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Nunthaboot N, Boonma T, Rajchakom C, Nutho B, Rungrotmongkol T. Efficiency of membrane fusion inhibitors on different hemagglutinin subtypes: insight from a molecular dynamics simulation perspective. J Biomol Struct Dyn 2024:1-12. [PMID: 38415365 DOI: 10.1080/07391102.2024.2322629] [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: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
The challenge in vaccine development, along with drug resistance issues, has encouraged the search for new anti-influenza drugs targeting different viral proteins. Hemagglutinin (HA) glycoprotein, crucial in the viral replication cycle, has emerged as a promising therapeutic target. CBS1117 and JNJ4796 were reported to exhibit similar potencies against infectious group 1 influenza, which included H1 and H5 HAs; however, their potencies were significantly reduced against group 2 HA. This study aims to explore the molecular binding mechanisms and group specificity of these fusion inhibitors against both group 1 (H5) and group 2 (H3) HA influenza viruses using molecular dynamics simulations. CBS1117 and JNJ4796 exhibit stronger interactions with key residues within the H5 HA binding pocket compared to H3-ligand complexes. Hydrogen bonding and hydrophobic interactions involving residues, such as H381, Q401, T3251 (H5-CBS1117), T3181 (H5-JNJ4796), W212, I452, V482, and V522 predominantly contribute to stabilizing H5-ligand systems. In contrast, these interactions are notably weakened in H3-inhibitor complexes. Predicted protein-ligand binding free energies align with experimental data, indicating CBS1117 and JNJ4796's preference for heterosubtypic group 1 HA binding. Understanding the detailed atomistic mechanisms behind the varying potencies of these inhibitors against the two HA groups can significantly contribute to the development and optimization of effective HA fusion inhibitors. To accomplish this, the knowledge of the transition of HA from its pre- to post-fusion states, the molecular size of ligands, and their potential binding regions, could be carefully considered.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nadtanet Nunthaboot
- Multidisciplinary Research Unit of Pure and Applied Chemistry and Supramolecular Chemistry Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Thitiya Boonma
- Multidisciplinary Research Unit of Pure and Applied Chemistry and Supramolecular Chemistry Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Chananya Rajchakom
- Multidisciplinary Research Unit of Pure and Applied Chemistry and Supramolecular Chemistry Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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Modanwal S, Mishra N. Identification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach. J Biomol Struct Dyn 2023; 41:1109-1127. [PMID: 34961392 DOI: 10.1080/07391102.2021.2020169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Obesity may have an effect on cancer outcomes, resulting in global inequalities in cancer survival and death. Microarray data analysis was done to identify differentially expressed genes (DEGs) in obese and cancer patients. Total 1977 differentially expressed genes among obesity and gastric cancer, breast cancer, pancreatic cancer, and colorectal cancer were used to build a gene interaction network, which was then analyzed by using Cytoscape software. It has been identified that JUN, CXCL12, and LEP genes show a higher degree and stress, and play an important role in obesity and cancer progression. Further, CXCL12 and LEP were taken for virtual screening study with coumarin and its derivatives to develop a drug against obesity and cancer. The interactions of CXCL12 and LEP with coumarins were studied by molecular docking and it shows good interaction as well as docking score as compared to the standard one. The ADME properties were predicted to check the drug-likeness activity of coumarins and the most of the drug-likeness activities are in admire range. The Binding free energy of the docked complex was calculated by performing MM-GBSA. The molecular docking, ADME properties prediction, and MM-GBSA was performed on Maestro 12.6. The top docked score compounds were further subjected to molecular dynamic simulation to check the stability by using GROMACS. The MM-PBSA study was performed to calculate the binding energy components as well as the energy contributions of specific amino acids. The resultant compounds could be a potent anti-obesity and anti-cancer drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shristi Modanwal
