1
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Puzari U, Fernandes PA, Mukherjee AK. Advances in the Therapeutic Application of Small-Molecule Inhibitors and Repurposed Drugs against Snakebite. J Med Chem 2021; 64:13938-13979. [PMID: 34565143 DOI: 10.1021/acs.jmedchem.1c00266] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The World Health Organization has declared snakebite as a neglected tropical disease. Antivenom administration is the sole therapy against venomous snakebite; however, several limitations of this therapy reinforce the dire need for an alternative and/or additional treatment against envenomation. Inhibitors against snake venoms have been explored from natural resources and are synthesized in the laboratory; however, repurposing of small-molecule therapeutics (SMTs) against the principal toxins of snake venoms to inhibit their lethality and/or obnoxious effect of envenomation has been garnering greater attention owing to their established pharmacokinetic properties, low-risk attributes, cost-effectiveness, ease of administration, and storage stability. Nevertheless, SMTs are yet to be approved and commercialized for snakebite treatment. Therefore, we have systematically reviewed and critically analyzed the scenario of small synthetic inhibitors and repurposed drugs against snake envenomation from 2005 to date and proposed novel approaches and commercialization strategies for the development of efficacious therapies against snake envenomation.
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Affiliation(s)
- Upasana Puzari
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur-784028, Assam, India
| | - Pedro Alexandrino Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Do Campo Alegre S/N, 4169-007 Porto, Portugal
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur-784028, Assam, India.,Institute of Advanced Study in Science and Technology, Vigyan Path Garchuk, Paschim Boragaon, Guwahati-781035, Assam, India
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2
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Wang LF, Wang Y, Yang ZY, Zhao J, Sun HB, Wu SL. Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:373-398. [PMID: 32496901 DOI: 10.1080/1062936x.2020.1748107] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Emerging evidences indicate bromodomain-containing proteins 2 and 4 (BRD2 and BRD4) play critical roles in cancers, inflammations, cardiovascular diseases and other pathologies. Multiple short molecular dynamics (MSMD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were applied to investigate the binding selectivity of three inhibitors 87D, 88M and 89G towards BRD2 over BRD4. The root-mean-square fluctuation (RMSF) analysis indicates that the structural flexibility of BRD4 is stronger than that of BRD2. Moreover the calculated distances between the Cα atoms in the centres of the ZA_loop and BC_loop of BRD4 are also bigger than that of BRD2. The rank of binding free energies calculated using MM-GBSA method agrees well with that determined by experimental data. The results show that 87D can bind more favourably to BRD2 than BRD4, while 88M has better selectivity on BRD4 over BRD2. Residue-based free-energy decomposition method was utilized to estimate the inhibitor-residue interaction spectrum and the results not only identify the hot interaction spots of inhibitors with BRD2 and BRD4, but also demonstrate that several common residues, including (W370, W374), (P371, P375), (V376, V380) and (L381, L385) belonging to (BRD2, BRD4), generate significant binding difference of inhibitors to BRD2 and BRD4.
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Affiliation(s)
- L F Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Y Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Z Y Yang
- Department of Physics, Jiangxi Agricultural University , Nanchang, China
| | - J Zhao
- School of Science, Shandong Jiaotong University , Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University , Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University , Jinan, China
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3
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Wang Y, Wang LF, Zhang LL, Sun HB, Zhao J. Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:149-170. [PMID: 31851834 DOI: 10.1080/1062936x.2019.1701075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
Recently, bromodomain-containing protein 9 (BRD9) has been a prospective therapeutic target for anticancer drug design. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were adopted to explore binding modes of three inhibitors (5SW, 5U2, and 5U6) to BRD9 and identify the hot spot of the inhibitor-BRD9 binding. The results indicate that the inhibitor 5SW has the strongest binding ability to BRD9 among the current three inhibitors. Furthermore, the rank of the binding free energies predicted by MM-GBSA approach agrees with that determined by the experimental values. In addition, inhibitor-residue interactions were computed by using residue-based free-energy decomposition method and the results suggest that residue His42 produces the CH-H interactions, residues Asn100, Ile53 and Val49 produce the CH-[Formula: see text] interactions with three inhibitors and Tyr106, Phe45 and Phe44 generate the π-π interactions with inhibitors. Notably, the residue Asn140 forms hydrogen bonding interactions with three inhibitors. This research is expected to provide useful molecular basis and dynamics information at atomic levels for the design of potent inhibitors inhibiting the activity of BRD9.
