1
|
Zhang X, Yang Y, Wang Y, Wu J, Fang Q, Wang Y, Zhao M, Peng S. (1R,3S)-THCCA-Asn: To show the discovery of selective inhibitor of thrombin by successfully combining virtual screening and biological assay. Eur J Med Chem 2022; 242:114681. [PMID: 36001936 DOI: 10.1016/j.ejmech.2022.114681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Thrombin is the most potent platelet aggregator. To discover the selective inhibitor of thrombin that is important to curing platelet aggregation-related diseases, docking experiments were performed to dock (1R,3S)-2,3,4,9-tetrahydro-β-carboline-3- carboxylic acid, [(1R,3S)-THCCA], and (1S,3S)-2,3,4,9-tetrahydro-β-carboline-3- carboxylic acid, [(1S,3S)-THCCA], into the p pocket of bovine thrombin. The ideal match supported that (1R,3S)-THCCA could be used as a potential lead compound. In this case 20 natural amino acids were theoretically introduced into the 3-carboxyl of (1R,3S)-THCCA and 20 derivatives, (1R,3S)-THCCA-amino acids, were docked into p pocket of bovine thrombin to perform virtual screening. The screening revealed that comparing to (1R,3S)-THCCA itself the DockScores of 16 derivatives were higher, and (1R,3S)-THCCA-Asn (4j) got the highest DockScore. Thus, 16 derivatives were synthesized for experimental study. The in vitro anti-platelet aggregation assay showed that at 100 μM of concentration the 16 derivatives failed to inhibit the platelet aggregation induced by both adenosine diphosphate and arachidonic acid. On the other hand, however, the IC50 value of the 16 derivatives inhibiting the platelet aggregation induced by platelet activating factor and thrombin ranged from 9.44 μM to 194.64 μM and from 0.07 μM to 9.56 μM, respectively. The in vitro anti-platelet aggregation assay suggested that the 16 derivatives selectively inhibited the platelet aggregation induced by thrombin. In particular, the IC50 of (1R,3S)-THCCA-Asn (4j) had the lowest value. On rat model at 1 nmol/kg of dosage the 16 derivatives effectively prevented thrombus formation. It is worth pointing out that even at 0.01 nmol/kg of dosage, 4j still effectively prevented thrombus formation. 4j hardly has effects on the proliferation of mammalian cells and rat tail bleeding time. In conclusion, the combination of virtual screening and biological assays successfully lead to the discovery of 4j as a promising candidate of selective inhibitor of thrombin.
Collapse
Affiliation(s)
- Xiaoyi Zhang
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Yifan Yang
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Yuji Wang
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Jianhui Wu
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Qiongyan Fang
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Yaonan Wang
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China
| | - Ming Zhao
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China.
| | - Shiqi Peng
- College of Pharmaceutical Sciences, Capital Medical University, Beijing, PR China.
| |
Collapse
|
2
|
Hellmers J, Hedegård ED, König C. Fragmentation-Based Decomposition of a Metalloenzyme-Substrate Interaction: A Case Study for a Lytic Polysaccharide Monooxygenase. J Phys Chem B 2022; 126:5400-5412. [PMID: 35833656 DOI: 10.1021/acs.jpcb.2c02883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel decomposition scheme for electronic interaction energies based on the flexible formulation of fragmentation schemes through fragment combination ranges (FCRs; J. Chem. Phys., 2021, 155, 164105). We devise a clear additive decomposition with contribution of nondisjoint fragments and correction terms for overlapping fragments and apply this scheme to the metalloenzyme-substrate complex of a lytic polysaccharide monooxygenase (LPMO) with an oligosaccharide. By this, we further illustrate the straightforward adaptability of the FCR-based schemes to novel systems. Our calculations suggest that the description of the electronic structure is a larger error source than the fragmentation scheme. In particular, we find a large impact of the basis set size on the interaction energies. Still, the introduction of three-body interaction terms in the fragmentation setup improves the agreement to the supermolecular reference. Yet, the qualitative results for the decomposition scheme with two-body terms only largely agree within the investigated electronic-structure approaches and basis sets, which are B97-3c, DFT (TPSS and B3LYP), and MP2 methods. The overlap contributions are found to be small, allowing analysis of the interaction energy into individual amino acid residues: We find a particularly strong interaction between the substrate and the LPMO copper active site.
