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Neuberger A, Trofimov YA, Yelshanskaya MV, Khau J, Nadezhdin KD, Khosrof LS, Krylov NA, Efremov RG, Sobolevsky AI. Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin. Nat Commun 2023; 14:4630. [PMID: 37532722 PMCID: PMC10397291 DOI: 10.1038/s41467-023-40362-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
The calcium-selective oncochannel TRPV6 is an important driver of cell proliferation in human cancers. Despite increasing interest of pharmacological research in developing synthetic inhibitors of TRPV6, natural compounds acting at this channel have been largely neglected. On the other hand, pharmacokinetics of natural small-molecule antagonists optimized by nature throughout evolution endows these compounds with a medicinal potential to serve as potent and safe next-generation anti-cancer drugs. Here we report the structure of human TRPV6 in complex with tetrahydrocannabivarin (THCV), a natural cannabinoid inhibitor extracted from Cannabis sativa. We use cryo-electron microscopy combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to identify THCV binding sites in the portals that connect the membrane environment surrounding the protein to the central cavity of the channel pore and to characterize the allosteric mechanism of TRPV6 inhibition. We also propose the molecular pathway taken by THCV to reach its binding site. Our study provides a foundation for the development of new TRPV6-targeting drugs.
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Affiliation(s)
- Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Yury A Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jeffrey Khau
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Lena S Khosrof
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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In silico pharmacokinetics, molecular docking and dynamic simulation studies of endolichenic fungi secondary metabolites: An implication in identifying novel kinase inhibitors as potential anticancer agents. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Lee HG, Kang S, Lee JS. Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G. Comput Struct Biotechnol J 2021; 19:3372-3383. [PMID: 34194664 PMCID: PMC8217638 DOI: 10.1016/j.csbj.2021.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 12/03/2022] Open
Abstract
In the wide array of physiological processes, protein-protein interactions and their binding are the most basal activities for achieving adequate biological metabolism. Among the studies on binding proteins, the examination of interactions between immunoglobulin G (IgG) and natural immunoglobulin-binding ligands, such as staphylococcal protein A (spA) and streptococcal protein G (spG), is essential in the development of pharmaceutical science, biotechnology, and affinity chromatography. The widespread utilization of IgG-spA/spG binding characteristics has allowed researchers to investigate these molecular interactions. However, the detailed binding strength of each ligand and the corresponding binding mechanisms have yet to be fully investigated. In this study, the authors analyzed the binding strengths of IgG-spA and IgG-spG complexes and identified the mechanisms enabling these bindings using molecular dynamics simulation, steered molecular dynamics, and advanced Poisson-Boltzmann Solver simulations. Based on the presented data, the binding strength of the spA ligand was found to significantly exceed that of the spG ligand. To find out which non-covalent interactions or amino acid sites have a dominant role in the tight binding of these ligands, further detailed analyses of electrostatic interactions, hydrophobic bonding, and binding free energies have been performed. In investigating their binding affinity, a relatively independent and different unbinding mechanism was found in each ligand. These distinctly different mechanisms were observed to be highly correlated to the protein secondary and tertiary structures of spA and spG ligands, as explicated from the perspective of hydrogen bonding.