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, U.P, India
| | - Nidhi Mishra
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, U.P, India
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Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective. Comput Biol Chem 2022; 101:107764. [DOI: 10.1016/j.compbiolchem.2022.107764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/07/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022]
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Studies on the Selectivity Mechanism of Wild-Type E. coli Thioesterase ‘TesA and Its Mutants for Medium- and Long-Chain Acyl Substrates. Catalysts 2022. [DOI: 10.3390/catal12091026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
E. coli thioesterase ‘TesA is an important enzyme in fatty acid production. Medium-chain fatty acids (MCFAs, C6-C10) are of great interest due to their similar physicochemical properties to petroleum-based oleo-chemicals. It has been shown that wild-type ‘TesA had better selectivity for long-chain acyl substrates (≥C16), while the two mutants ‘TesAE142D/Y145G and ‘TesAM141L/E142D/Y145G had better selectivity for medium-chain acyl substrates. However, it is difficult to obtain the selectivity mechanism of substrates for proteins by traditional experimental methods. In this study, in order to obtain more MCFAs, we analyzed the binding mode of proteins (‘TesA, ‘TesAE142D/Y145G and ‘TesAM141L/E142D/Y145G) and substrates (C16/C8-N-acetylcysteamine analogs, C16/C8-SNAC), the key residues and catalytic mechanisms through molecular docking, molecular dynamics simulations and the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA). The results showed that several main residues related to catalysis, including Ser10, Asn73 and His157, had a strong hydrogen bond interaction with the substrates. The mutant region (Met141-Tyr146) and loop107–113 were mainly dominated by Van der Waals contributions to the substrates. For C16-SNAC, except for ‘TesAM141L/E142D/Y145G with large conformational changes, there were strong interactions at both head and tail ends that distorted the substrate into a more favorable high-energy conformation for the catalytic reaction. For C8-SNAC, the head and tail found it difficult to bind to the enzyme at the same time due to insufficient chain length, which made the substrate binding sites more variable, so ‘TesAM141L/E142D/Y145G with better binding sites had the strongest activity, and ‘TesA had the weakest activity, conversely. In short, the matching substrate chain and binding pocket length are the key factors affecting selectivity. This will be helpful for the further improvement of thioesterases.
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Lu Y, Wang Y, Huang D, Bian Z, Lu P, Fan D, Wang X. Inhibitory mechanism of angiotensin-converting enzyme inhibitory peptides from black tea. J Zhejiang Univ Sci B 2021; 22:575-589. [PMID: 34269010 DOI: 10.1631/jzus.b2000520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this work is to discover the inhibitory mechanism of tea peptides and to analyse the affinities between the peptides and the angiotensin-converting enzyme (ACE) as well as the stability of the complexes using in vitro and in silico methods. Four peptide sequences identified from tea, namely peptides I, II, III, and IV, were used to examine ACE inhibition and kinetics. The half maximal inhibitory concentration (IC50) values of the four peptides were (210.03±18.29), (178.91±5.18), (196.31±2.87), and (121.11±3.38) μmol/L, respectively. The results of Lineweaver-Burk plots showed that peptides I, II, and IV inhibited ACE activity in an uncompetitive manner, which requires the presence of substrate. Peptide III inhibited ACE in a non-competitive manner, for which the presence of substrate is not necessary. The docking simulations showed that the four peptides did not bind to the active sites of ACE, indicating that the four peptides are allosteric inhibitors. The binding free energies calculated from molecular dynamic (MD) simulation were -72.47, -42.20, -52.10, and -67.14 kcal/mol (1 kcal=4.186 kJ), respectively. The lower IC50 value of peptide IV may be attributed to its stability when docking with ACE and changes in the flexibility and unfolding of ACE. These four bioactive peptides with ACE inhibitory ability can be incorporated into novel functional ingredients of black tea.