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Affiliation(s)
- Y Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
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4
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Wang L, Wang Y, Sun H, Zhao J, Wang Q. Theoretical insight into molecular mechanisms of inhibitor bindings to bromodomain-containing protein 4 using molecular dynamics simulations and calculations of binding free energies. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136785] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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7
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Chen J, Wang J, Lai F, Wang W, Pang L, Zhu W. Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations. RSC Adv 2018; 8:25456-25467. [PMID: 35539786 PMCID: PMC9082529 DOI: 10.1039/c8ra05042b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/10/2018] [Indexed: 11/21/2022] Open
Abstract
Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment. The current work integrates molecular dynamics (MD) simulations, calculations of binding free energy, and principal component (PC) analysis with scanning of inhibitor-residue interaction to probe the binding modes of inhibitors YK9, YKJ and YKI to Hsp90 and identify the hot spot of the inhibitor-Hsp90 binding. The results suggest that the introductions of two groups G1 and G2 into YKJ and YKI strengthen the binding ability of YKJ and YKI to Hsp90 compared to YK9. PC analysis based MD trajectories prove that inhibitor bindings exert significant effects on the conformational changes, internal dynamics and motion modes of Hsp90, especially for the helix α2 and the loops L1 and L2. The calculations of residue-based free energy decomposition and scanning of the inhibitor-Hsp90 interaction suggest that six residues L107, G108, F138, Y139, W162 and F170 construct the common hot spot of the inhibitor-residue interactions. Moreover the substitutions of the groups G1 and G2 in YKJ and YKI lead to two additional hydrogen bonding interactions and multiple hydrophobic interactions for bindings of YKJ and YKI to Hsp90. This work is also expected to contribute theoretical hints for the design of potent inhibitors toward Hsp90.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250014 China
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Fengbo Lai
- School of Science, Shandong Jiaotong University Jinan 250014 China
| | - Wei Wang
- School of Science, Shandong Jiaotong University Jinan 250014 China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University Jinan 250014 China
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
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8
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Wong KY, Xu Y, Xu L. Pitfall in Free-Energy Simulations on Simplest Systems. ChemistrySelect 2017. [DOI: 10.1002/slct.201601160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kin-Yiu Wong
- Department of Physics; High Performance Cluster Computing Centre; Institute of Computational and Theoretical Studies; Hong Kong Baptist University; 224 Waterloo Road Kowloon Tong Hong Kong
- Institute of Research and Continuing Education; Hong Kong Baptist University (Shenzhen); Shenzhen China
| | - Yuqing Xu
- Department of Physics; High Performance Cluster Computing Centre; Institute of Computational and Theoretical Studies; Hong Kong Baptist University; 224 Waterloo Road Kowloon Tong Hong Kong
- Institute of Research and Continuing Education; Hong Kong Baptist University (Shenzhen); Shenzhen China
| | - Liang Xu
- Department of Physics; High Performance Cluster Computing Centre; Institute of Computational and Theoretical Studies; Hong Kong Baptist University; 224 Waterloo Road Kowloon Tong Hong Kong
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9
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Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today 2017; 22:249-269. [DOI: 10.1016/j.drudis.2016.11.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022]
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10
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Chen J. Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis. J Biomol Struct Dyn 2017; 36:351-361. [PMID: 28030988 DOI: 10.1080/07391102.2016.1277783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular dynamics (MD) simulations coupled with principal component (PC) analysis were carried out to study functional roles of Mg2+ binding to extracellular signal-regulated kinase 2 (ERK2). The results suggest that Mg2+ binding heavily decreases eigenvalue of the first principal component and totally inhibits motion strength of ERK2, which favors stabilization of ERK2 structure. Binding free energy predictions indicate that Mg2+ binding produces an important effect on binding ability of adenosine triphosphate (ATP) to ERK2 and strengthens the ATP binding. The calculations of residue-based free energy decomposition show that lack of Mg2+ weakens interactions between the hydrophobic rings of ATP and five residues I29, V37, A50, L105, and L154. Hydrogen bond analyses also prove that Mg2+ binding increases occupancies of hydrogen bonds formed between ATP and residues K52, Q103, D104, and M106. We expect that this study can provide a significant theoretical hint for designs of anticancer drugs targeting ERK2.
