenname: Ashok P. surname: Giri fullname: Giri, Ashok P. email: rs.joshi@ncl.res.in, mj.kulkarni@ncl.res.in, ap.giri@ncl.res.in organization: Academy of Scientific and Innovative Research (AcSIR) – sequence: 9 givenname: Mahesh J. surname: Kulkarni fullname: Kulkarni, Mahesh J. email: rs.joshi@ncl.res.in, mj.kulkarni@ncl.res.in, ap.giri@ncl.res.in organization: Academy of Scientific and Innovative Research (AcSIR) |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32329408$$D View this record in MEDLINE/PubMed |
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| Copyright | 2020 Informa UK Limited, trading as Taylor & Francis Group 2020 2020 Informa UK Limited, trading as Taylor & Francis Group 2020 Informa UK Limited, trading as Taylor & Francis Group |
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| Issue | 9 |
| Keywords | COVID-19 protease inhibitor Coronavirus MPro RdRp SARS-CoV-2 virus hACE-2 multi-target-directed ligand |
| Language | English |
| License | This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Authors contributed equally We would like to dedicate this research article to all the frontline workers who are working selflessly in extreme situations to serve society and to control the pandemic COVID-19. |
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| PublicationTitle | Journal of biomolecular structure & dynamics |
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| Snippet | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over... |
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| SubjectTerms | Coronavirus COVID-19 hACE-2 Humans Ligands MPro multi-target-directed ligand Pandemics Peptide Hydrolases Pharmaceutical Preparations Phylogeny protease inhibitor Protease Inhibitors - pharmacology RdRp SARS-CoV-2 SARS-CoV-2 virus |
| Title | Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease |
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