Collapse
Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
| |
Collapse
|
3
|
Wang T, Wu F, Luo L, Zhang Y, Ma J, Hu Y. Efficient synthesis and cytotoxic activity of polysubstituted thieno[2,3-d]pyrimidine derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
4
|
Tang X, Zheng A, Wu F, Liao C, Hu Y, Luo C. Synthesis and anticancer activities of diverse furo[2,3- d]pyrimidine and benzofuro[3,2- d]pyrimidine derivatives. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2060117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xiaoyu Tang
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Aihua Zheng
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Fengxu Wu
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Chujie Liao
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Yanggen Hu
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, China
| | - Chao Luo
- School of Pharmaceutical Sciences and Institute of Medicinal Chemistry, Hubei University of Medicine, Shiyan, China
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| |
Collapse
|
5
|
Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
Collapse
|
6
|
Zhao J, Wang L, Bao H, Chen J. Cluster analysis on conformational changes of the GDP/KRAS complex induced by A59G and D33E. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Amaral JL, Souza PFN, Oliveira JTA, Freire VN, Sousa DOB. Computational approach, scanning electron and fluorescence microscopies revealed insights into the action mechanisms of anticandidal peptide Mo-CBP 3-PepIII. Life Sci 2021; 281:119775. [PMID: 34186044 DOI: 10.1016/j.lfs.2021.119775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 06/09/2021] [Accepted: 06/20/2021] [Indexed: 11/17/2022]
Abstract
AIMS The Candida genus is composed of opportunistic pathogens that threaten public health. Given the increase in resistance to current drugs, it is necessary to develop new drugs to treat infections by these pathogens. Antimicrobial peptides are promising alternative molecules with low cost, broad action spectrum and low resistance induction. This study aimed to clarify the action mechanisms of synthetic peptides against Candida albicans. MAIN METHODS The mode of action of the anticandidal peptides Mo-CBP3-PepIII were analyzed through molecular dynamics and quantum biochemistry methods against Exo-β-1,3-glucanase (EXG), vital to cell wall metabolism. Furthermore, scanning electron (SEM) and fluorescence (FM) microscopies were employed to corroborate the in silico data. KEY FINDINGS Mo-CBP3-PepIII strongly interacted with EXG (-122.2 kcal mol-1) at the active site, higher than the commercial inhibitor pepstatin. Also, molecular dynamics revealed the insertion of Mo-CBP3-PepIII into the yeast membrane. SEM analyses revealed that Mo-CBP3-PepIII induced cracks and scars of the cell wall and FM analyses confirmed the pore formation on the Candida membrane. SIGNIFICANCE Mo-CBP3-PepIII has strong potential as a new drug with a broad spectrum of action, given its different mode of action compared to conventional drugs.
Collapse
Affiliation(s)
- Jackson L Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil; Department of Physics, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil.
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil
| | - Jose T A Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil
| | - Valder N Freire
- Department of Physics, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil
| | - Daniele O B Sousa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará CEP 60.440-554, Brazil.
| |
Collapse
|
8
|
Yin YY, Zhao J, Zhang LL, Xu XY, Liu JQ. Molecular mechanisms of inhibitor bindings to A-FABP deciphered by using molecular dynamics simulations and calculations of MM-GBSA. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:293-315. [PMID: 33655818 DOI: 10.1080/1062936x.2021.1891966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Adipocyte fatty-acid binding protein (A-FABP) plays a central role in many aspects of metabolic diseases. It is an important target in drug design for treatment of FABP-related diseases. In this study, molecular dynamics (MD) simulations followed by calculations of molecular mechanics generalized Born surface area (MM-GBSA) and principal components analysis (PCA) were implemented to decipher molecular mechanism correlating with binding of inhibitors 57Q, 57P and L96 to A-FABP. The results show that van der Waals interactions are the leading factors to control associations of 57Q, 57P, and L96 with A-FABP, which reveals an energetic basis for designing of clinically available inhibitors towards A-FABP. The information from PCA and cross-correlation analysis rationally unveils that inhibitor bindings affect conformational changes of A-FABP and change relative movements between residues. Decomposition of binding affinity into contributions of individual residues not only detects hot spots of inhibitor/A-FABP binding but also shows that polar interactions of the positively charged residue Arg126 with three inhibitors provide a significant contribution for stabilization of the inhibitor/A-FABP bindings. Furthermore, the binding strength of L96 to residues Ser55, Phe57 and Lys58 are stronger than that of inhibitors 57Q and 57P to these residues.
