1
|
Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
Collapse
Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| |
Collapse
|
2
|
Jain S, Vanka K. Can the solvent enhance the rate of chemical reactions through C-H/π interactions? insights from theory. Phys Chem Chem Phys 2019; 21:14821-14831. [PMID: 31225546 DOI: 10.1039/c9cp02646k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The current computational study with density functional theory (DFT) shows that the rate of chemical reactions can be influenced through non-covalent C-H/π interactions between substrates and the solvent. It is shown that intramolecular carbon-carbon interaction and CO2 activation by a low valent silicon complex are both favourably affected by the explicit presence of the solvent toluene, due to C-H/π interactions between toluene and the silicon complex. Furthermore, ab initio molecular dynamics (AIMD) simulations demonstrate that even if the C-H/π interacting solvent molecule is displaced from the complex, another would quickly take its place, thus maintaining the interaction. Hence, the current work shows how non-covalent interactions between solvent and substrate can enhance the rate of the reaction and expands our understanding of the role and influence of the solvent in effecting important chemical transformations.
Collapse
Affiliation(s)
- Shailja Jain
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Kumar Vanka
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
3
|
Mishra BK, Venkatnarayan R. Substituents’ influence on the C–H···π interaction in the T-shaped benzene dimer. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2249-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
4
|
Poongavanam V, Namasivayam V, Vanangamudi M, Al Shamaileh H, Veedu RN, Kihlberg J, Murugan NA. Integrative approaches in
HIV
‐1 non‐nucleoside reverse transcriptase inhibitor design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1328] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical ChemistrySree Vidyanikethan College of Pharmacy Tirupathi India
| | | | - Rakesh N Veedu
- Centre for Comparative GenomicsMurdoch University Perth Australia
- Perron Institute for Neurological and Translational Science Perth Australia
| | - Jan Kihlberg
- Department of Chemistry‐BMCUppsala University Uppsala Sweden
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of BiotechnologyKTH‐Royal Institute of Technology Stockholm Sweden
| |
Collapse
|
5
|
Momeni Z, Ebrahimi A. The influence of CH…π interaction on hydrogen bonding ability of –CONH2 functional group of benzamide. Struct Chem 2016. [DOI: 10.1007/s11224-016-0745-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
6
|
Khanh PN, Ngan VT, Hong Man NT, Ai Nhung NT, Chandra AK, Trung NT. An insight into Csp–H⋯π hydrogen bonds and stability of complexes formed by acetylene and its substituted derivatives with benzene and borazine. RSC Adv 2016. [DOI: 10.1039/c6ra21557b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Theoretical calculations at the MP2/aug-cc-pVDZ level are used to investigate the Csp–H⋯π interactions of C2HX (X = H, F, Cl, Br, CH3, NH2) with C6H6 and B3N3H6 molecules.
Collapse
Affiliation(s)
- Pham Ngoc Khanh
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Vu Thi Ngan
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Nguyen Thi Hong Man
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| | - Nguyen Thi Ai Nhung
- Department of Chemistry
- Hue University of Sciences – Hue University
- Hue City
- Vietnam
| | - Asit K. Chandra
- Department of Chemistry
- North-Eastern Hill University
- Shillong
- India
| | - Nguyen Tien Trung
- Laboratory of Computational Chemistry and Modelling
- Department of Chemistry
- Quy Nhon University
- Vietnam
| |
Collapse
|
7
|
Raju RK, Bengali AA, Brothers EN. A unified set of experimental organometallic data used to evaluate modern theoretical methods. Dalton Trans 2016; 45:13766-78. [DOI: 10.1039/c6dt02763f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We applied a test set of ligand dissociation enthalpies derived entirely from a unified experimental approach to evaluate the efficacy of various methods for modeling organometallic chemistry.
Collapse
Affiliation(s)
- Rajesh K. Raju
- Department of Chemistry
- Texas A&M University at Qatar
- Doha
- Qatar
| | | | | |
Collapse
|
8
|
Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
| | | | | | | | | |
Collapse
|
9
|
Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| |
Collapse
|
10
|
Yilmazer ND, Korth M. Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J 2015; 13:169-75. [PMID: 25848495 PMCID: PMC4372622 DOI: 10.1016/j.csbj.2015.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/21/2022] Open
Abstract
Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.