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Affiliation(s)
- Yating Lu
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Danyi Huang
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhuang Bian
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Peng Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Dongmei Fan
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaochang Wang
- Tea Research Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. J Phys Chem B 2020; 124:10034-10047. [PMID: 33112147 PMCID: PMC7605337 DOI: 10.1021/acs.jpcb.0c05994] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/07/2020] [Indexed: 12/11/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means that the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also has implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in silico Ala-scanning and long-timescale MD simulations highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637962 DOI: 10.1101/2020.06.27.175448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious.
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How Different Substitution Positions of F, Cl Atoms in Benzene Ring of 5-Methylpyrimidine Pyridine Derivatives Affect the Inhibition Ability of EGFR L858R/T790M/C797S Inhibitors: A Molecular Dynamics Simulation Study. Molecules 2020; 25:molecules25040895. [PMID: 32085409 PMCID: PMC7071101 DOI: 10.3390/molecules25040895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the most frequent cause of cancer-related deaths worldwide, and mutations in the kinase domain of the epidermal growth factor receptor (EGFR) are a common cause of non-small-cell lung cancers, which is a major subtype of lung cancers. Recently, a series of 5-methylpyrimidine-pyridinone derivatives have been designed and synthesized as novel selective inhibitors of EGFR and EGFR mutants. However, the binding-based inhibition mechanism has not yet been determined. In this study, we carried out molecular dynamic simulations and free-energy calculations for EGFR derivatives to fill this gap. Based on the investigation, the three factors that influence the inhibitory effect of inhibitors are as follows: (1) The substitution site of the Cl atom is the main factor influencing the activity through steric effect; (2) The secondary factors are repulsion between the F atom (present in the inhibitor) and Glu762, and the blocking effect of Lys745 on the phenyl ring of the inhibitor. (3) The two factors function synergistically to influence the inhibitory capacity of the inhibitor. The theoretical results of this study can provide further insights that will aid the design of oncogenic EGFR inhibitors with high selectivity.
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Kalyan G, Junghare V, Bhattacharya S, Hazra S. Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources. J Biomol Struct Dyn 2020; 39:635-649. [PMID: 32048568 DOI: 10.1080/07391102.2020.1715836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Functional foods are emerging as essential healthy nutritional component due to their abundant wellbeing benefits. Especially the food-derived peptides are considered as key components for playing their biologically active roles. One such robust therapeutics that already exploited with food peptides that help treating high blood pressure via targeting Angiotensin-Converting Enzyme (ACE). This in silico study demonstrated the inhibitory potential of antihypertensive peptides derived from food sources. This study involves an intensive structure-based analysis of enzyme-peptide interactions using Molecular Dynamics (MD) simulations. Interestingly, this study will help us to get deeper understanding on how food peptides achieve successful inhibition of ACE. In this study, the peptide-enzyme complexes revealed two binding pockets, A and B, on either side of the active site Zn atom. Pocket B has a smaller binding site volume than pocket A, comprised of β-sheets and the active site opening cleft. The interface of the binding sites showed that the enzyme structure was negative to neutral charge, and the peptide structure was positive to neutral charge. The dynamics of complex structures of seven highly potential peptides were performed for 20 ns each at 300 K. Comparative analysis of RMSD, RMSF and binding energies show the enzyme-peptide complexes and the overall stability of apo-enzyme. Importantly, two peptides AFKAWAVAR and IWHHTF showed the highest variation in their RMSD as compared to the apo-enzyme. This study will further be useful for the assessment of the characteristics to predict novel inhibitory peptides that can be generated from food proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gazal Kalyan
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vivek Junghare
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sourya Bhattacharya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Centre of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Guan S, Zhu K, Dong Y, Li H, Yang S, Wang S, Shan Y. Exploration of Binding Mechanism of a Potential Streptococcus pneumoniae Neuraminidase Inhibitor from Herbaceous Plants by Molecular Simulation. Int J Mol Sci 2020; 21:ijms21031003. [PMID: 32028720 PMCID: PMC7038148 DOI: 10.3390/ijms21031003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 01/11/2023] Open