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Affiliation(s)
- Jianzhong Chen
- a School of Science, Shandong Jiaotong University , Jinan 250357 , China
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11
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Chen J. Clarifying binding difference of ATP and ADP to extracellular signal-regulated kinase 2 by using molecular dynamics simulations. Chem Biol Drug Des 2016; 89:548-558. [PMID: 27696674 DOI: 10.1111/cbdd.12877] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/03/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
Extracellular signal-regulated kinase 2 is a promising target for designs and development of anticancer drugs. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann method were applied to study binding difference of ADP and ATP to extracellular signal-regulated kinase 2. The results prove that the binding ability of ATP to extracellular signal-regulated kinase 2 is stronger than that of ADP. Principal component analysis performed by using molecular dynamics trajectories suggests that binding of ADP and ATP to extracellular signal-regulated kinase 2 change motion directions of two helices α1 and α2. Residue-based free energy decomposition method was adopted to calculate contributions of separate residues to associations of ADP and ATP with extracellular signal-regulated kinase 2. The results show that ADP and ATP produce strong CH-π interactions with five residues Ile29, Val37, Ala50, Leu105, and Leu154. In addition, five hydrogen bonding interactions of ADP and ATP with residues Lys52, Gln103, Asp104, and Met106 also stabilize bindings of ADP and ATP to extracellular signal-regulated kinase 2. Overall, the CH-π interactions of ATP with five residues Ile29, Val37, Ala50, Leu105, and Leu154 are stronger than ADP. This study is expected to contribute a significant theoretical hint for designs of anticancer drugs targeting extracellular signal-regulated kinase 2.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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12
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Meng XM, Hu WJ, Mu YG, Sheng XH. Effect of allosteric molecules on structure and drug affinity of HIV-1 protease by molecular dynamics simulations. J Mol Graph Model 2016; 70:153-162. [PMID: 27723563 DOI: 10.1016/j.jmgm.2016.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 11/16/2022]
Abstract
Recent experiments show that small molecules can bind onto the allosteric sites of HIV-1 protease (PR), which provides a starting point for developing allosteric inhibitors. However, the knowledge of the effect of such binding on the structural dynamics and binding free energy of the active site inhibitor and PR is still lacking. Here, we report 200ns long molecular dynamics simulation results to gain insight into the influences of two allosteric molecules (1H-indole-6-carboxylic acid, 1F1 and 2-methylcyclohexano, 4D9). The simulations demonstrate that both allosteric molecules change the PR conformation and stabilize the structures of PR and the inhibitor; the residues of the flaps are sensitive to the allosteric molecules and the flexibility of the residues is pronouncedly suppressed; the additions of the small molecules to the allosteric sites strengthen the binding affinities of 3TL-PR by about 12-15kal/mol in the binding free energy, which mainly arises from electrostatic term. Interestingly, it is found that the action mechanisms of 1F1 and 4D9 are different, the former behaviors like a doorman that keeps the inhibitor from escape and makes the flaps (door) partially open; the latter is like a wedge that expands the allosteric space and meanwhile closes the flaps. Our data provide a theoretical support for designing the allosteric inhibitor.
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Affiliation(s)
- Xian-Mei Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Wei-Jun Hu
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
| | - Yu-Guang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 639815, Singapore.
| | - Xie-Huang Sheng
- School of Chemistry, Shandong Normal University, Jinan 250014, China
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13
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Metalloproteases Affecting Blood Coagulation, Fibrinolysis and Platelet Aggregation from Snake Venoms: Definition and Nomenclature of Interaction Sites. Toxins (Basel) 2016; 8:toxins8100284. [PMID: 27690102 PMCID: PMC5086644 DOI: 10.3390/toxins8100284] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 01/08/2023] Open
Abstract
Snake venom metalloproteases, in addition to their contribution to the digestion of the prey, affect various physiological functions by cleaving specific proteins. They exhibit their activities through activation of zymogens of coagulation factors, and precursors of integrins or receptors. Based on their structure–function relationships and mechanism of action, we have defined classification and nomenclature of functional sites of proteases. These metalloproteases are useful as research tools and in diagnosis and treatment of various thrombotic and hemostatic conditions. They also contribute to our understanding of molecular details in the activation of specific factors involved in coagulation, platelet aggregation and matrix biology. This review provides a ready reference for metalloproteases that interfere in blood coagulation, fibrinolysis and platelet aggregation.