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Key Words
- AFM, Atomic Force Microscopy
- APBS, Advanced Poisson–Boltzmann Solver
- Affinity chromatography
- BIR, Between Protein–Protein Interface Residues
- ELISA, Enzyme-linked Immunosorbent Assays
- Fc, Fragment Crystallizable
- IgG, Immunoglobulin G
- Immunoglobulin G
- MD, Molecular Dynamics
- MM/PBSA, Molecular Mechanics Poisson–Boltzmann Surface Area
- Molecular dynamics
- Protein A
- Protein G
- Protein docking
- RMSD, Root Mean Square Deviation
- SASA, Solvent Accessible Surface Area
- SMD, Steered Molecular Dynamics
- spA, Staphylococcal Protein A
- spG, Streptococcal Protein G
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Affiliation(s)
- Hae Gon Lee
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Shinill Kang
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Joon Sang Lee
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
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Singh A, Mishra A. Molecular dynamics simulation and free energy calculation studies of Coagulin L as dipeptidyl peptidase-4 inhibitor. J Biomol Struct Dyn 2020; 40:1128-1138. [PMID: 33078683 DOI: 10.1080/07391102.2020.1822917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Plant derived product can be used as other alternatives to currently used drugs for controlling chronic diseases like Diabetes mellitus. The potential of Coagulin L (a constituent of Withania coagulans) as dipeptidyl peptidase-4 (DPP-4) inhibitor was evaluated by molecular modelling study. It was observed that amino acid residues such as Glu205, Glu206, Tyr 547, His 740, and Try662 interacts with Coagulin L and Saxagliptin (a known DPP-4 inhibitor). Other nonbonded interactions of Coagulin L and Saxagliptin with DPP-4 binding residues were also found similar. The docking energy of Coagulin L was found to be -7.69 Kcal/mol whereas -8.44 kcal/mol was recorded for Saxagliptin. MD simulation study revealed stable binding throughout 100 ns simulation. RMSD plot of the complex was stabilized in 43 ns and remained stable during entire simulation(100 ns). RMSF plot of DPP-4 Coagulin L interaction showed major fluctuations at residue 246 and 766, however, Arg 125, Glu 205, Ser 209 and His 740 showed no major perturbations. Principal Component Analysis showed that important dynamics of the protein remain unchanged during entire simulation since the non-polar, van der waals, ionic interaction and solvation energy, altogether play important role in the complex stability. The molecular modelling study of DPP-4 with Coagulin L was an effort to establish correlation with traditional practices of Withania coagulans as antidiabetic agent in Indian subcontinent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Singh
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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Guerra RF, Melo GFD, Faria RR, de Sousa Neto LR, Franca EDF. Molecular modelling to understand AFM tip functionalisation and imazaquin-AHAS interactions in order to design a new nanobiosensor. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Renan Faria Guerra
- Laboratory of Crystallography and Computational Chemistry, Chemistry Institute, Federal University of Uberlândia – UFU, Santa Mônica, Brazil
| | | | - Roberto Ribeiro Faria
- Laboratory of Crystallography and Computational Chemistry, Chemistry Institute, Federal University of Uberlândia – UFU, Santa Mônica, Brazil
| | - Lourival Rodrigues de Sousa Neto
- Laboratory of Crystallography and Computational Chemistry, Chemistry Institute, Federal University of Uberlândia – UFU, Santa Mônica, Brazil
| | - Eduardo de Faria Franca
- Laboratory of Crystallography and Computational Chemistry, Chemistry Institute, Federal University of Uberlândia – UFU, Santa Mônica, Brazil
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Hu JP, Wu ZX, Xie T, Liu XY, Yan X, Sun X, Liu W, Liang L, He G, Gan Y, Gou XJ, Shi Z, Zou Q, Wan H, Shi HB, Chang S. Applications of Molecular Simulation in the Discovery of Antituberculosis Drugs: A Review. Protein Pept Lett 2019; 26:648-663. [PMID: 31218945 DOI: 10.2174/0929866526666190620145919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/10/2019] [Accepted: 05/03/2019] [Indexed: 02/05/2023]
Abstract
After decades of efforts, tuberculosis has been well controlled in most places. The existing drugs are no longer sufficient for the treatment of drug-resistant Mycobacterium tuberculosis due to significant toxicity and selective pressure, especially for XDR-TB. In order to accelerate the development of high-efficiency, low-toxic antituberculosis drugs, it is particularly important to use Computer Aided Drug Design (CADD) for rational drug design. Here, we systematically reviewed the specific role of molecular simulation in the discovery of new antituberculosis drugs. The purpose of this review is to overview current applications of molecular simulation methods in the discovery of antituberculosis drugs. Furthermore, the unique advantages of molecular simulation was discussed in revealing the mechanism of drug resistance. The comprehensive use of different molecular simulation methods will help reveal the mechanism of drug resistance and improve the efficiency of rational drug design. With the help of molecular simulation methods such as QM/MM method, the mechanisms of biochemical reactions catalyzed by enzymes at atomic level in Mycobacterium tuberculosis has been deeply analyzed. QSAR and virtual screening both accelerate the development of highefficiency, low-toxic potential antituberculosis drugs. Improving the accuracy of existing algorithms and developing more efficient new methods for CADD will always be a hot topic in the future. It is of great value to utilize molecular dynamics simulation to investigate complex systems that cannot be studied in experiments, especially for drug resistance of Mycobacterium tuberculosis.