Collapse
Affiliation(s)
| | - Martin Korth
- Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany
| |
Collapse
|
11
|
Mishra BK, Deshmukh MM, Venkatnarayan R. C-H···π interactions and the nature of the donor carbon atom. J Org Chem 2014; 79:8599-606. [PMID: 25157745 DOI: 10.1021/jo501251s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The influence of multiple substituents (F, CH3, NO2, CN, Cl, OH and NH2) on the C-H···π interaction in benzene-ethylene complex was investigated using the estimated CCSD(T) method and complete basis set limit. The results were compared with our earlier reported complexes of benzene-acetylene and benzene-methane, thus completing the sp, sp(2) and sp(3) series of C-H donors. The stabilization energy values for multiple fluoro-substituted benzene-ethylene complexes are found to be very close to those of the multiple fluoro-substituted benzene-methane complexes. Expectedly, the stabilization energies for the multiple methyl-substituted benzene-ethylene complexes lie between those of the multiple methyl-substituted benzene-methane and benzene-acetylene complexes. Energy decomposition analysis using the DFT-SAPT method predicts the dispersion energy to be dominant, similar to the benzene-methane complexes. For the symmetrically disubstituted complexes (-OH, -Cl, -NH2, -CN and -NO2), additional C-H···X interaction was observed, possibly due to the angular orientation of the ethylene molecule. Multidimensional correlation analysis between the electrostatic, dispersion and exchange-repulsion with the C-H···π interaction distance (r), Hammett constant (σ) and the molar refractivity (MR) revealed strong correlation between dispersion energy and the C-H···π interaction distance (r) as well as molar refractivity (MR).
Collapse
Affiliation(s)
- Brijesh Kumar Mishra
- International Institute of Information Technology Bangalore , Bangalore 560100, Karnataka, India
| | | | | |
Collapse
|
12
|
Wheeler SE, Bloom JWG. Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 2014; 118:6133-47. [PMID: 24937084 DOI: 10.1021/jp504415p] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.
Collapse
Affiliation(s)
- Steven E Wheeler
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | | |
Collapse
|
13
|
Galembeck SE, Bickelhaupt FM, Fonseca Guerra C, Galembeck E. Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X. J Mol Model 2014; 20:2332. [DOI: 10.1007/s00894-014-2332-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/30/2014] [Indexed: 01/15/2023]
|
14
|
Tan C, Li W, Wang W. Localized frustration and binding-induced conformational change in recognition of 5S RNA by TFIIIA zinc finger. J Phys Chem B 2013; 117:15917-25. [PMID: 24266699 DOI: 10.1021/jp4052165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein TFIIIA is composed of nine tandemly arranged Cys2His2 zinc fingers. It can bind either to the 5S RNA gene as a transcription factor or to the 5S RNA transcript as a chaperone. Although structural and biochemical data provided valuable information on the recognition between the TFIIIIA and the 5S DNA/RNA, the involved conformational motions and energetic factors contributing to the binding affinity and specificity remain unclear. In this work, we conducted MD simulations and MM/GBSA calculations to investigate the binding-induced conformational changes in the recognition of the 5S RNA by the central three zinc fingers of TFIIIA and the energetic factors that influence the binding affinity and specificity at an atomistic level. Our results revealed drastic interdomain conformational changes between these three zinc fingers, involving the exposure/burial of several crucial DNA/RNA binding residues, which can be related to the competition between DNA and RNA for the binding of TFIIIA. We also showed that the specific recognition between finger 4/finger 6 and the 5S RNA introduces frustrations to the nonspecific interactions between finger 5 and the 5S RNA, which may be important to achieve optimal binding affinity and specificity.
