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Qiu X, Zhang Q, Li Z, Zhang J, Liu H. Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis. Int J Mol Sci 2024; 25:3764. [PMID: 38612573 PMCID: PMC11011931 DOI: 10.3390/ijms25073764] [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: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
With the rapid emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently, the identification of new anti-TB targets and drugs is critically urgent. DNA gyrase subunit B (GyrB) has been identified as a potential anti-TB target, with novobiocin and SPR719 proposed as inhibitors targeting GyrB. Therefore, elucidating the molecular interactions between GyrB and its inhibitors is crucial for the discovery and design of efficient GyrB inhibitors for combating multidrug-resistant TB. In this study, we revealed the detailed binding mechanisms and dissociation processes of the representative inhibitors, novobiocin and SPR719, with GyrB using classical molecular dynamics (MD) simulations, tau-random acceleration molecular dynamics (τ-RAMD) simulations, and steered molecular dynamics (SMD) simulations. Our simulation results demonstrate that both electrostatic and van der Waals interactions contribute favorably to the inhibitors' binding to GyrB, with Asn52, Asp79, Arg82, Lys108, Tyr114, and Arg141 being key residues for the inhibitors' attachment to GyrB. The τ-RAMD simulations indicate that the inhibitors primarily dissociate from the ATP channel. The SMD simulation results reveal that both inhibitors follow a similar dissociation mechanism, requiring the overcoming of hydrophobic interactions and hydrogen bonding interactions formed with the ATP active site. The binding and dissociation mechanisms of GyrB with inhibitors novobiocin and SPR719 obtained in our work will provide new insights for the development of promising GyrB inhibitors.
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Affiliation(s)
- Xiaofei Qiu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Qianqian Zhang
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
| | - Zhaoguo Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Juan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; (X.Q.); (Z.L.); (J.Z.)
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, China;
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2
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Meng H, Cui Z, Yu Y, Li Y, Jiang S, Liu Y. From Molecular Dynamics to Taste Sensory Perception: A Comprehensive Study on the Interaction of Umami Peptides with the T1R1/T1R3-VFT Receptor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6533-6543. [PMID: 38488059 DOI: 10.1021/acs.jafc.3c09598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The research on the umami receptor-ligand interaction is crucial for understanding umami perception. This study integrated molecular simulations, sensory evaluation, and biosensor technology to analyze the interaction between umami peptides and the umami receptor T1R1/T1R3-VFT. Molecular dynamics simulations were used to investigate the dissociation process of seven umami peptides with the umami receptor T1R1/T1R3-VFT, and by calculating the potential mean force curve using the Jarzynski equation, it was found that the binding free energy of umami peptide is between -58.80 and -12.17 kcal/mol, which had a strong correlation with the umami intensity obtained by time intensity sensory evaluation. Through correlation analysis, the dissociation rate constants (0.0126-0.394 1/s) of umami peptides were found to have a great impact on umami perception. The faster the dissociation rate of umami peptides from receptors, the stronger the perceived intensity of the umami taste. This research aims to elucidate the relationship between the umami peptide-receptor interaction and umami perception, providing theoretical support for the exploration of umami perception mechanisms.
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Affiliation(s)
- Hengli Meng
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Cui
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanyang Yu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingqiu Li
- Secondary College of Cereals and Tourism, Guangxi Vocational College of Technology and Business, Nanning 530005, China
| | - Shui Jiang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Liu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Hasse T, Mantei E, Shahoei R, Pawnikar S, Wang J, Miao Y, Huang YMM. Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein. PLoS Comput Biol 2024; 20:e1011955. [PMID: 38452125 PMCID: PMC10959368 DOI: 10.1371/journal.pcbi.1011955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/22/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024] Open
Abstract
The COVID-19 pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spurred an urgent need for effective therapeutic interventions. The spike glycoprotein of the SARS-CoV-2 is crucial for infiltrating host cells, rendering it a key candidate for drug development. By interacting with the human angiotensin-converting enzyme 2 (ACE2) receptor, the spike initiates the infection of SARS-CoV-2. Linoleate is known to bind the spike glycoprotein, subsequently reducing its interaction with ACE2. However, the detailed mechanisms underlying the protein-ligand interaction remain unclear. In this study, we characterized the pathways of ligand dissociation and the conformational changes associated with the spike glycoprotein by using ligand Gaussian accelerated molecular dynamics (LiGaMD). Our simulations resulted in eight complete ligand dissociation trajectories, unveiling two distinct ligand unbinding pathways. The preference between these two pathways depends on the gate distance between two α-helices in the receptor binding domain (RBD) and the position of the N-linked glycan at N343. Our study also highlights the essential contributions of K417, N121 glycan, and N165 glycan in ligand unbinding, which are equally crucial in enhancing spike-ACE2 binding. We suggest that the presence of the ligand influences the motions of these residues and glycans, consequently reducing accessibility for spike-ACE2 binding. These findings enhance our understanding of ligand dissociation from the spike glycoprotein and offer significant implications for drug design strategies in the battle against COVID-19.
