1
|
Pham MQ, Vu KB, Han Pham TN, Thuy Huong LT, Tran LH, Tung NT, Vu VV, Nguyen TH, Ngo ST. Correction: Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations. RSC Adv 2022; 12:35778. [PMID: 36545115 PMCID: PMC9751897 DOI: 10.1039/d2ra90114e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
[This corrects the article DOI: 10.1039/D0RA06212J.].
Collapse
Affiliation(s)
- Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Natural Products Chemistry, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Khanh B. Vu
- School of Biotechnology, International UniversityHo Chi Minh CityVietnam,Vietnam National UniversityHo Chi Minh CityVietnam
| | - T. Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang UniversityHo Chi Minh CityVietnam
| | - Le Thi Thuy Huong
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Natural Products Chemistry, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Linh Hoang Tran
- Vietnam National UniversityHo Chi Minh CityVietnam,Faculty of Civil Engineering, Ho Chi Minh University of Technology (HCMUT)Ho Chi MinhVietnam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Materials Science, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh UniversityHo Chi Minh CityVietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang UniversityHo Chi Minh CityVietnam,Faculty of Applied Sciences, Ton Duc Thang UniversityHo Chi Minh CityVietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang UniversityHo Chi Minh CityVietnam,Faculty of Applied Sciences, Ton Duc Thang UniversityHo Chi Minh CityVietnam
| |
Collapse
|
2
|
Thai QM, Pham TNH, Hiep DM, Pham MQ, Tran PT, Nguyen TH, Ngo ST. Searching for AChE inhibitors from natural compounds by using machine learning and atomistic simulations. J Mol Graph Model 2022; 115:108230. [DOI: 10.1016/j.jmgm.2022.108230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022]
|
3
|
Pham TNH, Nguyen TH, Tam NM, Y Vu T, Pham NT, Huy NT, Mai BK, Tung NT, Pham MQ, V Vu V, Ngo ST. Improving ligand-ranking of AutoDock Vina by changing the empirical parameters. J Comput Chem 2021; 43:160-169. [PMID: 34716930 DOI: 10.1002/jcc.26779] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 01/09/2023]
Abstract
AutoDock Vina (Vina) achieved a very high docking-success rate, p ^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking-success rate p ^ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment R set 1 = 0.556 ± 0.025 compared with R Default = 0.493 ± 0.028 obtained by the original Vina and R Vina 1.2 = 0.503 ± 0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R ≥ 0.500 for 32/48 targets, compared with the default package, giving R ≥ 0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient ( R set 1 = 0.617 ± 0.017 ) than the default package ( R Default = 0.543 ± 0.020 ) and Vina version 1.2 ( R Vina 1.2 = 0.540 ± 0.020 ). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand-binding affinity using Autodock Vina.
Collapse
Affiliation(s)
- T Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nhat Truong Pham
- Faculty of Electrical and Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| |
Collapse
|
4
|
Pham MQ, Vu KB, Han Pham TN, Thuy Huong LT, Tran LH, Tung NT, Vu VV, Nguyen TH, Ngo ST. Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations. RSC Adv 2020; 10:31991-31996. [PMID: 35518150 PMCID: PMC9056572 DOI: 10.1039/d0ra06212j] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/10/2020] [Indexed: 01/30/2023] Open
Abstract
Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations. The approaches were initially validated over a set of eleven available inhibitors. Both Autodock Vina and FPL calculations produced consistent results with the experiments with correlation coefficients of R Dock = 0.72 ± 0.14 and R W = -0.76 ± 0.10, respectively. The combined approaches were then utilized to predict possible inhibitors that were selected from a ZINC15 sub-database for SARS-CoV-2 Mpro. Twenty compounds were suggested to be able to bind well to SARS-CoV-2 Mpro. Among them, five top-leads are periandrin V, penimocycline, cis-p-Coumaroylcorosolic acid, glycyrrhizin, and uralsaponin B. The obtained results could probably lead to enhance the COVID-19 therapy.
Collapse
Affiliation(s)
- Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Khanh B Vu
- School of Biotechnology, International University Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Vietnam
| | - T Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Le Thi Thuy Huong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Linh Hoang Tran
- Vietnam National University Ho Chi Minh City Vietnam
- Faculty of Civil Energeering, Ho Chi Minh University of Technology (HCMUT) Ho Chi Minh Vietnam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Materials Science, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| |
Collapse
|
5
|
Nguyen NT, Nguyen TH, Pham TNH, Huy NT, Bay MV, Pham MQ, Nam PC, Vu VV, Ngo ST. Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. J Chem Inf Model 2019; 60:204-211. [DOI: 10.1021/acs.jcim.9b00778] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Thanh Nguyen
- Department of Theoretical Physics, Ho Chi Minh City University of Science, Ho Chi Minh City 700000, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - T. Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Mai Van Bay
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| |
Collapse
|