1
|
Sk MF, Haridev S, Roy R, Kar P. Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:941-962. [PMID: 34787532 DOI: 10.1080/1062936x.2021.1999318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A detailed computational study was performed to investigate the conformational changes of flap region and the mechanism underlying the binding of the inhibitor TMC-126 to HIV-1 protease (PR1) and its mutant variants through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation. Further, we have studied the effectiveness of the inhibitor against HIV-2 protease (PR2). The MM-PBSA calculation suggests that TMC-126 loses its potency against mutant variants and PR2 compared to wild-type PR1 mainly due to the loss in intermolecular electrostatic interactions. The potency of the inhibitor decreases in the order: wild type PR1 > M46L > MDR20 > I50V > PR2 > V32I > A28S. Our study reveals that the flap of PR1 adopts a semi-open conformation due to the mutation I50V or MDR20. The dissimilar nature of the movement of the flap tip of both monomers is evident from the dynamic cross-correlation map. The protein structural network analysis displays that mutation causes structural rearrangements and changes the communication path between residues. Overall, we believe our study may help explore and accelerate the development of novel HIV-1/HIV-2 protease inhibitors with better potency.
Collapse
Affiliation(s)
- M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - S Haridev
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | - R Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| |
Collapse
|
2
|
Yu YX, Wang W, Sun HB, Zhang LL, Wu SL, Liu WT. Insights into effect of the Asp25/Asp25' protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:615-641. [PMID: 34157882 DOI: 10.1080/1062936x.2021.1939149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.
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
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- School of Science, Shandong Jiaotong University, Jinan, China
| |
Collapse
|
3
|
Shi S, Sui K, Liu W, Lei Y, Zhang S, Zhang Q. Revealing binding selectivity of ligands toward murine double minute 2 and murine double minute X based on molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2019; 38:5081-5094. [PMID: 31755361 DOI: 10.1080/07391102.2019.1695671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
It is well known that the interactions of p53 with murine double minute 2 and murine double minute X, namely MDM2 and MDMX, have been significant targets of efficient anti-cancer drug design. In this study, molecular dynamics (MD) simulations, principal component (PC) analysis and binding free energy calculations are combined to recognize binding selectivity of three ligands to MDM2 and MDMX. The binding free energies were estimated by using molecular mechanics generalized Born surface area (MM-GBSA) method and the obtained results display that the increase in the binding enthalpy of three ligands to MDM2 relative to MDMX mainly drives the binding selectivity of them toward MDM2 and MDMX. The information obtained from PC analysis shows that the associations of ligands exert important impacts on internal dynamics of MDM2 and MDMX. Meanwhile, the calculations of residue-based free energy decomposition not only identify the hot interaction spots of ligands with MDM2 and MDMX, but also show the residues (L54, M53), (Y67, Y66), (V93, V92), (H96, P95), (I99, I98) and (Y100, Y99) in (MDM2, MDMX) are responsible for most contributions to the binding selectivity of three ligands toward MDM2 and MDMX. It is believed that this work can provide useful information for design of highly selective and dual inhibitors targeting MDM2 and MDMX.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shuhua Shi
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Kai Sui
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Weizhe Liu
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Yanzi Lei
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
| |
Collapse
|
4
|
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]
|
5
|
Ding JN, Zhang YJ, Zhong H, Ao CC, Han JG. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. J Biomol Struct Dyn 2018; 36:1009-1028. [DOI: 10.1080/07391102.2017.1307143] [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]
Affiliation(s)
- Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
- Department of Clinical Medicine, Anqing Medical College, Anqing 246052, People’s Republic of China
| | - Yan-Jun Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Hui Zhong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Cheng-Cheng Ao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Ju-Guang Han
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| |
Collapse
|
6
|
Ding JN, Zhang YJ, Zhong H, Ao CC, Li J, Han JG. An all-atom molecular dynamics study of the anti-interferon signaling of Ebola virus: interaction mechanisms of EBOV VP24 binding to Karyopherin alpha5. MOLECULAR BIOSYSTEMS 2018; 13:1031-1045. [PMID: 28418440 DOI: 10.1039/c7mb00136c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ebola virus (EBOV) is highly lethal due to virally encoded immune antagonists, and the combination of EBOV VP24 with karyopherin alpha (KPNA) will trigger anti-interferon (IFN) signaling. The crystal structure of VP24-KPNA5 has been proposed in recent studies, but the precise binding mechanisms are still unclear. In order to explore the VP24-KPNA5 protein binding micro-mechanisms, Molecular Dynamic (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation are performed. The obtained results show that EBOV VP24 binding to KPNA5 will rigidify their binding-face, and both proteins will be compacted during binding. According to the analyses of binding free energies of WT and the eight mutant systems, MUT3 makes the most effective contributions to the interaction; additionally MUT4, R398A and the double mutant have the second most effective influence. Hydrogen bond analysis demonstrates that inhibitors which can interfere with the formation of hydrogen bonds D480-T138, E483-R137 and D205-R396 will prevent the anti-IFN effect. Meanwhile, by combining the decomposition of binding free energies (DC) with computational alanine scanning (CAS) results, it is shown that VP24 residues R137 and T138 will be potential targets for EBOV VP24 inhibitors, and KPNA5 residues R396, R398, R480, Y477 and F484 will be potential targets to prevent KPNA5 binding to VP24, which will ultimately block anti-IFN signaling. Our investigations provide theoretical data to understand the binding modes of VP24-KPNA5. The precise binding mechanisms of the complex may shed light on the development of potential novel inhibitors against EBOV infection.
