In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations
The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts...
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| Veröffentlicht in: | Interdisciplinary sciences : computational life sciences 2021-09, Vol.13 (3), p.521-534 |
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| creator | Khan, Abbas Umbreen, Shaheena Hameed, Asma Fatima, Rida Zahoor, Ujala Babar, Zainib Waseem, Muhammad Hussain, Zahid Rizwan, Muhammad Zaman, Nasib Ali, Shahid Suleman, Muhammad Shah, Abdullah Ali, Liaqat Ali, Syed Shujait Wei, Dong-Qing |
| description | The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.
Graphic abstract |
| doi_str_mv | 10.1007/s12539-021-00447-2 |
| format | Article |
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Graphic abstract</description><identifier>ISSN: 1913-2751</identifier><identifier>EISSN: 1867-1462</identifier><identifier>DOI: 10.1007/s12539-021-00447-2</identifier><identifier>PMID: 34324157</identifier><language>eng</language><publisher>Singapore: Springer Singapore</publisher><subject>Affinity ; Antiviral Agents - chemistry ; Antiviral Agents - pharmacology ; Antiviral Agents - therapeutic use ; Binding ; Biomedical and Life Sciences ; Computational Biology/Bioinformatics ; Computational Science and Engineering ; Computer Appl. in Life Sciences ; Computer Simulation ; Coronavirus 3C Proteases - antagonists & inhibitors ; Coronaviruses ; COVID-19 ; COVID-19 - drug therapy ; COVID-19 - virology ; Dynamic stability ; Dynamic structural analysis ; Free energy ; Health Sciences ; Humans ; Life Sciences ; Mathematical analysis ; Mathematical and Computational Physics ; Medicine ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutagenesis ; Original ; Original Research Article ; Peptides ; Peptides - chemistry ; Peptides - genetics ; Peptides - pharmacology ; Protease Inhibitors - chemistry ; Protease Inhibitors - pharmacology ; Protease Inhibitors - therapeutic use ; Residues ; SARS Virus - chemistry ; SARS Virus - genetics ; SARS-CoV-2 - drug effects ; SARS-CoV-2 - enzymology ; Severe acute respiratory syndrome coronavirus 2 ; Stability analysis ; Statistics for Life Sciences ; Theoretical ; Theoretical and Computational Chemistry ; Thermodynamics ; Vaccines ; Viral diseases</subject><ispartof>Interdisciplinary sciences : computational life sciences, 2021-09, Vol.13 (3), p.521-534</ispartof><rights>International Association of Scientists in the Interdisciplinary Areas 2021</rights><rights>2021. International Association of Scientists in the Interdisciplinary Areas.</rights><rights>International Association of Scientists in the Interdisciplinary Areas 2021.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-9dff7554592aa6f68c8dbf618982551db67257b6de6129d631ebb6f203f080733</citedby><cites>FETCH-LOGICAL-c474t-9dff7554592aa6f68c8dbf618982551db67257b6de6129d631ebb6f203f080733</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12539-021-00447-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12539-021-00447-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34324157$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Khan, Abbas</creatorcontrib><creatorcontrib>Umbreen, Shaheena</creatorcontrib><creatorcontrib>Hameed, Asma</creatorcontrib><creatorcontrib>Fatima, Rida</creatorcontrib><creatorcontrib>Zahoor, Ujala</creatorcontrib><creatorcontrib>Babar, Zainib</creatorcontrib><creatorcontrib>Waseem, Muhammad</creatorcontrib><creatorcontrib>Hussain, Zahid</creatorcontrib><creatorcontrib>Rizwan, Muhammad</creatorcontrib><creatorcontrib>Zaman, Nasib</creatorcontrib><creatorcontrib>Ali, Shahid</creatorcontrib><creatorcontrib>Suleman, Muhammad</creatorcontrib><creatorcontrib>Shah, Abdullah</creatorcontrib><creatorcontrib>Ali, Liaqat</creatorcontrib><creatorcontrib>Ali, Syed Shujait</creatorcontrib><creatorcontrib>Wei, Dong-Qing</creatorcontrib><title>In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations</title><title>Interdisciplinary sciences : computational life sciences</title><addtitle>Interdiscip Sci Comput Life Sci</addtitle><addtitle>Interdiscip Sci</addtitle><description>The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.