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14
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Guo G, Cao Y, Zhu G, Tian Z, Gou Y, Chen C, Liu M. Screening, tandem expression and immune activity appraisal of Deinagkistrodon acutus (pit viper) venom mimotopes from a phage display 12-mer peptide library. Biotechnol Lett 2016; 38:1867-1873. [PMID: 27421965 DOI: 10.1007/s10529-016-2172-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/05/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To design a specific polyclonal antibody against Deinagkistrodon acutus venom (DA-pAb) by immunizating New Zealand white rabbits. RESULTS The IgG fraction was purified by affinity chromatography, and specific antibodies were purified by immunoaffinity chromatography. Polyclonal antibodies were subjected to ELISA and western blotting to evaluate their immune reactivity. We identified the mimotopes by screening a phage display 12-mer peptide library against D. acutus venom. After three rounds of biopanning with DA-pAb, 30 positive clones were identified. Eighteen phage clones were sequenced, and their corresponding amino acid sequences were deduced. Additional immunoassays with the peptides and DA-pAb identified five sequences as possible epitopes. Recombinant antigens synthesized with the five epitopes were used for the immunization of BALB/c mice. CONCLUSION The antibodies induced by these peptides recognized the recombinant antigen and D. acutus venom and protected mice against the hemorrhagic effects of the venom.
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Affiliation(s)
- Guoning Guo
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China
| | - Yuliang Cao
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China
| | - Guoyan Zhu
- Department of Health Management, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Zhu Tian
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China
| | - Yajun Gou
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China
| | - Cong Chen
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China
| | - Minghua Liu
- Department of Emergency, Southwest Hospital, Third Military Medical University, Chongqing, 400038, People's Republic of China.
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Chen J, Wang X, Zhu T, Zhang Q, Zhang JZH. A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. J Chem Inf Model 2015; 55:1903-13. [DOI: 10.1021/acs.jcim.5b00173] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jianzhong Chen
- School
of Science, Shandong Jiaotong University, Jinan 250357 China
| | - Xingyu Wang
- NYU−ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Tong Zhu
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
| | - Qinggang Zhang
- Collage
of Physics and Electronic Science, Shandong Normal University, Jinan 250014, China
| | - John Z. H. Zhang
- NYU−ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
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16
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Zhu W, Liu Y. Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Wenyou Zhu
- Key
Laboratory of Colloid and Interface Chemistry, Ministry of Education,
School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key
Laboratory of Colloid and Interface Chemistry, Ministry of Education,
School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
- Key
Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau
Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
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17
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Review of computer simulations of isotope effects on biochemical reactions: From the Bigeleisen equation to Feynman's path integral. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1782-94. [PMID: 25936775 DOI: 10.1016/j.bbapap.2015.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
Abstract
Enzymatic reactions are integral components in many biological functions and malfunctions. The iconic structure of each reaction path for elucidating the reaction mechanism in details is the molecular structure of the rate-limiting transition state (RLTS). But RLTS is very hard to get caught or to get visualized by experimentalists. In spite of the lack of explicit molecular structure of the RLTS in experiment, we still can trace out the RLTS unique "fingerprints" by measuring the isotope effects on the reaction rate. This set of "fingerprints" is considered as a most direct probe of RLTS. By contrast, for computer simulations, oftentimes molecular structures of a number of TS can be precisely visualized on computer screen, however, theoreticians are not sure which TS is the actual rate-limiting one. As a result, this is an excellent stage setting for a perfect "marriage" between experiment and theory for determining the structure of RLTS, along with the reaction mechanism, i.e., experimentalists are responsible for "fingerprinting", whereas theoreticians are responsible for providing candidates that match the "fingerprints". In this Review, the origin of isotope effects on a chemical reaction is discussed from the perspectives of classical and quantum worlds, respectively (e.g., the origins of the inverse kinetic isotope effects and all the equilibrium isotope effects are purely from quantum). The conventional Bigeleisen equation for isotope effect calculations, as well as its refined version in the framework of Feynman's path integral and Kleinert's variational perturbation (KP) theory for systematically incorporating anharmonicity and (non-parabolic) quantum tunneling, are also presented. In addition, the outstanding interplay between theory and experiment for successfully deducing the RLTS structures and the reaction mechanisms is demonstrated by applications on biochemical reactions, namely models of bacterial squalene-to-hopene polycyclization and RNA 2'-O-transphosphorylation. For all these applications, we used our recently-developed path-integral method based on the KP theory, called automated integration-free path-integral (AIF-PI) method, to perform ab initio path-integral calculations of isotope effects. As opposed to the conventional path-integral molecular dynamics (PIMD) and Monte Carlo (PIMC) simulations, values calculated from our AIF-PI path-integral method can be as precise as (not as accurate as) the numerical precision of the computing machine. Lastly, comments are made on the general challenges in theoretical modeling of candidates matching the experimental "fingerprints" of RLTS. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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18
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Chen J, Wang J, Zhang Q, Chen K, Zhu W. A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation. J Biomol Struct Dyn 2015; 33:2606-18. [PMID: 25562613 DOI: 10.1080/07391102.2014.1003146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.
