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Zhang Y, Chen L, Wang Z, Zhu Y, Jiang H, Xu J, Xiong F. Design of novel DABO derivatives as HIV-1 RT inhibitors using molecular docking, molecular dynamics simulations and ADMET properties. J Biomol Struct Dyn 2024; 42:4196-4213. [PMID: 37272892 DOI: 10.1080/07391102.2023.2219331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
HIV-1 reverse transcriptase is an important target for developing effective anti-HIV-1 inhibitors. Different types of small molecules have been designed based on this target, showing different levels of inhibitory activity against various types of HIV-1 strains. The relationship between structure and activity of DABO derivatives was investigated by means of 3D-QSAR molecular model, molecular docking, molecular dynamics and ADMET properties. The statistical results of molecular models show that the CoMFA and CoMSIA models have good internal stability (CoMFA: q2 = 0.623, r2 = 0.946; CoMSIA: q2 = 0.668, r2 = 0.983) and external prediction ability (CoMFA: rpred2 = 0.961; CoMSIA: rpred2 = 0.961). In addition, molecular docking has explored the mechanism of action between small molecules and receptor proteins, and the results show that hydrogen bonding between amino acid Lys101 and small molecules can improve the affinity of ligands to receptor binding. A total of 12 novel molecules were designed and their activities were predicted based on the 3D-QSAR model and molecular docking results. The results showed that the designed molecules had higher predictive activity. Subsequently, 100 ns MD simulation and binding free energy verified the stability of molecular docking results. Finally, the pharmacokinetic properties of the novel designed molecule were verified by using ADMET to predict its properties. These results can provide reference for the design and development of novel and effective HIV-1 RT inhibitors, and provide new ideas for the design of subsequent drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhonghua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Huifang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Jie Xu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
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Xiong F, Zhang YJ, Jiang HY, Wang ZH. Exploring the Efficacy of Noncovalent SARS-CoV-2 Main Protease Inhibitors: A Computational Simulation Analysis Study. Chem Biodivers 2024; 21:e202302089. [PMID: 38526531 DOI: 10.1002/cbdv.202302089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 03/26/2024]
Abstract
The SARS-CoV-2 main protease, as a key target for antiviral therapeutics, is instrumental in maintaining virus stability, facilitating translation, and enabling the virus to evade innate immunity. Our research focused on designing non-covalent inhibitors to counteract the action of this protease. Utilizing a 3D-QSAR model and contour map, we successfully engineered eight novel non-covalent inhibitors. Further evaluation and comparison of these novel compounds through methodologies including molecular docking, ADMET analysis, frontier molecular orbital studies, molecular dynamics simulations, and binding free energy revealed that the inhibitors N02 and N03 demonstrated superior research performance (N02 ΔGbind=-206.648 kJ/mol, N03 ΔGbind=-185.602 kJ/mol). These findings offer insightful guidance for the further refinement of molecular structures and the development of more efficacious inhibitors. Consequently, future investigations can draw upon these findings to unearth more potent inhibitors, thereby amplifying their impact in the treatment and prevention of associated diseases.
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Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yan-Jun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Hui-Ying Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhong-Hua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
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Jiang H, Li Y, Wang Z, Li S, Wu T, Xiong F. 3D-QSAR, molecular docking, and molecular dynamics analysis of novel biphenyl-substituted pyridone derivatives as potent HIV-1 NNRTIs. J Biomol Struct Dyn 2023:1-16. [PMID: 37909494 DOI: 10.1080/07391102.2023.2276885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/14/2023] [Indexed: 11/03/2023]
Abstract
When designing new medications targeting HIV-1, drug designers concentrate on reverse transcriptase (RT), the central enzyme of their concern. This is due to its vital role in converting single-stranded RNA into double-stranded DNA throughout the life cycle of HIV-1. In recent reports, a series of newly discovered pyridone derivatives with biphenyl substitutions have emerged as highly potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), displaying impressive antiviral activity. To analyse the three-dimensional quantitative structure-activity relationship (3D-QSAR) of pyridone inhibitors with biphenyl substitutions, we employed CoMFA and CoMSIA methods in this study. The dataset comprises a total of 51 compounds. The findings of this research demonstrate that both the CoMFA (q2=0.688, r2=0.976, rpred2=0.831) and CoMSIA/SHE (q2=0.758, r2=0.968, rpred2=0.828) models exhibit excellent predictive capability and reliable estimation stability. According to the findings of the model, we designed a collection of eleven molecules that exhibit the potential for significantly improved predictive activity. We proceeded to investigate the binding patterns of these compounds to receptor proteins utilizing the molecular docking technique. To ensure the reliability of the docking results, we went on to validate them by conducting molecular dynamics simulations and performing accurate calculations of the binding free energy. Moreover, based on initial ADMET predictions, the results consistently indicate that the newly created molecule possesses favourable pharmacokinetic properties. This study will help to facilitate the development of efficient novel inhibitors that specifically target HIV-1's non-nucleoside reverse transcriptase (NNRTIs).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huifang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P.R. China
| | - Yeji Li
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P.R. China
| | - Zhonghua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P.R. China
| | - Shaotong Li
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P.R. China
| | - Tianle Wu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P.R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P.R. China
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Belghalia E, Ouabane M, El Bahi S, Rehman HM, Sbai A, Lakhlifi T, Bouachrine M. In silico research on new sulfonamide derivatives as BRD4 inhibitors targeting acute myeloid leukemia using various computational techniques including 3D-QSAR, HQSAR, molecular docking, ADME/Tox, and molecular dynamics. J Biomol Struct Dyn 2023:1-19. [PMID: 37656159 DOI: 10.1080/07391102.2023.2250460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