Graphic abstract</description><subject>Affinity</subject><subject>Antiviral Agents - chemistry</subject><subject>Antiviral Agents - pharmacology</subject><subject>Antiviral Agents - therapeutic use</subject><subject>Binding</subject><subject>Biomedical and Life Sciences</subject><subject>Computational Biology/Bioinformatics</subject><subject>Computational Science and Engineering</subject><subject>Computer Appl. in Life Sciences</subject><subject>Computer Simulation</subject><subject>Coronavirus 3C Proteases - antagonists & inhibitors</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 - drug therapy</subject><subject>COVID-19 - virology</subject><subject>Dynamic stability</subject><subject>Dynamic structural analysis</subject><subject>Free energy</subject><subject>Health Sciences</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Mathematical analysis</subject><subject>Mathematical and Computational Physics</subject><subject>Medicine</subject><subject>Molecular Docking Simulation</subject><subject>Molecular Dynamics Simulation</subject><subject>Mutagenesis</subject><subject>Original</subject><subject>Original Research Article</subject><subject>Peptides</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Peptides - pharmacology</subject><subject>Protease Inhibitors - chemistry</subject><subject>Protease Inhibitors - pharmacology</subject><subject>Protease Inhibitors - therapeutic use</subject><subject>Residues</subject><subject>SARS Virus - chemistry</subject><subject>SARS Virus - genetics</subject><subject>SARS-CoV-2 - drug effects</subject><subject>SARS-CoV-2 - enzymology</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Stability analysis</subject><subject>Statistics for Life Sciences</subject><subject>Theoretical</subject><subject>Theoretical and Computational Chemistry</subject><subject>Thermodynamics</subject><subject>Vaccines</subject><subject>Viral diseases</subject><issn>1913-2751</issn><issn>1867-1462</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kc1u1DAURiMEoqXwAiyQJTawMPjfMQukMLQw0iCgKWwtJ3ZSVxl7sB2keQsemcCUFjasbOme-91POlX1GKMXGCH5MmPCqYKIYIgQYxKSO9UxroWEmAlyd_krTCGRHB9VD3K-QkiwmqL71RFllDDM5XH1Yx1A6yffR_BhLmZ0wWWf4RuTnQXnbhutmyYfRhAH0DbnLVzFrxCDT25XvHXgWXOx-dysm_Y5KBGsw6XvfLkFySvQljT3ZU5mgm_3wWx9n4EJFpwl58BpcGncg5WZ-nkyxceQH1b3BjNl9-j6Pam-nJ1erN7Dzcd361WzgT2TrEBlh0FyzrgixohB1H1tu0HgWtWEc2w7IQmXnbBOYKKsoNh1nRgIogOqkaT0pHp9yN3N3dbZ3oWydNS75Lcm7XU0Xv87Cf5Sj_G7rilWQqkl4Ol1QIrfZpeLvopzCktnTbjASBGB2UKRA9WnmHNyw80FjPQvi_pgUS8W9W-LmixLT_7udrPyR9sC0AOQl1EYXbq9_Z_Yn3Ynpt8</recordid><startdate>20210901</startdate><enddate>20210901</enddate><creator>Khan, Abbas</creator><creator>Umbreen, Shaheena</creator><creator>Hameed, Asma</creator><creator>Fatima, Rida</creator><creator>Zahoor, Ujala</creator><creator>Babar, Zainib</creator><creator>Waseem, Muhammad</creator><creator>Hussain, Zahid</creator><creator>Rizwan, Muhammad</creator><creator>Zaman, Nasib</creator><creator>Ali, Shahid</creator><creator>Suleman, Muhammad</creator><creator>Shah, Abdullah</creator><creator>Ali, Liaqat</creator><creator>Ali, Syed Shujait</creator><creator>Wei, Dong-Qing</creator><general>Springer Singapore</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>5PM</scope></search><sort><creationdate>20210901</creationdate><title>In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations</title><author>Khan, Abbas ; Umbreen, Shaheena ; Hameed, Asma ; Fatima, Rida ; Zahoor, Ujala ; Babar, Zainib ; Waseem, Muhammad ; Hussain, Zahid ; Rizwan, Muhammad ; Zaman, Nasib ; Ali, Shahid ; Suleman, Muhammad ; Shah, Abdullah ; Ali, Liaqat ; Ali, Syed Shujait ; Wei, Dong-Qing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-9dff7554592aa6f68c8dbf618982551db67257b6de6129d631ebb6f203f080733</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Affinity</topic><topic>Antiviral Agents - 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chemistry</topic><topic>Peptides - genetics</topic><topic>Peptides - pharmacology</topic><topic>Protease Inhibitors - chemistry</topic><topic>Protease Inhibitors - pharmacology</topic><topic>Protease Inhibitors - therapeutic use</topic><topic>Residues</topic><topic>SARS Virus - chemistry</topic><topic>SARS Virus - genetics</topic><topic>SARS-CoV-2 - drug effects</topic><topic>SARS-CoV-2 - enzymology</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Stability analysis</topic><topic>Statistics for Life Sciences</topic><topic>Theoretical</topic><topic>Theoretical and Computational Chemistry</topic><topic>Thermodynamics</topic><topic>Vaccines</topic><topic>Viral