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Affiliation(s)
- Jian-Ping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Zhi-Xiang Wu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Tao Xie
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xin-Yu Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiao Yan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Wei Liu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Li Liang
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Gang He
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Ya Gan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Xiao-Jun Gou
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Zheng Shi
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Qiang Zou
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
| | - Hu-Bing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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Hu F, Liu XT, Zhang JL, Zheng QC, Eglitis RI, Zhang HX. MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor. J Chem Inf Model 2019; 59:1554-1562. [PMID: 30884225 DOI: 10.1021/acs.jcim.8b00844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of three intermediate states in the binding process. The analysis of the simulation trajectories demonstrates that, in the intermediate structures, KAR1 is stabilized by some hydrophobic residues (Phe26, Phe134, Leu142, Trp153, Phe157, Leu160, Phe194), along with several bridging water molecules, and meanwhile, the significant shifting occurs in the local conformation of the protein as the ligand's binding. A series of the residues (Gln141-Phe157) on the so-called "cap domain" are proposed to be responsible for capturing the ligand at the initial stage of the binding. Besides, the changes of the ligand's poses are also quantitatively characterized by the proper choice of the coordinate system. Our work will contribute to the more penetrating understanding of the ligand binding process and the receptor affinity difference between several members in the KAR family and help design new, more effective germination stimulants.
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Affiliation(s)
- Fei Hu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , Jilin , People's Republic of China
| | - Xiao-Ting Liu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , Jilin , People's Republic of China
| | - Ji-Long Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , Jilin , People's Republic of China
| | - Qing-Chuan Zheng
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , Jilin , People's Republic of China
| | - Roberts I Eglitis
- Institute of Solid State Physics , University of Latvia , 8 Kengaraga Str. , Riga LV1067 , Latvia
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , Jilin , People's Republic of China
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Esmaeeli R, Mehrnejad F, Mir-Derikvand M, Gopalpoor N. Computational insights into pH-dependence of structure and dynamics of pyrazinamidase: A comparison of wild type and mutants. J Cell Biochem 2019; 120:2502-2514. [PMID: 30304542 DOI: 10.1002/jcb.27543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 01/24/2023]
Abstract
The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs of molecular dynamics simulations coupled with essential dynamics and binding pocket analysis at neutral (pH = 7) and acidic (pH = 4) ambient conditions. The 51-71 flap region exhibited drastic displacement leading to enlargement of binding cavity, especially at the lower pH. Accessibility of solvent to the active site of the mutant enzymes was also reduced. The protonation of key surface residues at low pH results in more contribution of these residues to structural stability and integrity of the enzyme and reduced interactions with solvent molecules, which acts as a cage, keeping the enzyme together. The observed results suggest a pattern of structural alterations due to point mutations in PZase, which is consistent with other experimental and theoretical investigations and, can be harnessed for drug design purposes.
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Affiliation(s)
- Reza Esmaeeli
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Mir-Derikvand
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Niloofar Gopalpoor
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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In silico approaches for investigating the binding propensity of apigenin and luteolin against class I HDAC isoforms. Future Med Chem 2018; 10:1925-1945. [PMID: 29992822 DOI: 10.4155/fmc-2018-0020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM Aberrant activity of class I histone deacetylases (HDACs) has strong implications for various cancers. Targeting these HDACs with synthetic HDAC inhibitors has shown significant side effects such as atrial fibrillation and QT prolongation emphasizing the need of natural inhibitors as substitutes to synthetic ones. RESULTS The binding propensity of the two plant-derived inhibitors apigenin and luteolin towards class I HDAC isoforms was checked using extra-precision molecular docking and implicit solvation MMGBSA. Apigenin showed a superior binding affinity against these isoforms as compared to luteolin. Both inhibitors docked stable to the binding pocket of these HDACs as determined by molecular dynamics simulation study. CONCLUSION Apigenin and luteolin may serve as substitutes to synthetic inhibitors for effective HDAC based anticancer therapy.
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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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Pohjolainen E, Malola S, Groenhof G, Häkkinen H. Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjug Chem 2017; 28:2327-2339. [DOI: 10.1021/acs.bioconjchem.7b00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmi Pohjolainen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Sami Malola
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Gerrit Groenhof
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Hannu Häkkinen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
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Ferreira MF, Franca EF, Leite FL. Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force. J Mol Graph Model 2017; 72:43-49. [PMID: 28033555 DOI: 10.1016/j.jmgm.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol-1. The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide.