Collapse
Affiliation(s)
- Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
7
|
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
|
8
|
Chen J. Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions. RSC Adv 2016. [DOI: 10.1039/c6ra09201b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular dynamics simulation and binding free energy calculations were used to probe drug resistance of HIV-1 protease mutations toward inhibitors.
Collapse
Affiliation(s)
- Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
| |
Collapse
|
9
|
Zhao RN, Fan S, Han JG, Liu G. Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein. J Biomol Struct Dyn 2014; 33:1067-81. [PMID: 24865469 DOI: 10.1080/07391102.2014.929028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mcl-1 has emerged as a potential therapeutic target in the treatment of several malignancies. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic Mcl-1 and this segment is responsible for modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-peptide interaction is required to develop potent inhibitors specific for Mcl-1. Molecular dynamics simulations were performed for Mcl-1 in complex with three different BH3 peptides derived from Mcl-1, Bax, and Bim. Accordingly, the calculated binding free energies using MM-PBSA method are obtained and comparison with the experimentally determined binding free energies is made. The interactions involving two conserved charged residues (Aspi, and Arg/Lysi-4) and three upstream conserved hydrophobic residues (Leui-5, Ile/Vali-2, and Glyi-1, respectively) of BH3 peptides play the important roles in the structural stability of the complexes. The calculated results exhibit that the interactions of Bim BH3 peptides to Mcl-1 is stronger than the complex with Bax 19BH3 peptides. The hydrophobic residues (position i - 9, i - 8 and i + 2) of BH3 peptides can be involved in their inhibitory specificity. The calculated results can be used for designing more effective MCL-1 inhibitors.
Collapse
Affiliation(s)
- Run-Ning Zhao
- a Institute of Applied Mathematics and Physics , Shanghai Dianji University , Shanghai 201306 , P.R. China
| | | | | | | |
Collapse
|
10
|
Li D, Zhang Y, Zhao RN, Fan S, Han JG. Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. J Mol Model 2014; 20:2122. [PMID: 24526384 DOI: 10.1007/s00894-014-2122-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/19/2013] [Indexed: 12/01/2022]
Abstract
Residue Gly86 is considered as the highly conversed residue in the HIV-1 protease. In our work, the detailed binding free energies for the wild-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and inhibitor are different than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively. Furthermore, free energy decomposition analysis for the WT and mutated complexes on the basis of per-residue indicates that the mutagenesis influences the energy contribution of the residue located at three regions: active site region (residue 24-32), the flap region, and the region around the mutated residue G86 (residue 79-88), especially the flap region. Finally, further hydrogen bonds and structure analysis are carried out to detect the relationship between the energy and conformation. In all, the G86 mutations change the flap region's conformation. The experimental results are in good agreement with available results.
Collapse
Affiliation(s)
- Dan Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
| | | | | | | | | |
Collapse
|
11
|
Yadav D, Paliwal S, Yadav R, Pal M, Pandey A. Identification of novel HIV 1--protease inhibitors: application of ligand and structure based pharmacophore mapping and virtual screening. PLoS One 2012; 7:e48942. [PMID: 23145032 PMCID: PMC3493599 DOI: 10.1371/journal.pone.0048942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/01/2012] [Indexed: 01/27/2023] Open
Abstract
A combined ligand and structure-based drug design approach provides a synergistic advantage over either methods performed individually. Present work bestows a good assembly of ligand and structure-based pharmacophore generation concept. Ligand-oriented study was accomplished by employing the HypoGen module of Catalyst in which we have translated the experimental findings into 3-D pharmacophore models by identifying key features (four point pharmacophore) necessary for interaction of the inhibitors with the active site of HIV-1 protease enzyme using a training set of 33 compounds belonging to the cyclic cyanoguanidines and cyclic urea derivatives. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, two hydrogen bond acceptors and two hydrophobic, showed a correlation (r) of 0.90 and a root mean square of 0.71 and cost difference of 56.59 bits between null cost and fixed cost. The model was validated using CatScramble technique, internal and external test set prediction. In the second phase of our study, a structure-based five feature pharmacophore hypothesis was generated which signifies the importance of hydrogen bond donor, hydrogen bond acceptors and hydrophobic interaction between the HIV-1 protease enzyme and its inhibitors. This work has taken a significant step towards the full integration of ligand and structure-based drug design methodologies as pharmacophoric features retrieved from structure-based strategy complemented the features from ligand-based study hence proving the accuracy of the developed models. The ligand-based pharmacophore model was used in virtual screening of Maybridge and NCI compound database resulting in the identification of four structurally diverse druggable compounds with nM activities.
Collapse
Affiliation(s)
- Divya Yadav
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Rakesh Yadav
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Mahima Pal
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| | - Anubhuti Pandey
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, India
| |
Collapse
|