diseases</topic><toplevel>online_resources</toplevel><creatorcontrib>Khan, Abbas</creatorcontrib><creatorcontrib>Umbreen, Shaheena</creatorcontrib><creatorcontrib>Hameed, Asma</creatorcontrib><creatorcontrib>Fatima, Rida</creatorcontrib><creatorcontrib>Zahoor, Ujala</creatorcontrib><creatorcontrib>Babar, Zainib</creatorcontrib><creatorcontrib>Waseem, Muhammad</creatorcontrib><creatorcontrib>Hussain, Zahid</creatorcontrib><creatorcontrib>Rizwan, Muhammad</creatorcontrib><creatorcontrib>Zaman, Nasib</creatorcontrib><creatorcontrib>Ali, Shahid</creatorcontrib><creatorcontrib>Suleman, Muhammad</creatorcontrib><creatorcontrib>Shah, Abdullah</creatorcontrib><creatorcontrib>Ali, Liaqat</creatorcontrib><creatorcontrib>Ali, Syed Shujait</creatorcontrib><creatorcontrib>Wei, Dong-Qing</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Interdisciplinary sciences : computational life sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Khan, Abbas</au><au>Umbreen, Shaheena</au><au>Hameed, Asma</au><au>Fatima, Rida</au><au>Zahoor, Ujala</au><au>Babar, Zainib</au><au>Waseem, Muhammad</au><au>Hussain, Zahid</au><au>Rizwan, Muhammad</au><au>Zaman, Nasib</au><au>Ali, Shahid</au><au>Suleman, Muhammad</au><au>Shah, Abdullah</au><au>Ali, Liaqat</au><au>Ali, Syed Shujait</au><au>Wei, Dong-Qing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations</atitle><jtitle>Interdisciplinary sciences : computational life sciences</jtitle><stitle>Interdiscip Sci Comput Life Sci</stitle><addtitle>Interdiscip Sci</addtitle><date>2021-09-01</date><risdate>2021</risdate><volume>13</volume><issue>3</issue><spage>521</spage><epage>534</epage><pages>521-534</pages><issn>1913-2751</issn><eissn>1867-1462</eissn><abstract>The prolific spread of COVID-19 caused by a novel coronavirus (SARS-CoV-2) from its epicenter in Wuhan, China, to every nook and cranny of the world after December 2019, jeopardize the prevailing health system in the world and has raised serious concerns about human safety. Multi-directional efforts are made to design small molecule inhibitors, and vaccines and many other therapeutic options are practiced, but their final therapeutic potential is still to be tested. Using the old drug or vaccine or peptides could aid this process to avoid such long experimental procedures. Hence, here, we have repurposed a small peptide (ATLQAIAS) from the previous study, which reported the inhibitory effects of this peptide. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. Furthermore, using MD simulation and free energy calculation confirmed its dynamics stability and stronger binding affinities. Per-residue energy decomposition analysis revealed that the specified substitution significantly increased the binding affinity at the residue level. Our wide-ranging analyses of binding affinities disclosed that our designed peptide owns the potential to hinder the SARS-CoV-2 and will reduce the progression of SARS-CoV-2-borne pneumonia. Our research strongly suggests the experimental and clinical validation of these peptides to curtail the recent corona outbreak.
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| ispartof | Interdisciplinary sciences : computational life sciences, 2021-09, Vol.13 (3), p.521-534 |
| issn | 1913-2751 1867-1462 |
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| subjects | Affinity Antiviral Agents - chemistry Antiviral Agents - pharmacology Antiviral Agents - therapeutic use Binding Biomedical and Life Sciences Computational Biology/Bioinformatics Computational Science and Engineering Computer Appl. in Life Sciences Computer Simulation Coronavirus 3C Proteases - antagonists & inhibitors Coronaviruses COVID-19 COVID-19 - drug therapy COVID-19 - virology Dynamic stability Dynamic structural analysis Free energy Health Sciences Humans Life Sciences Mathematical analysis Mathematical and Computational Physics Medicine Molecular Docking Simulation Molecular Dynamics Simulation Mutagenesis Original Original Research Article Peptides Peptides - chemistry Peptides - genetics Peptides - pharmacology Protease Inhibitors - chemistry Protease Inhibitors - pharmacology Protease Inhibitors - therapeutic use Residues SARS Virus - chemistry SARS Virus - genetics SARS-CoV-2 - drug effects SARS-CoV-2 - enzymology Severe acute respiratory syndrome coronavirus 2 Stability analysis Statistics for Life Sciences Theoretical Theoretical and Computational Chemistry Thermodynamics Vaccines Viral diseases |
| title | In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations |
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