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Affiliation(s)
- Moacir F Ferreira
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil.
| | - Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil
| | - Fábio L Leite
- Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil
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Karmakar T, Roy S, Balaram H, Prakash MK, Balasubramanian S. Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase. J Chem Inf Model 2016; 56:1528-38. [PMID: 27404508 DOI: 10.1021/acs.jcim.6b00203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Atomistic molecular dynamics (MD) simulations coupled with the metadynamics technique were carried out to delineate the product (PPi.2Mg and IMP) release mechanisms from the active site of both human (Hs) and Plasmodium falciparum (Pf) hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (HG(X)PRT). An early movement of PPi.2Mg from its binding site has been observed. The swinging motion of the Asp side chain (D134/D145) in the binding pocket facilitates the detachment of IMP, which triggers the opening of flexible loop II, the gateway to the bulk solvent. In PfHGXPRT, PPi.2Mg and IMP are seen to be released via the same path in all of the biased MD simulations. In HsHGPRT too, the product molecules follow similar routes from the active site; however, an alternate but minor escape route for PPi.2Mg has been observed in the human enzyme. Tyr 104 and Phe 186 in HsHGPRT and Tyr 116 and Phe 197 in PfHGXPRT are the key residues that mediate the release of IMP, whereas the motion of PPi.2Mg away from the reaction center is guided by the negatively charged Asp and Glu and a few positively charged residues (Lys and Arg) that line the product release channels. Mutations of a few key residues present in loop II of Trypanosoma cruzi (Tc) HGPRT have been shown to reduce the catalytic efficiency of the enzyme. Herein, in silico mutation of corresponding residues in loop II of HsHGPRT and PfHGXPRT resulted in partial opening of the flexible loop (loop II), thus exposing the active site to bulk water, which offers a rationale for the reduced catalytic activity of these two mutant enzymes. Investigations of the product release from these HsHGPRT and PfHGXPRT mutants delineate the role of these important residues in the enzymatic turnover.
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Affiliation(s)
- Tarak Karmakar
- Chemistry and Physics of Materials Unit, ‡Molecular Biology and Genetics Unit, and §Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Sourav Roy
- Chemistry and Physics of Materials Unit, ‡Molecular Biology and Genetics Unit, and §Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Hemalatha Balaram
- Chemistry and Physics of Materials Unit, ‡Molecular Biology and Genetics Unit, and §Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Meher K Prakash
- Chemistry and Physics of Materials Unit, ‡Molecular Biology and Genetics Unit, and §Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, ‡Molecular Biology and Genetics Unit, and §Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
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Qian M, Guan S, Shan Y, Zhang H, Wang S. Structural and molecular basis of cellulase Cel48F by computational modeling: Insight into catalytic and product release mechanism. J Struct Biol 2016; 194:347-56. [DOI: 10.1016/j.jsb.2016.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 11/26/2022]
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15
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Zhang W, Wang ML, Cranford SW. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics. Sci Rep 2016; 6:18659. [PMID: 26750747 PMCID: PMC4707552 DOI: 10.1038/srep18659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022] Open
Abstract
DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.
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Affiliation(s)
- Wenjun Zhang
- Laboratory for Nanotechnology In Civil Engineering (NICE), Boston, MA 02115 United States
- Interdisciplinary Engineering Program, College of Engineering, Northeastern University, Boston, MA 02115 United States
| | - Ming L. Wang
- Department of Civil & Environmental Engineering, Northeastern University, Boston, MA 02115 United States.
| | - Steven W. Cranford
- Laboratory for Nanotechnology In Civil Engineering (NICE), Boston, MA 02115 United States
- Department of Civil & Environmental Engineering, Northeastern University, Boston, MA 02115 United States.