Collapse
Affiliation(s)
- Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - X Y Xu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Q Liu
- School of Science, Shandong Jiaotong University, Jinan, China
| |
Collapse
|
9
|
Quantum biochemistry in cancer immunotherapy: New insights about CTLA-4/ipilimumab and design of ipilimumab-derived peptides with high potential in cancer treatment. Mol Immunol 2020; 127:203-211. [DOI: 10.1016/j.molimm.2020.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 01/22/2023]
|
10
|
Wu SL, Wang LF, Sun HB, Wang W, Yu YX. Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:547-570. [PMID: 32657160 DOI: 10.1080/1062936x.2020.1777584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.
Collapse
Affiliation(s)
- S L Wu
- School of Science, Shandong Jiaotong University , Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University , Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Y X Yu
- School of Science, Shandong Jiaotong University , Jinan, China
| |
Collapse
|
11
|
Santos de Oliveira FL, Vieira Carletti J, Azevedo FFN, Freitas de Sousa FJ, Caetano EWS, Freire VN, Zanatta G. mTOR–mLST8 interaction: hot spot identification through quantum biochemistry calculations. NEW J CHEM 2020. [DOI: 10.1039/d0nj04099a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quantum calculation of mTOR–mLST8 interaction.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Geancarlo Zanatta
- Department of Physics at Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
- Postgraduate Research Program in Biochemistry at Federal University of Ceará
- Fortaleza
| |
Collapse
|
12
|
Zhong S, Huang K, Xiao Z, Sheng X, Li Y, Duan L. Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method. J Phys Chem B 2019; 123:8704-8716. [DOI: 10.1021/acs.jpcb.9b08064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Zhengrong Xiao
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Xiehuang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
13
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
14
|
Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Effect of double mutations T790M/L858R on conformation and drug-resistant mechanism of epidermal growth factor receptor explored by molecular dynamics simulations. RSC Adv 2018; 8:39797-39810. [PMID: 35558225 PMCID: PMC9091310 DOI: 10.1039/c8ra06844e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/18/2018] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is one of the most promising targets for the treatment of cancers. Double mutations T790M/L858R lead to different degrees of drug resistance toward inhibitors. In this study, molecular dynamics (MD) simulations followed by principal component analysis are performed to study the conformational changes of EGFR induced by T790M/L858R. The results suggest that T790M/L858R cause obvious disturbance of the structural stability of EGFR. Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) and residue-based free energy decomposition methods are integrated to explore the drug-resistant mechanism of T790M/L858R toward inhibitors. The results show that the decrease in van der Waals interactions of inhibitors with the mutated EFGR relative to the wild-type (WT) one is the main force inducing drug resistance of T790M/L858R toward inhibitors TAK-285, while drug resistance toward W2P and HKI-272 is dominated by the decrease in van der Waals interactions and the increase in polar interactions. We expect that the information obtained from this study can aid rational design of effective drugs to relieve drug resistance of EGFR induced by T790M/L858R.
Collapse
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
| |
Collapse
|
15
|
Patra P, Ghosh M, Banerjee R, Chakrabarti J. Quantum chemical studies on anion specificity of C αNN motif in functional proteins. J Comput Aided Mol Des 2018; 32:929-936. [PMID: 30182143 DOI: 10.1007/s10822-018-0157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
Anion binding CαNN motif is found in functionally important regions of protein structures. This motif based only on backbone atoms from three adjacent residues, recognizes free sulphate or phosphate ion as well as phosphate groups in nucleotides and in a variety of cofactors. The mode of anion recognition and microscopic picture of binding interaction remains unclear. Here we perform self-consistent quantum chemical calculations considering sulphate and phosphate bound CαNN motif fragments from crystal structures of functional proteins in order to figure out microscopic basis of anion recognition. Our calculations indicate that stability and preference of the anion in the motif depends on the sequence of the motif. The stabilization energy is larger in case of polar residue containing motif fragment. Nitrogen atom of the polar residue of motif mainly participates in the coordination at the lowest energy levels. Anion replacement decreases stabilization energy along with coordination between motif atoms and oxygen atoms of anion shifted to higher energies, suggesting preference of the motif residues to specific anion. Our analysis may be helpful to understand microscopic basis of interaction between proteins and ionic species.