Acute myeloid leukemia, a serious condition affecting stem cells, drives uncontrollable myeloblast proliferation, leading to accumulation. Extensive research seeks rapid, effective chemotherapeutics. A potential option is a BRD4 inhibitor, known for suppressing cell proliferation. Sulfonamide derivatives probed essential structural elements for potent BRD4 inhibitors. To achieve this goal, we employed 3D-QSAR molecular modeling techniques, including CoMFA, CoMSIA, and HQSAR models, along with molecular docking and molecular dynamics simulations. The validation of the 2D/3D QSAR models, both internally and externally, underscores their robustness and reliability. The contour plots derived from CoMFA, CoMSIA, and HQSAR analyses played a pivotal role in shaping the design of effective BRD4 inhibitors. Importantly, our findings highlight the advantageous impact of incorporating bulkier substituents on the pyridinone ring and hydrophobic/electrostatic substituents on the methoxy-substituted phenyl ring, enhancing interactions with the BRD4 target. The interaction mode of the new compounds with the BRD4 receptor (PDB ID: 4BJX) was investigated using molecular docking simulations, revealing favorable binding energies, supported by the formation of hydrogen and hydrophobic bonds with key protein residues. Moreover, these novel inhibitors exhibited good oral bioavailability and demonstrated non-toxic properties based on ADMET analysis. Furthermore, the newly designed compounds along with the most active one from series 58, underwent a molecular dynamics simulation to analyze their behavior. The simulation provided additional evidence to support the molecular docking results, confirming the sustained stability of the analyzed molecules over the trajectory. This outcome could serve as a valuable reference for designing and developing novel and effective BRD4 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Etibaria Belghalia
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohamed Ouabane
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- Chemistry- Biologie Applied to the Environment URL CNRT 13, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Salma El Bahi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | | | - Abdelouahid Sbai
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Higher School of Technology - Khenifra (EST-Khenifra), University of Sultan My Slimane, Beni Mellal, Morocco
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Mak LY, Hui RWH, Cheung KS, Fung J, Seto WK, Yuen MF. Advances in determining new treatments for hepatitis B infection by utilizing existing and novel biomarkers. Expert Opin Drug Discov 2023; 18:401-416. [PMID: 36943183 DOI: 10.1080/17460441.2023.2192920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Chronic hepatitis B (CHB) infection is a major global health threat and accounts for significant liver-related morbidity and mortality. An improved understanding of how hepatitis B virus (HBV) interacts with the host immune system allows the discovery of novel biomarkers and new treatment options. Viral biomarkers including hepatitis B surface antigen (HBsAg) and newer ones like HBV RNA and hepatitis B core-related antigen appear to be useful to select patients who are likely to benefit from cessation of long-term antiviral therapy. These markers can also help to confirm target engagement for novel compounds, and efficacy in HBsAg reduction and seroclearance is deemed essential as this is how the current treatment endpoint of functional cure is defined. AREAS COVERED In this review, the authors discuss the current standard of care and the gaps between such standard and the ideal goals for treatment in CHB. The authors highlight novel viral and immunological biomarkers that are potentially useful to evaluate treatment response. Novel treatment approaches in relation to these novel biomarkers are also evaluated. EXPERT OPINION Novel serum viral biomarkers and immunological markers are indispensable in the HBV functional cure program. These will likely become part of standard monitoring soon.
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Affiliation(s)
- Lung-Yi Mak
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rex Wan-Hin Hui
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
| | - Ka-Shing Cheung
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
| | - James Fung
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wai-Kay Seto
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Man-Fung Yuen
- Department of Medicine, School of Clinical Medicine, Pokfulam, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong
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Xiong F, Chen L, Zhang YJ, Zhu YR, Sun C, Ma C, Zhang SJ, Wang ZH. Molecular Modeling and Docking Studies of 2,4,5-Trisubstituted Pyrimidines as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2141274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Yan-jun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Yi-ren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Chen Sun
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Chao Ma
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Shuai-jun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, PR China
| | - Zhong-hua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, PR China
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Zhang YJ, Chen L, Xu J, Jiang HF, Zhu YR, Wang ZH, Xiong F. Evaluation of novel HIV-1 protease inhibitors with DRV-resistance by utilizing 3D-QSAR molecular docking and molecular dynamics simulation. NEW J CHEM 2022. [DOI: 10.1039/d2nj04492g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular dynamics simulations were performed to explore the interaction mode of DRV derivatives binding to target proteins and to identify new potential HIV-1 PR inhibitors with stronger activity.
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Affiliation(s)
- Yan-Jun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Jie Xu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Hui-Fang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Yi-Ren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Zhong-Hua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
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Chen L, Liu WG, Xiong F, Ma C, Sun C, Zhu YR, Zhang XG, Wang ZH. 3D-QSAR, molecular docking and molecular dynamics simulations analyses of a series of heteroaryldihydropyrimidine derivatives as hepatitis B virus capsid assembly inhibitors. NEW J CHEM 2021. [DOI: 10.1039/d1nj02542b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In silico design of heteroaryldihydropyrimidine-based selective HBV capsid assembly inhibitors.
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Affiliation(s)
- Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Wen-Guang Liu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Chao Ma
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Chen Sun
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Yi-Ren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Xing-Guang Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China
| | - Zhong-Hua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, People's Republic of China
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