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16
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Pang CL, Yuan HB, Cao TG, Su JG, Chen YF, Liu H, Yu H, Zhang HL, Zhan Y, An HL, Han YB. Molecular simulation assisted identification of Ca(2+) binding residues in TMEM16A. J Comput Aided Mol Des 2015; 29:1035-43. [PMID: 26481648 DOI: 10.1007/s10822-015-9876-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/12/2015] [Indexed: 01/31/2023]
Abstract
Calcium-activated chloride channels (CaCCs) play vital roles in a variety of physiological processes. Transmembrane protein 16A (TMEM16A) has been confirmed as the molecular counterpart of CaCCs which greatly pushes the molecular insights of CaCCs forward. However, the detailed mechanism of Ca(2+) binding and activating the channel is still obscure. Here, we utilized a combination of computational and electrophysiological approaches to discern the molecular mechanism by which Ca(2+) regulates the gating of TMEM16A channels. The simulation results show that the first intracellular loop serves as a Ca(2+) binding site including D439, E444 and E447. The experimental results indicate that a novel residue, E447, plays key role in Ca(2+) binding. Compared with WT TMEM16A, E447Y produces a 30-fold increase in EC50 of Ca(2+) activation and leads to a 100-fold increase in Ca(2+) concentrations that is needed to fully activate the channel. The following steered molecular dynamic (SMD) simulation data suggests that the mutations at 447 reduce the Ca(2+) dissociation energy. Our results indicated that both the electrical property and the size of the side-chain at residue 447 have significant effects on Ca(2+) dependent gating of TMEM16A.
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Affiliation(s)
- Chun-Li Pang
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Hong-Bo Yuan
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Tian-Guang Cao
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Ji-Guo Su
- School of Sciences, Yanshan University, Qinhuangdao, China
| | - Ya-Fei Chen
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Hui Liu
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Hui Yu
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
| | - Hai-Ling Zhang
- Key Laboratory of Neural and Vascular Biology, Ministry of Education, Shijiazhuang, China
- The Key Laboratory of Pharmacology and Toxicology for New Drug, Shijiazhuang, Hebei Province, China
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Yong Zhan
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China.
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China.
| | - Hai-Long An
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China.
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China.
| | - Yue-Bin Han
- Key laboratory of Molecular Biophysics, Tianjin, Hebei Province, China
- Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin, China
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17
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Wang D, Jin H, Wang J, Guan S, Zhang Z, Han W. Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations. J Biomol Struct Dyn 2015; 34:749-61. [PMID: 26155973 DOI: 10.1080/07391102.2015.1052097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Acylpeptide hydrolases (APH) catalyze the removal of an N-acylated amino acid from blocked peptides. APH is significantly more sensitive than acetylcholinesterase, a target of Alzheimer's disease, to inhibition by organophosphorus (OP) compounds. Thus, OP compounds can be used as a tool to probe the physiological functions of APH. Here, we report the results of a computational study of molecular dynamics simulations of APH bound to the OP compounds and an exploration of the chlorpyrifos escape pathway using steered molecular dynamics (SMD) simulations. In addition, we apply SMD simulations to identify potential escape routes of chlorpyrifos from hydrolase hydrophobic cavities in the APH-inhibitor complex. Two previously proposed APH pathways were reliably identified by CAVER 3.0, with the estimated relative importance of P1 > P2 for its size. We identify the major pathway, P2, using SMD simulations, and Arg526, Glu88, Gly86, and Asn65 are identified as important residues for the ligand leaving via P2. These results may help in the design of APH-targeting drugs with improved efficacy, as well as in understanding APH selectivity of the inhibitor binding in the prolyl oligopeptidase family.
