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Lu G, Ou K, Zhang Y, Zhang H, Feng S, Yang Z, Sun G, Liu J, Wei S, Pan S, Chen Z. Structural Analysis, Multi-Conformation Virtual Screening and Molecular Simulation to Identify Potential Inhibitors Targeting pS273R Proteases of African Swine Fever Virus. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020570. [PMID: 36677630 PMCID: PMC9866604 DOI: 10.3390/molecules28020570] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The African Swine Fever virus (ASFV) causes an infectious viral disease in pigs of all ages. The development of antiviral drugs primarily aimed at inhibition of proteases required for the proteolysis of viral polyproteins. In this study, the conformation of the pS273R protease in physiological states were investigated, virtually screened the multi-protein conformation of pS273R target proteins, combined various molecular docking scoring functions, and identified five potential drugs from the Food and Drug Administration drug library that may inhibit pS273R. Subsequent validation of the dynamic interactions of pS273R with the five putative inhibitors was achieved using molecular dynamics simulations and binding free energy calculations using the molecular mechanics/Poison-Boltzmann (Generalized Born) (MM/PB(GB)SA) surface area. These findings demonstrate that the arm domain and Thr159-Lys167 loop region of pS273R are significantly more flexible compared to the core structural domain, and the Thr159-Lys167 loop region can serve as a "gatekeeper" in the substrate channel. Leucovorin, Carboprost, Protirelin, Flavin Mononucleotide, and Lovastatin Acid all have Gibbs binding free energies with pS273R that were less than -20 Kcal/mol according to the MM/PBSA analyses. In contrast to pS273R in the free energy landscape, the inhibitor and drug complexes of pS273R showed distinct structural group distributions. These five drugs may be used as potential inhibitors of pS273R and may serve as future drug candidates for treating ASFV.
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Affiliation(s)
- Gen Lu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Kang Ou
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Yihan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Shouhua Feng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Zuofeng Yang
- The Preventive and Control Center of Animal Disease of Liaoning Province, Liaoning Agricultural Development Service Center, No. 95, Renhe Road, Shenbei District, Shenyang 110164, China
| | - Guo Sun
- Qianyuanhao Biological Co., Ltd., Building 20, District 11, No. 188 South Fourth Ring West Road, Fengtai District, Beijing 100070, China
| | - Jinling Liu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Shu Wei
- The Preventive and Control Center of Animal Disease of Liaoning Province, Liaoning Agricultural Development Service Center, No. 95, Renhe Road, Shenbei District, Shenyang 110164, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Shude Pan
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
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Gu K, Ma P, Song Z, Yang M, Yang X, Li C, Zhou C, Ju Z, Zhao Y, Li H, Yang X, Lei C, Wang H. Ferritin-displayed antigen nanoparticles and nanobody-horseradish peroxidase fusions based-competitive ELISA for the rapid and sensitive detection of antibody against African swine fever virus. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Prediction of African Swine Fever Virus Inhibitors by Molecular Docking-Driven Machine Learning Models. Molecules 2021; 26:molecules26123592. [PMID: 34208385 PMCID: PMC8231271 DOI: 10.3390/molecules26123592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/23/2021] [Accepted: 06/09/2021] [Indexed: 01/31/2023] Open
Abstract
African swine fever virus (ASFV) causes a highly contagious and severe hemorrhagic viral disease with high mortality in domestic pigs of all ages. Although the virus is harmless to humans, the ongoing ASFV epidemic could have severe economic consequences for global food security. Recent studies have found a few antiviral agents that can inhibit ASFV infections. However, currently, there are no vaccines or antiviral drugs. Hence, there is an urgent need to identify new drugs to treat ASFV. Based on the structural information data on the targets of ASFV, we used molecular docking and machine learning models to identify novel antiviral agents. We confirmed that compounds with high affinity present in the region of interest belonged to subsets in the chemical space using principal component analysis and k-means clustering in molecular docking studies of FDA-approved drugs. These methods predicted pentagastrin as a potential antiviral drug against ASFVs. Finally, it was also observed that the compound had an inhibitory effect on AsfvPolX activity. Results from the present study suggest that molecular docking and machine learning models can play an important role in identifying potential antiviral drugs against ASFVs.
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