Abstract
Streptococcus pneumoniae can cause diseases such as pneumonia. Broad-spectrum antibiotic therapy for Streptococcus pneumoniae is increasingly limited due to the emergence of drug-resistant strains. The development of novel drugs is still currently of focus. Abundant polyphenols have been demonstrated to have antivirus and antibacterial ability. Chlorogenic acid is one of the representatives that has been proven to have the potential to inhibit both the influenza virus and Streptococcus pneumoniae. However, for such a potential neuraminidase inhibitor, the interaction mechanism studies between chlorogenic acid and Streptococcus pneumoniae neuraminidase are rare. In the current study, the binding mechanism of chlorogenic acid and Streptococcus pneumoniae neuraminidase were investigated by molecular simulation. The results indicated that chlorogenic acid might establish the interaction with Streptococcus pneumoniae neuraminidase via hydrogen bonds, salt bridge, and cation-π. The vital residues involved Arg347, Ile348, Lys440, Asp372, Asp417, and Glu768. The side chain of Arg347 might form a cap-like structure to lock the chlorogenic acid to the active site. The results from binding energy calculation indicated that chlorogenic acid had strong binding potential with neuraminidase. The results predicted a detailed binding mechanism of a potential Streptococcus pneumoniae neuraminidase inhibitor, which will be provide a theoretical basis for the mechanism of new inhibitors.
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Affiliation(s)
- Shanshan Guan
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
| | - Ketong Zhu
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Yanjiao Dong
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Shuang Yang
- College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Jilin, China; (K.Z.); (Y.D.); (H.L.); (S.Y.)
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun 130052, Jilin, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, Jilin, China;
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
- Correspondence: (S.G.); (Y.S.); Tel.: +86-4318-172-1319 (S.G. & Y.S.)
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Han F, Liu Y, E J, Guan S, Han W, Shan Y, Wang S, Zhang H. Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study. Biopolymers 2018; 109:e23238. [PMID: 30484856 DOI: 10.1002/bip.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/21/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Analysis of simulation results suggests that the binding free energies between the substrate and WT-Cbh9A are lower than those of Y555S and W678G mutants. The pull forces and energy barrier in Y555S and W678G mutants also reduced significantly during the steered molecular dynamics (SMD) simulation compared with that of the WT-Cbh9A. And the potential mean force calculations showed that the pulling energy barrier of Y555S and W678G mutants is much lower than that of WT-Cbh9A.
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Affiliation(s)
- Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Shanshan Guan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Yaming Shan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
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Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations. PLoS One 2018; 13:e0207234. [PMID: 30444912 PMCID: PMC6239307 DOI: 10.1371/journal.pone.0207234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023] Open
Abstract
Adenosine deaminase (ADA) catalyzes the deamination of adenosine, which is important in purine metabolism. ADA is ubiquitous to almost all human tissues, and ADA abnormalities have been reported in various diseases, including rheumatoid arthritis. ADA can be divided into two conformations based on the inhibitor that it binds to: open and closed forms. Here, we chose three ligands, namely, FR117016 (FR0), FR221647 (FR2) (open form), and HDPR (PRH, closed form), to investigate the inhibition mechanism of ADA and its effect on ADA through molecular dynamics simulations. In open forms, Egap and electrostatic potential (ESP) indicated that electron transfer might occur more easily in FR0 than in FR2. Binding free energy and hydrogen bond occupation revealed that the ADA-FR0 complex had a more stable structure than ADA-FR2. The probability of residues Pro159 to Lys171 of ADA-FR0 and ADA-FR2 to form a helix moderately increased compared with that in nonligated ADA. In comparison with FR0 and FR2 PRH could maintain ADA in a closed form to inhibit the function of ADA. The α7 helix (residues Thr57 to Ala73) of ADA in the closed form was mostly unfastened because of the effect of PRH. The number of H bonds and the relative superiority of the binding free energy indicated that the binding strength of PRH to ADA was significantly lower than that of an open inhibitor, thereby supporting the comparison of the inhibitory activities of the three ligands. Alanine scanning results showed that His17, Gly184, Asp295, and Asp296 exerted the greatest effects on protein energy, suggesting that they played crucial roles in binding to inhibitors. This study served as a theoretical basis for the development of new ADA inhibitors.