Collapse
Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as WBUT), BF-142, Sector-I, Salt Lake, Kolkata, 700064, India.
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as WBUT), BF-142, Sector-I, Salt Lake, Kolkata, 700064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India. .,The Thematic Unit of Excellence on Computational Materials Science, S.N. Bose National Centre for Basic Sciences, Sector-III, Block JD, Salt Lake, Kolkata, 700106, India.
| |
Collapse
|
16
|
Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5. Int J Mol Sci 2018; 19:ijms19092496. [PMID: 30142969 PMCID: PMC6164837 DOI: 10.3390/ijms19092496] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 12/11/2022] Open
Abstract
Designing highly selective inhibitors of fatty acid binding proteins 4 and 5 (FABP4 and FABP5) is of importance for treatment of some diseases related with inflammation, metabolism, and tumor growth. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were performed to probe binding selectivity of three inhibitors (5M7, 65X, and 65Z) to FABP4/FABP5 with Ki values of 0.022/0.50 μM, 0.011/0.086 μM, and 0.016/0.12 μM, respectively. The results not only suggest that all inhibitors associate more tightly with FABP4 than FABP5, but also prove that the main forces driving the selective bindings of inhibitors to FABP4 and FABP5 stem from the difference in the van der Waals interactions and polar interactions of inhibitors with two proteins. Meanwhile, a residue-based free energy decomposition method was applied to reveal molecular basis that inhibitors selectively interact with individual residues of two different proteins. The calculated results show that the binding difference of inhibitors to the residues (Phe16, Phe19), (Ala33, Gly36), (Phe57, Leu60), (Ala75, Ala78), (Arg126, Arg129), and (Tyr128, Tyr131) in (FABP4, FABP5) drive the selectivity of inhibitors toward FABP4 and FABP5. This study will provide great help for further design of effective drugs to protect against a series of metabolic diseases, arteriosclerosis, and inflammation.
Collapse
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
| |
Collapse
|
17
|
Chen J, Wang J, Zhu W. Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling. Phys Chem Chem Phys 2018; 19:3067-3075. [PMID: 28079218 DOI: 10.1039/c6cp08105c] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The hydrolysis of a β-lactam core ring caused by new Delphi metallo-β-lactamase 1 (NDM-1) with the help of two zinc cofactors induces significant resistance toward β-lactam antibiotics. Molecular dynamics (MD) simulations and the umbrella sampling method are integrated to study the conformational change mechanism of NDM-1 mediated by zinc ion binding. The statistical analyses of interaction contacts of the antibiotic ampicillin (AMP) with residues based on MD trajectories suggest that two Zn ions are essential for maintaining the binding of AMP with NDM-1. Umbrella sampling simulations further reveal that double-Zn coordination exerts strong restriction on the motions of loop L10 relative to loops L3 and L4. Principal component (PC) analysis also demonstrates that zinc ion binding totally inhibits the motion extent of NDM-1 and changes internal motion modes in NDM-1. We expect that the current study can provide significant dynamical information involving conformational changes of NDM-1 for the development of efficient inhibitors to decrease drug resistance of NDM-1 toward antibiotics.
Collapse
Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250014, 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.
| | - 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.
| |
Collapse
|
18
|
Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. A theoretical insight into selectivity of inhibitors toward two domains of bromodomain-containing protein 4 using molecular dynamics simulations. Chem Biol Drug Des 2017; 91:828-840. [DOI: 10.1111/cbdd.13148] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/22/2017] [Accepted: 11/01/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jing Su
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Xinguo Liu
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Shaolong Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Fangfang Yan
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Qinggang Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Jianzhong Chen
- School of Science; Shandong Jiaotong University; Jinan China
| |
Collapse
|
19
|
Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3636-3650. [DOI: 10.1080/07391102.2017.1394221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| |
Collapse
|
20
|
de Sousa B, Oliveira J, Albuquerque E, Fulco U, Amaro V, Blaha C. Molecular modelling and quantum biochemistry computations of a naturally occurring bioremediation enzyme: Alkane hydroxylase from Pseudomonas putida P1. J Mol Graph Model 2017; 77:232-239. [DOI: 10.1016/j.jmgm.2017.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/24/2017] [Accepted: 08/26/2017] [Indexed: 12/29/2022]
|
21
|
Shi S, Zhang S, Zhang Q. Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation. J Biomol Struct Dyn 2017; 36:981-992. [PMID: 28279118 DOI: 10.1080/07391102.2017.1305296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH-π and CH-CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.