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Affiliation(s)
- Dongmei Wang
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , College of Life Science, Jilin University , Changchun 130023 , China
| | - Hanyong Jin
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , College of Life Science, Jilin University , Changchun 130023 , China
| | - Junling Wang
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , College of Life Science, Jilin University , Changchun 130023 , China
| | - Shanshan Guan
- b State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun 130023 , China
| | - Zuoming Zhang
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , College of Life Science, Jilin University , Changchun 130023 , China
| | - Weiwei Han
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , College of Life Science, Jilin University , Changchun 130023 , China
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18
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Doustdar F, Pazhang M, Mehrnejad F, Safarzadeh M, Rabiei D, Chaparzadeh N, Falahati H, Mir-Derikvand M. Biochemical Characterization and Computational Identification of Mycobacterium tuberculosis Pyrazinamidase in Some Pyrazinamide-Resistant Isolates of Iran. Protein J 2015; 34:181-92. [DOI: 10.1007/s10930-015-9610-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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19
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Guan SS, Han WW, Zhang H, Wang S, Shan YM. Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation. J Biomol Struct Dyn 2015; 34:15-28. [PMID: 25582663 DOI: 10.1080/07391102.2015.1007167] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Angiotensin-converting enzyme (ACE), a membrane-bound zinc metallopeptidase, catalyzes the formation of Angiotensin-II (AngII) and the deactivation of bradykinin in the renin-angiotensin-aldosterone and kallikrein-kinin systems. As a hydrolysis product of ACE, AngII is regarded as an inhibitor and displays stronger competitive inhibition in the C-domain than the N-domain of ACE. However, the AngII binding differences between the two domains and the mechanisms behind AngII dissociation from the C-domain are rarely explored. In this work, molecular docking, Molecular Mechanics/Poisson-Boltzmann Surface Area calculation, and steered molecular dynamics (SMD) are applied to explore the structures and interactions in the binding or unbinding of AngII with the two domains of human somatic ACE. Calculated free energy values suggest that the C-domain-AngII complex is more stable than the N-domain-AngII complex, consistent with available experimental data. SMD simulation results imply that electrostatic interaction is dominant in the dissociation of AngII from the C-domain. Moreover, Gln106, Asp121, Glu123, and Tyr213 may be the key residues in the unbinding pathway of AngII. The simulation results in our work provide insights into the interactions between the two domains of ACE and its natural peptide inhibitor AngII at a molecular level. Moreover, the results provide theoretical clues for the design of new inhibitors.
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Affiliation(s)
- Shan-shan Guan
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Wei-wei Han
- b Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education , School of Life Sciences, Jilin University , Changchun 130023 , People's Republic of China
| | - Hao Zhang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Song Wang
- a State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China
| | - Ya-ming Shan
- c School of Life Sciences , Jilin University , Changchun 130012 , People's Republic of China
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20
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Abstract
Nicotinamidase (Pnc1) is a member of Zn-dependent amidohydrolases that hydrolyzes nicotinamide (NAM) to nicotinic acid (NA), which is a key step in the salvage pathway of NAD(+) biosynthesis. In this paper, the catalytic mechanism of Pnc1 has been investigated by using a combined quantum-mechanical/molecular-mechanical (QM/MM) approach based on the recently obtained crystal structure of Pnc1. The reaction pathway, the detail of each elementary step, the energetics of the whole catalytic cycle, and the roles of key residues and Zn-binding site are illuminated. Our calculation results indicate that the catalytic water molecule comes from the bulk solvent, which is then deprotonated by residue D8. D8 functions as a proton transfer station between C167 and NAM, while the activated C167 serves as the nucleophile. The residue K122 only plays a role in stabilizing intermediates and transition states. The oxyanion hole formed by the amide backbone nitrogen atoms of A163 and C167 has the function to stabilize the hydroxyl anion of nicotinamide. The Zn-binding site rather than a single Zn(2+) ion acts as a Lewis acid to influence the reaction. Two elementary steps, the activation of C167 in the deamination process and the decomposition of catalytic water in the hydrolysis process, correspond to the large energy barriers of 25.7 and 28.1 kcal mol(-1), respectively, meaning that both of them contribute a lot to the overall reaction barrier. Our results may provide useful information for the design of novel and efficient Pnc1 inhibitors and related biocatalytic applications.
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Affiliation(s)
- Xiang Sheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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21
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Kalyaanamoorthy S, Chen YPP. A steered molecular dynamics mediated hit discovery for histone deacetylases. Phys Chem Chem Phys 2014; 16:3777-91. [PMID: 24429775 DOI: 10.1039/c3cp53511h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The inhibitors of class I histone deacetylases (HDACIs) have gained significant interest in cancer therapeutics. Virtual high throughput screening (vHTS) is one of the popular approaches used in the identification of novel scaffolds of HDACIs. However, an accurate description of ligand-protein flexibilities in the vHTS remains challenging. In this work, we implement an integrated approach, which combines the vHTS with the 'state-of-the-art' steered molecular dynamics (SMD). This approach serves as an efficient tool to identify potential hits and characterize their binding potencies against the class I HDACs in a flexible solvent environment. A hybrid pharmacophore-based and structure-based vHTS method identifies the hits with more favourable physico-chemical features against the class I HDACs. Our pharmacophore-based screening enhanced the quality of the vHTS outcomes. Further, the molecular interactions between the hits and the HDACs are investigated using the SMD-driven force profiles, which in turn resulted in filtering the hits with higher binding potencies against the HDACs. Our results, therefore, reveal that vHTS and SMD can be a complementary and effective analytical tool for accelerating the hit identification phase in structure-based drug design.