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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Zhang J, Zhang L, Xu Y, Jiang S, Shao Y. Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex. PLoS One 2018; 13:e0196651. [PMID: 29715320 PMCID: PMC5929560 DOI: 10.1371/journal.pone.0196651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Flavonoids, a class of natural compounds with variable phenolic structures, have been found to possess anti-cancer activities by modulating different enzymes and receptors like CDK6. To understand the binding behavior of flavonoids that inhibit the active CDK6, molecular dynamics (MD) simulations were performed on six inhibitors, chrysin (M01), fisetin (M03), galangin (M04), genistein (M05), quercetin (M06) and kaempferol (M07), complexed with CDK6/cyclin D. For all six flavonoids, the 3'-OH and 4'-OH of B-ring were found to be favorable for hydrogen bond formation, but the 3-OH on the C-ring and 5-OH on the A-ring were unfavorable, which were confirmed by the MD simulation results of the test molecule, 3', 4', 7-trihydroxyflavone (M15). The binding efficiencies of flavonoids against the CDK6/cyclin D complex were mainly through the electrostatic (especially the H-bond force) and vdW interactions with residues ILE19, VAL27, ALA41, GLU61, PHE98, GLN103, ASP163 and LEU152. The order of binding affinities of these flavonoids toward the CDK6/cyclin D was M03 > M01 > M07 > M15 > M06 > M05 > M04. It is anticipated that the binding features of flavonoid inhibitors studied in the present work may provide valuable insights for the development of CDK6 inhibitors.
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Affiliation(s)
- Jingxiao Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Lilei Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Yangcheng Xu
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Shanshan Jiang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Yueyue Shao
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
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15
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Anbarasu K, Jayanthi S. Identification of curcumin derivatives as human LMTK3 inhibitors for breast cancer: a docking, dynamics, and MM/PBSA approach. 3 Biotech 2018; 8:228. [PMID: 29719770 DOI: 10.1007/s13205-018-1239-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/02/2018] [Indexed: 02/04/2023] Open
Abstract
Human lemur tyrosine kinase-3 (LMTK3) is primarily involved in regulation of estrogen receptor-α (ERα) by phosphorylation activity. LMTK3 acts as key biomarker for ERα positive breast cancer and identified as novel drug target for breast cancer. Due to the absence of experimental reports, the computational approach has been followed to screen LMTK3 inhibitors from natural product curcumin derivatives based on rational inhibitor design. The initial virtual screening and re-docking resulted in identification of top three leads with favorable binding energy and strong interactions in critical residues of ATP-binding cavity. ADME prediction confirmed the pharmacological activity of the leads with various properties. The stability and binding affinity of leads were well refined in dynamic system from 25 ns MD simulations. The behavior of protein motion towards closure of ATP-binding cavity was evaluated based on eigenvectors by PCA. In addition, MM/PBSA calculations also confirmed the relative binding free energy of LMTK3-lead complexes in favor of the effective binding. From our study, novel LMTK3 inhibitors tetrahydrocurcumin, curcumin 4,4'-diacetate, and demethoxycurcumin have been proposed with inhibition mechanism. Further experimental evaluation on reported lead candidates might prove its role in breast cancer therapeutics.