Collapse
Affiliation(s)
- Shuhua Shi
- a School of Science , Shandong Jianzhu University , Jinan 250101 , China
| | - Shaolong Zhang
- b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China
| | - Qinggang Zhang
- b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China
| |
Collapse
|
22
|
Neto JXL, Bezerra KS, Manso DN, Mota KB, Oliveira JIN, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Energetic description of cilengitide bound to integrin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02166f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ quantum chemistry methods to investigate the binding energy features of the cyclic RGD pentapeptide cilengitide interacting with the integrin receptor αVβ3.
Collapse
Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Dalila N. Manso
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Kyvia B. Mota
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | | | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| |
Collapse
|
23
|
Predicting bioactive conformations and binding modes of macrocycles. J Comput Aided Mol Des 2016; 30:841-849. [DOI: 10.1007/s10822-016-9973-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/12/2016] [Indexed: 11/26/2022]
|
24
|
Mota K, Lima Neto J, Lima Costa A, Oliveira J, Bezerra K, Albuquerque E, Caetano E, Freire V, Fulco U. A quantum biochemistry model of the interaction between the estrogen receptor and the two antagonists used in breast cancer treatment. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
25
|
Sikdar S, Ghosh M, De Raychaudhury M, Chakrabarti J. Quantum chemical studies on nucleophilic sites in calcium ion bound zwitterionic calmodulin loops. RSC Adv 2016. [DOI: 10.1039/c6ra10846f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Quantum chemical calculation on Ca2+ bound zwitterionic calmodulin-loops shows terminal capping contributions localized near HOMO and LUMO, which decay exponentially and presence of nucleophilic site at the phenyl-ring Oh of Y99.
Collapse
Affiliation(s)
- Samapan Sikdar
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700098
- India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700098
- India
| | | | - J. Chakrabarti
- Department of Chemical, Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700098
- India
| |
Collapse
|
26
|
Sousa BL, Barroso-Neto IL, Oliveira EF, Fonseca E, Lima-Neto P, Ladeira LO, Freire VN. Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis. RSC Adv 2016. [DOI: 10.1039/c6ra16712h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quantum biochemistry computations are applied to precisely describe important protein–protein interactions, providing a basis for the design of inhibitory peptides against osteoporosis.
Collapse
Affiliation(s)
- Bruno L. Sousa
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Ito L. Barroso-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | | | - Emerson Fonseca
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Pedro Lima-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Luiz O. Ladeira
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| |
Collapse
|
27
|
Sikdar S, Ghosh M, De Raychaudhury M, Chakrabarti J. Quantum Chemical Studies on Stability and Chemical Activities in Calcium Ion Bound Calmodulin Loops. J Phys Chem B 2015; 119:14652-9. [PMID: 26515023 DOI: 10.1021/acs.jpcb.5b09713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum chemical (QC) calculations for macromolecules require truncation of the molecule, highlighting the portion of interest due to heavy computation cost. As a result, an estimation of the effects of truncation is important to interpret the energy spectrum of such calculations. We perform density functional theory based QC calculations on calcium ion bound EF-hand loops of Calmodulin isolated from the crystal structure in an implicit solvent. We find that the terminal contributions of neutral capping are negligible across the entire ground-state energy spectrum. The coordination energy range and the nature of hybridization of the coordination state molecular orbitals remain qualitatively similar across these loops. While the HOMO and LUMO of loops in the N-terminal domain are dominated by the acidic aspartates, and the polar/hydrophobic residues, respectively, these levels of the C-terminal domain loops show strong localized electron density on the phenyl rings of the tyrosines. The Fukui index calculation identifies the hydroxyl oxygen in the phenyl ring of Y99 as a potent nucleophile. Our analysis indicates a general way of interpreting the electronic energy spectra to understand stability and functions of large biomolecules where the truncation of the molecule and, hence, the terminal capping effects are inevitable.