Collapse
Affiliation(s)
- Cheng Tan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University , Nanjing, Jiangsu 210093, China
| | | | | |
Collapse
|
15
|
Karthikeyan S, Ramanathan V, Mishra BK. Influence of the Substituents on the CH...π Interaction: Benzene–Methane Complex. J Phys Chem A 2013; 117:6687-94. [DOI: 10.1021/jp404972f] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- S. Karthikeyan
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea
| | - V. Ramanathan
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | | |
Collapse
|
16
|
Rao L, Zhang IY, Guo W, Feng L, Meggers E, Xu X. Nonfitting protein-ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors. J Comput Chem 2013; 34:1636-46. [DOI: 10.1002/jcc.23303] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 03/25/2013] [Accepted: 04/03/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | | | | | - Li Feng
- Department of Chemistry; Philipps-University Marburg; Hans-Meerwein-Strasse; Marburg; 35032; Germany
| | | | | |
Collapse
|
17
|
Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
18
|
Safi M, Lilien RH. Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA. J Chem Inf Model 2012; 52:1529-41. [DOI: 10.1021/ci200626m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Maria Safi
- Department of Computer Science, University of Toronto,
Toronto, Ontario M5S 3G4, Canada
| | - Ryan H. Lilien
- Department of Computer Science, University of Toronto,
Toronto, Ontario M5S 3G4, Canada
| |
Collapse
|
19
|
Zhang Y, Pan D, Shen Y, Jin N, Liu H, Yao X. Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations. J Mol Model 2012; 18:4517-27. [PMID: 22643972 DOI: 10.1007/s00894-012-1450-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 04/30/2012] [Indexed: 01/02/2023]
Abstract
VRC01 is one of the most broadly and potently neutralizing HIV-1 antibodies known-it has been shown to neutralize 91 % of the tested primary isolate Env pseudoviruses by recognizing the viral envelope glycoprotein gp120. To explore the mechanism of HIV-1 neutralization by VRC01 and thus obtain valuable information for vaccine design, we performed molecular dynamics simulations and binding free energy calculations for apo-VRC01, apo-gp120, and the gp120-VRC01 complex. For gp120, residue energy decomposition analysis showed that the hotspot residues Asn280, Lys282, Asp368, Ile371, and Asp457 are located in three primary loops, including the CD4-binding loop, loop D, and loop V5. For VRC01, the hotspot residues Trp47, Trp50, Asn58, Arg61, Gln64, Trp100, and Tyr91 mainly come from CDR2 of the heavy chain. By decomposing the binding free energy into different components, intermolecular van der Waals interactions and nonpolar solvation were found to dominate the binding process. Principal component analysis of loops D and V5, which are related to neutralization resistance, indicated that these two areas have a larger conformational space in apo-gp120 compared to bound gp120. A comparison of three representative structures from the cluster analysis of loops D and V5 indicated that changes primarily occur at the tip of loop V5, and are caused by fluctuations in the terminal Glu1 residue of the antibody. This information can be used to guide the design of vaccines and small molecule inhibitors.
Collapse
Affiliation(s)
- Yan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | | | | | | | | | | |
Collapse
|
20
|
Pan D, Xue W, Wang X, Guo J, Liu H, Yao X. Molecular mechanism of the enhanced virulence of 2009 pandemic Influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. J Mol Model 2012; 18:4355-66. [DOI: 10.1007/s00894-012-1423-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/02/2012] [Indexed: 11/30/2022]
|
21
|
Mishra BK, Karthikeyan S, Ramanathan V. Tuning the C–H···π Interaction by Different Substitutions in Benzene–Acetylene Complexes. J Chem Theory Comput 2012; 8:1935-42. [DOI: 10.1021/ct300100h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - S. Karthikeyan
- Department of Theoretical and
Computational Molecular Science, Institute of Molecular Science, Myodaiji, Okazaki 444-8585, Aichi, Japan
| | - V. Ramanathan
- Third Institute of Physics, University of Stuttgart, 57 Pfaffenwaldring, 70569
Stuttgart, Germany
| |
Collapse
|
22
|
Pan D, Sun H, Shen Y, Liu H, Yao X. Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation. Antiviral Res 2011; 92:424-33. [DOI: 10.1016/j.antiviral.2011.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/23/2011] [Accepted: 09/23/2011] [Indexed: 11/26/2022]
|
23
|
Minkara MS, Davis PH, Radhakrishnan ML. Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT. Proteins 2011; 80:573-90. [DOI: 10.1002/prot.23221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/13/2011] [Accepted: 10/06/2011] [Indexed: 11/09/2022]
|
24
|
Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
Collapse
Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | | | | | | |
Collapse
|
25
|
Boonsri P, Kuno M, Hannongbua S. Key interactions of the mutant HIV-1 reverse transcriptase/efavirenz: an evidence obtained from ONIOM method. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00162k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|