Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CLPro) activity in silico and in vitro
Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new...
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| Published in | Scientific reports Vol. 13; no. 1; pp. 17106 - 16 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
10.10.2023
Nature Publishing Group Nature Portfolio |
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| Online Access | Get full text |
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| Abstract | Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CL
Pro
compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from
Taiwanofungus camphoratus
that targets 3CL
Pro
activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CL
Pro
. Further, these compounds were subjected to study their inhibitory effects on 3CL
Pro
activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets. |
|---|---|
| AbstractList | Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets.Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets. Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CL Pro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CL Pro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CL Pro . Further, these compounds were subjected to study their inhibitory effects on 3CL Pro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets. Abstract Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets. Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets. |
| ArticleNumber | 17106 |
| Author | Pérez-Sánchez, Horacio Wang, Sheng-Yang Dakpa, Gyaltsen Kumar, K. J. Senthil Nelen, Jochem |
| Author_xml | – sequence: 1 givenname: Gyaltsen surname: Dakpa fullname: Dakpa, Gyaltsen organization: Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Graduate Institute of Biotechnology, National Chung Hsing University – sequence: 2 givenname: K. J. Senthil surname: Kumar fullname: Kumar, K. J. Senthil organization: Bachelor Program of Biotechnology, National Chung Hsing University – sequence: 3 givenname: Jochem surname: Nelen fullname: Nelen, Jochem organization: Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM) – sequence: 4 givenname: Horacio surname: Pérez-Sánchez fullname: Pérez-Sánchez, Horacio organization: Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM) – sequence: 5 givenname: Sheng-Yang surname: Wang fullname: Wang, Sheng-Yang email: taiwanfir@drgon.nchu.edu.tw organization: Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Department of Forestry, National Chung Hsing University, Special Crop and Metabolome Discipline Cluster, Academy of Circle Economy, National Chung Hsing University, Agricultural Biotechnology Research Center, Academia Sinica |
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| Snippet | Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19)... Abstract Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019... |
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| SubjectTerms | 631/154 631/45/607 631/92 692/699/255/1901 Affinity Chymotrypsin Coronaviruses COVID-19 Cytotoxicity Humanities and Social Sciences Molecular dynamics Molecular modelling mRNA multidisciplinary Replication Science Science (multidisciplinary) Severe acute respiratory syndrome coronavirus 2 Taiwanofungus camphoratus Vaccines |
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| Title | Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CLPro) activity in silico and in vitro |
| URI | https://link.springer.com/article/10.1038/s41598-023-44476-x https://www.proquest.com/docview/2875226394 https://www.proquest.com/docview/2875852069 https://pubmed.ncbi.nlm.nih.gov/PMC10564890 https://doaj.org/article/6cf2639a8d5040b49f1fb9e59fb82bc7 |
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