Collapse
Affiliation(s)
| | | | - Molly De Raychaudhury
- Department of Physics, West Bengal State University , Barasat, Kolkata 700126, India
| | | |
Collapse
|
28
|
Cheng W, Liang Z, Wang W, Yi C, Li H, Zhang S, Zhang Q. Insight into binding modes of p53 and inhibitors to MDM2 based on molecular dynamic simulations and principal component analysis. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1087598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
29
|
Lima Neto JX, Fulco UL, Albuquerque EL, Corso G, Bezerra EM, Caetano EWS, da Costa RF, Freire VN. A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors. Phys Chem Chem Phys 2015; 17:13092-103. [DOI: 10.1039/c4cp05630b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil detailed binding energy features of willardiines co-crystallized with the AMPA receptor.
Collapse
Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Gilberto Corso
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Eveline M. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Roner F. da Costa
- Departamento de Física
- Universidade Federal Rural do Semi-Árido
- 59780-000 Caraúbas-RN
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| |
Collapse
|
30
|
Rodrigues C, Oliveira J, Fulco U, Albuquerque E, Moura R, Caetano E, Freire V. Quantum biochemistry study of the T3-785 tropocollagen triple-helical structure. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.12.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
31
|
Barroso-Neto IL, Marques JPC, da Costa RF, Caetano EWS, Cavada BS, Gottfried C, Freire VN. Inactivation of Ovine Cyclooxygenase-1 by Bromoaspirin and Aspirin: A Quantum Chemistry Description. J Phys Chem B 2012; 116:3270-9. [DOI: 10.1021/jp206397z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ito L. Barroso-Neto
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - João Paulo C. Marques
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Roner F. da Costa
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| | - Ewerton W. S. Caetano
- Instituto
Federal de Educação, Ciência e Tecnologia do Ceará, Fortaleza 60040-531, Ceará,
Brazil
| | - Benildo S. Cavada
- Department of Biochemistry, Universidade Federal do Ceará, Fortaleza 60455-760, Ceará, Brazil
| | - Carmem Gottfried
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre
90035-003, Rio Grande do Sul, Brazil
| | - Valder N. Freire
- Department of Physics, Universidade Federal do Ceará, Fortaleza 60455-760,
Ceará, Brazil
| |
Collapse
|
32
|
Meher BR, Wang Y. Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies. J Phys Chem B 2012; 116:1884-900. [PMID: 22239286 DOI: 10.1021/jp2074804] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the present work, the binding of inhibitor TMC114 (darunavir) to wild-type (WT), single (I50V) as well as double (I50L/A71V) mutant HIV-proteases (HIV-pr) was investigated with all-atom molecular dynamics (MD) simulations as well as molecular mechanic-Poisson-Boltzmann surface area (MM-PBSA) calculation. For both the apo and complexed HIV-pr, many intriguing effects due to double mutant, I50L/A71V, are observed. For example, the flap-flap distance and the distance from the active site to the flap residues in the apo I50L/A71V-HIV-pr are smaller than those of WT- and I50V-HIV-pr, probably making the active site smaller in volume and closer movement of flaps. For the complexed HIV-pr with TMC114, the double mutant I50L/A71V shows a less curling of the flap tips and less flexibility than WT and the single mutant I50V. As for the other previous studies, the present results also show that the single mutant I50V decreases the binding affinity of I50V-HIV-pr to TMC, resulting in a drug resistance; whereas the double mutant I50L/A71V increases the binding affinity, and as a result of the stronger binding, the I50L/A71V may be well adapted by the TMC114. The energy decomposition analysis suggests that the increase of the binding for the double mutant I50L/A71V-HIV-pr can be mainly attributed to the increase in electrostatic energy by -5.52 kacl/mol and van der Waals by -0.42 kcal/mol, which are canceled out in part by the increase of polar solvation energy of 1.99 kcal/mol. The I50L/A71V mutant directly increases the binding affinity by approximately -0.88 (Ile50 to Leu50) and -0.90 (Ile50' to Leu50') kcal/mol, accounting 45% for the total gain of the binding affinity. Besides the direct effects from the residues Leu50 and Leu50', the residue Gly49' increases the binding affinity of I50L/A71V-HIV-pr to the inhibitor by -0.74 kcal/mol, to which the electrostatic interaction of Leu50's backbone contributes by -1.23 kcal/mol. Another two residues Ile84 and Ile47' also increase the binding affinity by -0.22 and -0.29 kcal/mol, respectively, which can be mainly attributed to van der Waals terms (ΔT(vdw) = -0.21 and -0.39 kcal/mol).
