Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs
Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CL<...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/29/1/225 |
| _version_ | 1827384607725584384 |
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| author | Pengxuan Ren Shiwei Li Shihang Wang Xianglei Zhang Fang Bai |
| author_facet | Pengxuan Ren Shiwei Li Shihang Wang Xianglei Zhang Fang Bai |
| author_sort | Pengxuan Ren |
| collection | DOAJ |
| description | Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CL<sup>pro</sup>), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CL<sup>pro</sup> or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CL<sup>pro</sup> with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CL<sup>pro</sup> and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds <b>1</b>–<b>2</b>, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs. |
| first_indexed | 2024-03-08T15:01:11Z |
| format | Article |
| id | doaj.art-3abed54470f146baadd7b0ebf1c6b4ce |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-08T15:01:11Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-3abed54470f146baadd7b0ebf1c6b4ce2024-01-10T15:04:33ZengMDPI AGMolecules1420-30492023-12-0129122510.3390/molecules29010225Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum DrugsPengxuan Ren0Shiwei Li1Shihang Wang2Xianglei Zhang3Fang Bai4School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, ChinaSchool of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, ChinaSchool of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, ChinaSchool of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, ChinaSchool of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, ChinaHuman society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CL<sup>pro</sup>), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CL<sup>pro</sup> or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CL<sup>pro</sup> with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CL<sup>pro</sup> and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds <b>1</b>–<b>2</b>, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.https://www.mdpi.com/1420-3049/29/1/225viral protease3CL<sup>pro</sup>PAPsinhibitor design strategiesdrug repurposing |
| spellingShingle | Pengxuan Ren Shiwei Li Shihang Wang Xianglei Zhang Fang Bai Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs Molecules viral protease 3CL<sup>pro</sup> PAPs inhibitor design strategies drug repurposing |
| title | Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs |
| title_full | Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs |
| title_fullStr | Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs |
| title_full_unstemmed | Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs |
| title_short | Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs |
| title_sort | computer aided prediction of the interactions of viral proteases with antiviral drugs antiviral potential of broad spectrum drugs |
| topic | viral protease 3CL<sup>pro</sup> PAPs inhibitor design strategies drug repurposing |
| url | https://www.mdpi.com/1420-3049/29/1/225 |
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