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Affiliation(s)
- Timothy Hasse
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - Esra Mantei
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - Rezvan Shahoei
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - Shristi Pawnikar
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jinan Wang
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Yinglong Miao
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Yu-ming M. Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
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Guo J, Liu H. The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics. Curr Med Chem 2024; 31:2839-2840. [PMID: 38904158 DOI: 10.2174/092986733120240405144035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Affiliation(s)
- Jingjing Guo
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
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Du Q, Tu G, Qian Y, Yang J, Yao X, Xue W. Unbiased molecular dynamics simulation of a first-in-class small molecule inhibitor binds to oncostatin M. Comput Biol Med 2023; 155:106709. [PMID: 36854228 DOI: 10.1016/j.compbiomed.2023.106709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023]
Abstract
Small molecule inhibitors (SMIs) targeting oncostatin M (OSM) signaling pathway represent new therapeutics to combat cancer, inflammatory bowel disease (IBD) and CNS disease. Recently, the first-in-class SMI named SMI-10B that target OSM and block its interaction with receptor (OSMR) were reported. However, the binding pocket and interaction mode of the compound on OSM remain poorly understood, which hampering the rational design of SMIs that target OSM. Here, using SMI-10B as a probe, the multiple pockets on OSM for small molecules binding were extensively explored by unbiased molecular dynamics (MD) simulations. Then, the near-native structure of the complex was identified by molecular mechanics generalized Born surface area (MM/GBSA) binding energy funnel. Moreover, the binding stabilities of the protein-ligand complexes in near- and non-native conformations were verified by additional independent MD runs and absolute free energy perturbation (FEP) calculation. In summary, the unique feature of SMI-10B spontaneously binds to OSM characterized here not only provide detailed information for understanding the molecular mechanism of SMI-10B binding to OSM, but also will facilitate the rational design of novel and more potent SMIs to block OSM signaling.
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Affiliation(s)
- Qingqing Du
- Depart of Pharmacy, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Gao Tu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Yan Qian
- Depart of Pharmacy, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Jingyi Yang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
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Sohraby F, Nunes-Alves A. Advances in computational methods for ligand binding kinetics. Trends Biochem Sci 2022; 48:437-449. [PMID: 36566088 DOI: 10.1016/j.tibs.2022.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms. In this review, we introduce and compare computational methods recently developed and applied to two systems, trypsin-benzamidine and kinase-inhibitor complexes. Methods involving enhanced sampling in molecular dynamics simulations or machine learning can be used not only to predict kinetic rates, but also to reveal factors modulating the duration of residence times, selectivity, and drug resistance to mutations. Methods which require less computational time to make predictions are highlighted, and suggestions to reduce the error of computed kinetic rates are presented.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
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Shinobu A, Re S, Sugita Y. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics. Front Mol Biosci 2022; 9:878830. [PMID: 35573746 PMCID: PMC9099257 DOI: 10.3389/fmolb.2022.878830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular dynamics (MD) simulations are increasingly used to study various biological processes such as protein folding, conformational changes, and ligand binding. These processes generally involve slow dynamics that occur on the millisecond or longer timescale, which are difficult to simulate by conventional atomistic MD. Recently, we applied a two-dimensional (2D) replica-exchange MD (REMD) method, which combines the generalized replica exchange with solute tempering (gREST) with the replica-exchange umbrella sampling (REUS) in kinase-inhibitor binding simulations, and successfully observed multiple ligand binding/unbinding events. To efficiently apply the gREST/REUS method to other kinase-inhibitor systems, we establish modified, practical protocols with non-trivial simulation parameter tuning. The current gREST/REUS simulation protocols are tested for three kinase-inhibitor systems: c-Src kinase with PP1, c-Src kinase with Dasatinib, and c-Abl kinase with Imatinib. We optimized the definition of kinase-ligand distance as a collective variable (CV), the solute temperatures in gREST, and replica distributions and umbrella forces in the REUS simulations. Also, the initial structures of each replica in the 2D replica space were prepared carefully by pulling each ligand from and toward the protein binding sites for keeping stable kinase conformations. These optimizations were carried out individually in multiple short MD simulations. The current gREST/REUS simulation protocol ensures good random walks in 2D replica spaces, which are required for enhanced sampling of inhibitor dynamics around a target kinase.
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Affiliation(s)
- Ai Shinobu
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- *Correspondence: Yuji Sugita,
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