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Affiliation(s)
- Jianzhong Chen
- a School of Science , Shandong Jiaotong University , Jinan , 250014 , China
| | - Jinan Wang
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Qinggang Zhang
- c College of Physics and Electronics , Shandong Normal University , Jinan , 250014 , China
| | - Kaixian Chen
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Weiliang Zhu
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
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A study of the interaction between HIV-1 protease and C 2-symmetric inhibitors by computational methods. J Mol Model 2014; 20:2369. [DOI: 10.1007/s00894-014-2369-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 06/29/2014] [Indexed: 12/14/2022]
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Wong KY, Xu Y, York DM. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J Comput Chem 2014; 35:1302-16. [PMID: 24841935 PMCID: PMC4096342 DOI: 10.1002/jcc.23628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/06/2014] [Indexed: 12/16/2022]
Abstract
Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2'-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2'-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a "gold-standard" coupled-cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path-integral method, that is, automated integration-free path-integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Physics, High Performance Cluster Computing Centre, Institute of Computational and Theoretical Studies, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong; Institute of Research and Continuing Education, Hong Kong Baptist University (Shenzhen), Shenzhen, China
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Hu G, Qi L, Dou X, Wang J. The influences of protonation state of histidine on aromatic/arginine region of aquaporin-1 protein. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.718438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Multiligand zinc(II) hydroxide complexes: Zn(OH)2X2Y and Zn(OH)2X1,2Y2; X=H2O, CH3OH and Y=NH3, C5H5N. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Li YL, Mei Y, Zhang DW, Xie DQ, Zhang JZH. Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization. J Phys Chem B 2011; 115:10154-62. [PMID: 21766867 DOI: 10.1021/jp203505v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures and dynamics of a recently designed dizinc metalloprotein (DFsc) (J. Mol. Biol. 2003, 334, 1101) are studied by molecular dynamics simulation using a dynamically adapted polarized force field derived from fragment quantum calculation for protein in solvent. To properly describe the effect of charge transfer and polarization in the present approach, quantum chemistry calculation of the zinc-binding group is periodically performed (on-the-fly) to update the atomic charges of the zinc-binding group during the MD simulation. Comparison of the present result with those obtained from simulations under standard AMBER force field reveals that charge transfer and polarization are critical to maintaining the correct asymmetric metal coordination in the DFsc. Detailed analysis of the result also shows that dynamic fluctuation of the zinc-binding group facilitates solvent interaction with the zinc ions. In particular, the dynamic fluctuation of the zinc-zinc distance is shown to be an important feature of the catalytic function of the di-ion zinc-binding group. Our study demonstrates that the dynamically adapted polarization approach is computationally practical and can be used to study other metalloprotein systems.
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Affiliation(s)
- Yong L Li
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Abstract
Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two-dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring-opening process takes place through an S(N)2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B-catalyzed cAMP hydrolysis is about 13 kcal·mol(-1) and an overall reaction free energy is about -17 kcal·mol(-1), both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol(-1). We found that the proton transfer from the general acid residue His234 to the O3' oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn(2+) and Mg(2+) in the active site as the reaction proceeds from the Michaelis complex to the transition state.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Chemistry, Digital Technology Center, University of Minnesota, Minneapolis, MN 55455, USA.
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Fujiwara T, Mochizuki Y, Komeiji Y, Okiyama Y, Mori H, Nakano T, Miyoshi E. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Jing YQ, Han KL. Quantum mechanical effect in protein–ligand interaction. Expert Opin Drug Discov 2009; 5:33-49. [DOI: 10.1517/17460440903440127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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