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Affiliation(s)
- Subha Kalyaanamoorthy
- Faculty of Science, Technology and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia.
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22
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Zhang JL, Zheng QC, Li ZQ, Zhang HX. Theoretical evaluation and improvement on the potency of the rhodanine-based inhibitors for human serotoninN-acetyltransferase. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.854894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Carneiro J, Duarte-Pereira S, Azevedo L, Castro LFC, Aguiar P, Moreira IS, Amorim A, Silva RM. The evolutionary portrait of metazoan NAD salvage. PLoS One 2013; 8:e64674. [PMID: 23724078 PMCID: PMC3665594 DOI: 10.1371/journal.pone.0064674] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022] Open
Abstract
Nicotinamide Adenine Dinucleotide (NAD) levels are essential for cellular homeostasis and survival. Main sources of intracellular NAD are the salvage pathways from nicotinamide, where Nicotinamide phosphoribosyltransferases (NAMPTs) and Nicotinamidases (PNCs) have a key role. NAMPTs and PNCs are important in aging, infection and disease conditions such as diabetes and cancer. These enzymes have been considered redundant since either one or the other exists in each individual genome. The co-occurrence of NAMPT and PNC was only recently detected in invertebrates though no structural or functional characterization exists for them. Here, using expression and evolutionary analysis combined with homology modeling and protein-ligand docking, we show that both genes are expressed simultaneously in key species of major invertebrate branches and emphasize sequence and structural conservation patterns in metazoan NAMPT and PNC homologues. The results anticipate that NAMPTs and PNCs are simultaneously active, raising the possibility that NAD salvage pathways are not redundant as both are maintained to fulfill the requirement for NAD production in some species.
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Affiliation(s)
- João Carneiro
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sara Duarte-Pereira
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Luísa Azevedo
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - L. Filipe C. Castro
- Interdisciplinary Centre for Marine and Environmental Research (CIIMAR), CIMAR Associate Laboratory, University of Porto, Porto, Portugal
| | - Paulo Aguiar
- CMUP - Centro de Matemática da Universidade do Porto, Porto, Portugal
| | - Irina S. Moreira
- REQUIMTE - Rede de Química e Tecnologia, Faculty of Sciences, University of Porto, Porto, Portugal
| | - António Amorim
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Raquel M. Silva
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- * E-mail:
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24
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Sánchez-Carrón G, García-García MI, Zapata-Pérez R, Takami H, García-Carmona F, Sánchez-Ferrer Á. Biochemical and mutational analysis of a novel nicotinamidase from Oceanobacillus iheyensis HTE831. PLoS One 2013; 8:e56727. [PMID: 23451075 PMCID: PMC3581539 DOI: 10.1371/journal.pone.0056727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/14/2013] [Indexed: 12/30/2022] Open
Abstract
Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia, an important reaction in the NAD(+) salvage pathway. This paper reports a new nicotinamidase from the deep-sea extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831 (OiNIC). The enzyme was active towards nicotinamide and several analogues, including the prodrug pyrazinamide. The enzyme was more nicotinamidase (kcat/Km = 43.5 mM(-1)s(-1)) than pyrazinamidase (kcat/Km = 3.2 mM(-1)s(-1)). Mutational analysis was carried out on seven critical amino acids, confirming for the first time the importance of Cys133 and Phe68 residues for increasing pyrazinamidase activity 2.9- and 2.5-fold, respectively. In addition, the change in the fourth residue involved in the ion metal binding (Glu65) was detrimental to pyrazinamidase activity, decreasing it 6-fold. This residue was also involved in a new distinct structural motif DAHXXXDXXHPE described in this paper for Firmicutes nicotinamidases. Phylogenetic analysis revealed that OiNIC is the first nicotinamidase described for the order Bacillales.