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Affiliation(s)
- K Anbarasu
- Computational Drug Design Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, TamilNadu 632014 India
| | - S Jayanthi
- Computational Drug Design Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, TamilNadu 632014 India
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16
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Guan S, Xu Y, Qiao Y, Kuai Z, Qian M, Jiang X, Wang S, Zhang H, Kong W, Shan Y. A novel small molecule displays two different binding modes during inhibiting H1N1 influenza A virus neuraminidases. J Struct Biol 2018; 202:142-149. [DOI: 10.1016/j.jsb.2017.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/08/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023]
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17
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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18
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Exploration of binding and inhibition mechanism of a small molecule inhibitor of influenza virus H1N1 hemagglutinin by molecular dynamics simulation. Sci Rep 2017. [PMID: 28630402 PMCID: PMC5476670 DOI: 10.1038/s41598-017-03719-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found. The results suggested that the binding of the inhibitor with HA under neutral conditions facilitates only its intake, while it interacts with HA under acidic conditions using a different mechanism at a new binding site. After a series of experiments, we believe that binding of the inhibitor can prevent the release of HA1 from HA2, further maintaining the rigidity of the HA2 loop and stabilizing the distance between the long helix and short helices. The investigated residues in the new binding site show high conservation, implying that the new binding pocket has the potential to be an effective drug target. The results of this study will provide a theoretical basis for the mechanism of new influenza virus inhibitors.
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19
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Medvedev KE, Kolchanov NA, Afonnikov DA. High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations. J Biomol Struct Dyn 2017; 36:68-82. [DOI: 10.1080/07391102.2016.1268070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill E. Medvedev
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolay A. Kolchanov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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20
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Qiao Y, Yang Q, Song C, Chang J. Computational insights into the origin of decrease/increase in potency of N-CDPCB analogues toward FTO. J Biomol Struct Dyn 2016; 35:1758-1765. [DOI: 10.1080/07391102.2016.1193445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yan Qiao
- Department of Pathophysiology, Basic Medical College of Zhengzhou University, Zhengzhou 450001, People’s Republic of China
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Qinghua Yang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
| | - Chuanjun Song
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
| | - Junbiao Chang
- Department of Pathophysiology, Basic Medical College of Zhengzhou University, Zhengzhou 450001, People’s Republic of China
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21
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Nagamani S, Muthusamy K, Marshal JJ. E-pharmacophore filtering and molecular dynamics simulation studies in the discovery of potent drug-like molecules for chronic kidney disease. J Biomol Struct Dyn 2016; 34:2233-2250. [PMID: 26513595 DOI: 10.1080/07391102.2015.1111168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic kidney disease (CKD) is a prominent health issue reported globally. The level of the vitamin D receptor (VDR) and cytochrome P450 enzyme 24-hydroxylase (CYP24A1) are crucial in the pathogenesis of secondary hyperparathyroidism (sHPT) in CKD. An elevated expression of the CYP24A1 leads to the deficiency of vitamin D and resistance to vitamin D therapy. Hence, VDR agonists and CYP24A1 antagonists are suggested to CKD patients for the management of biochemical complications. CTA-018 is a recently reported analog and acts as a potent CYP24A1 inhibitor. It inhibits CYP24A1 with an IC50 27 ± 6 nM, about 10 times more potentially than the non-selective inhibitor ketoconazole (253 ± 20 nM), and it is also been reported to induce the VDR expression. Thus, CTA-018 is under clinical trial among CKD patients. In this study, combined molecular docking and pharmacophore filtering were employed to identify compounds better than CTA-018. A huge set of 9127 compounds from Sweet Lead database were docked into the active site of VDR using Glide XP program. E-pharmacophore was developed from both the targets along with CTA-018. The compounds retrieved from the two different pharmacophore-based screening were re-docked into the active site of CYP24A1. The hits that bind well at both the active sites and matched with the pharmacophore models were considered as possible dual functional molecules against VDR and CYP24A1. Further, molecular dynamics simulation and subsequent energy decomposition analyses were also performed to study the role of specific amino acids in the active site of both VDR and CYP24A1.
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Affiliation(s)
- Selvaraman Nagamani
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
| | | | - J John Marshal
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
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