Collapse
Affiliation(s)
- Biswa Ranjan Meher
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, Georgia 31705, USA
| | | |
Collapse
|
33
|
Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein. Amino Acids 2011; 43:557-65. [DOI: 10.1007/s00726-011-1150-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
|
34
|
Söderhjelm P, Kongsted J, Ryde U. Ligand Affinities Estimated by Quantum Chemical Calculations. J Chem Theory Comput 2010; 6:1726-37. [DOI: 10.1021/ct9006986] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden, and Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden, and Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden, and Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| |
Collapse
|
35
|
Söderhjelm P, Kongsted J, Genheden S, Ryde U. Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdiscip Sci 2010; 2:21-37. [DOI: 10.1007/s12539-010-0083-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/29/2009] [Accepted: 11/11/2009] [Indexed: 12/01/2022]
|
36
|
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]
|
37
|
Zhu XL, Ge-Fei H, Zhan CG, Yang GF. Computational simulations of the interactions between acetyl-coenzyme-A carboxylase and clodinafop: resistance mechanism due to active and nonactive site mutations. J Chem Inf Model 2009; 49:1936-43. [PMID: 19594140 DOI: 10.1021/ci900174d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Grass weed populations resistant to acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides represent a major problem for the sustainable development of modern agriculture. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecular mechanics-Poisson-Boltzmann surface area (MM/PBSA) calculations, have been carried out to uncover the detailed molecular mechanism of Alopecurus myosuroides resistance to clodinafop, a commercial herbicide targeting ACCase. All the computational model and energetic results indicated that W374C, I388N, D425G, and G443A mutations have great effects on the conformational change of the binding pocket and the hydrogen-bonding interactions. The pi-pi interaction between ligand and the residue of Phe377 and Tyr161', playing an important contribution to the binding affinity, were decreased after mutations. In addition, the hydrogen-bonding interactions between clodinafop and the residues (Ile158' and Ala54') disappeared or decreased significantly upon mutation. As a result, the mutant-type ACCase has a lower affinity for the inhibitor binding than the wild-type enzyme, which accounts for the molecular basis of herbicidal resistance. The structural and mechanistic insights obtained from the present study will provide a valuable clue for future designing of a promising inhibitor to reduce drug resistance associated with both active and nonactive site mutations.
Collapse
Affiliation(s)
- Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, PR China
| | | | | | | |
Collapse
|
38
|
Chen J, Zhang S, Liu X, Zhang Q. Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation. J Mol Model 2009; 16:459-68. [PMID: 19629548 DOI: 10.1007/s00894-009-0553-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 06/11/2009] [Indexed: 12/01/2022]
Abstract
The single mutations D30N and I50V are considered as the key residue mutations of the HIV-1 protease drug resistance to inhibitors in clinical use. In this work, molecular dynamics (MD) simulations combined with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method have been performed to investigate the drug-resistant mechanisms of D30N and I50V to an inhibitor TMC-114. The analyses of absolute binding free energies using the separate trajectory approach suggests that the decrease in the van der Waals energy and electrostatic energy in the gas phase results in the drug resistance of D30N to TMC-114, while for I50V, the decrease in the electrostatic energy mainly drive its drug resistance to TMC-114. Detailed binding free energies between TMC-114 and individual protein residues are computed by using a per-residue basis decomposition method, which provides insights into the inhibitor-protein binding mechanism and also explains the drug-resistant mechanisms of mutations D30N and I50V to TMC-114. The study shows that the loss of the hydrogen bond between TMC-114 and the side chain of Asn30' is the main driving force of the resistance of D30N to TMC-114, and in the case of I50V, the increase in the polar solvation energies between TMC-114 and two residues Val50' and Asp30' definitively drives the resistance of I50V to TMC-114. We expect that this work can provide some helpful insights into the nature of mutational effect and aid the future design of better inhibitors.
Collapse
Affiliation(s)
- Jianzhong Chen
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | | | | | | |
Collapse
|