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Affiliation(s)
- Guiomar Sánchez-Carrón
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, Murcia, Spain
| | - María Inmaculada García-García
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, Murcia, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Rubén Zapata-Pérez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, Murcia, Spain
| | - Hideto Takami
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Francisco García-Carmona
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, Murcia, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Álvaro Sánchez-Ferrer
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Campus Espinardo, Murcia, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
- * E-mail:
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25
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Rajendran V, Sethumadhavan R. Drug resistance mechanism of PncA in Mycobacterium tuberculosis. J Biomol Struct Dyn 2013; 32:209-21. [PMID: 23383724 DOI: 10.1080/07391102.2012.759885] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tuberculosis continues to be a global health threat. Pyrazinamide (PZA) is an important first-line drug in multidrug-resistant tuberculosis treatment. The emergence of strains resistant to PZA represents an important public health problem, as both first- and second-line treatment regimens include PZA. It becomes toxic to Mycobacterium tuberculosis when converted to pyrazinoic acid by the bacterial pyrazinamidase (PncA) enzyme. Resistance to PZA is caused mainly by the loss of enzyme activity by mutation, the mechanism of resistance is not completely understood. In our studies, we analysed three mutations (D8G, S104R and C138Y) of PncA which are involved in resistance towards PZA. Binding pocket analysis solvent accessibility analysis, molecular docking and interaction analysis were performed to understand the interaction behaviour of mutant enzymes with PZA. Molecular dynamics simulations were conducted to understand the three-dimensional (3D) conformational behaviour of native and mutants PncA. Our analysis clearly indicates that the mutation (D8G, S104R and C138Y) in PncA is responsible for rigid binding cavity which in turn abolishes conversion of PZA to its active form and is the sole reason for PZA resistance. Excessive hydrogen bonding between PZA binding cavity residues and their neighbouring residues are the reason of rigid binding cavity during simulation. We present an exhaustive analysis of the binding site flexibility and its 3D conformations that may serve as new starting points for structure-based drug design and helps the researchers to design new inhibitors with consideration of rigid criterion of binding residues due to mutation of this essential target. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:11.
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Affiliation(s)
- Vidya Rajendran
- a Bioinformatics Division, School of Bio Sciences and Technology (SBST) , Vellore Institute of Technology University , Vellore , 632014 , TN , India
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26
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Zhang JL, Zheng QC, Li ZQ, Zhang HX. How does (E)-2-(acetamidomethylene)succinate bind to its hydrolase? From the binding process to the final result. PLoS One 2013; 8:e53811. [PMID: 23308285 PMCID: PMC3538738 DOI: 10.1371/journal.pone.0053811] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
The binding of (E)-2-(acetamidomethylene)succinate (E-2AMS) to E-2AMS hydrolase is crucial for biological function of the enzyme and the last step reaction of vitamin B(6) biological degradation. In the present study, several molecular simulation methods, including molecular docking, conventional molecular dynamics (MD), steered MD (SMD), and free energy calculation methods, were properly integrated to investigate the detailed binding process of E-2AMS to its hydrolase and to assign the optimal enzyme-substrate complex conformation. It was demonstrated that the substrate binding conformation with trans-form amide bond is energetically preferred conformation, in which E-2AMS's pose not only ensures hydrogen bond formation of its amide oxygen atom with the vicinal oxyanion hole but also provides probability of the hydrophobic interaction between its methyl moiety and the related enzyme's hydrophobic cavity. Several key residues, Arg146, Arg167, Tyr168, Arg179, and Tyr259, orientate the E-2AMS's pose and stabilize its conformation in the active site via the hydrogen bond interaction with E-2AMS. Sequentially, the binding process of E-2AMS to E-2AMS hydrolase was studied by SMD simulation, which shows the surprising conformational reversal of E-2AMS. Several important intermediate structures and some significant residues were identified in the simulation. It is stressed that Arg146 and Arg167 are two pivotal residues responsible for the conformational reversal of E-2AMS in the binding or unbinding. Our research has shed light onto the full binding process of the substrate to E-2AMS hydrolase, which could provide more penetrating insight into the interaction of E-2AMS with the enzyme and would help in the further exploration on the catalysis mechanism.
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Affiliation(s)
- Ji-Long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, People's Republic of China
| | - Qing-Chuan Zheng
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, People's Republic of China
| | - Zheng-Qiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, People's Republic of China
- * E-mail:
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