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Functionalized carbon nanotubes as an alternative to traditional anti-HIV-1 protease inhibitors: An understanding towards Nano-medicine development through MD simulations. J Mol Graph Model 2022; 117:108280. [PMID: 35963109 DOI: 10.1016/j.jmgm.2022.108280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/14/2023]
Abstract
The Human Immunodeficiency Virus (HIV) has been the source of epidemic infection of AIDS for a longer period. One of the most difficult tasks is identifying novel medications that can help to decrease or control this global health hazard by overcoming drug resistance. In recent decades' nanoparticles are emerging as extremely relevant in drug delivery platforms. In the current study, the pristine (SWCNT) and hydroxyl functionalized (SWCNT-OH) versions of the SWCNT were investigated as inhibitors against the wild-type (WT) and three key mutants of HIV-1 protease (HIV-pr) (I50V, V82A, and I84V). Molecular docking of SWCNT in the catalytic domain and running all-atom MD simulations of all complexes are also part of this project. A thorough inspection of conformational dynamics from 50 ns trajectories reveals that both the pristine and SWCNT-OH can fit right to the pocket region of HIV-pr and govern flap dynamics. The binding affinity of the four HIV-pr-SWCNT/SWCNT-OH complexes was further investigated using MM-PBSA-dependent binding free energy studies. In most mutants and WT systems, SWCNT-OH was reported to bind proportionately many folds (kcal/mol) more than pristine SWCNTs. Hence, SWCNTs are possible HIV-pr inhibitors in terms of their stable existence in the pocket area, stronger binding to the protease, and regulation of flap dynamics in controlling the active site volume, which have vast potential for applications against drug resistance.
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2
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Zhang Q, Yang Y, Gong X, Zhao N, Zhang Y, Liu H. Thermodynamic integration combined with molecular dynamic simulations to explore the
cross‐resistance
mechanism of isoniazid and ethionamide. Proteins 2022; 90:1142-1151. [DOI: 10.1002/prot.26295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/25/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022]
Affiliation(s)
| | - Yuwei Yang
- School of Pharmacy Lanzhou University Lanzhou China
| | - Xiaoqing Gong
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry Lanzhou University Lanzhou China
| | - Nannan Zhao
- School of Pharmacy Lanzhou University Lanzhou China
| | - Yang Zhang
- Supercomputing Center of Lanzhou University Lanzhou China
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3
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations and Energy Analysis Unravel the Dynamic Properties and Binding Mechanism of Mutants HIV-1 Protease with DRV and CA-p2. Microbiol Spectr 2022; 10:e0074821. [PMID: 35319278 PMCID: PMC9045218 DOI: 10.1128/spectrum.00748-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
Abstract
PRS17, a variant of human immunodeficiency virus type I protease (HIV-1 PR), has 17 mutated residues showing high levels of multidrug resistance. To describe the effects of these mutated residues on the dynamic properties and the binding mechanism of PR with substrate and inhibitor, focused on six systems (two complexes of WT PR and PRS17 with inhibitor Darunavir (DRV), two complexes of WT PR and PRS17 with substrate analogue CA-p2, two unligand WT PR and PRS17), we performed multiple molecular dynamics (MD) simulations combined with MM-PBSA and solvated interaction energy (SIE) methods. For both the unligand PRs and ligand-PR complexes, the results from simulations revealed 17 mutated residues alter the flap-flap distance, the distance from flap regions to catalytic sites, and the curling degree of the flap tips. These mutated residues changed the flexibility of the flap region in PR, and thus affected its binding energy with DRV and CA-p2, resulting in differences in sensitivity. Hydrophobic cavity makes an important contribution to the binding of PR and ligands. And most noticeable of all, the binding of the guanidine group in CA-p2 and Arg8' of PRS17 is useful for increasing their binding ability. These results have important guidance for the further design of drugs against multidrug resistant PR. IMPORTANCE Developing effective anti-HIV inhibitors is the current requirement to cope with the emergence of the resistance of mutants. Compared with the experiments, MD simulations along with energy calculations help reduce the time and cost of designing new inhibitors. Based on our simulation results, we propose two factors that may help design effective inhibitors against HIV-1 PR: (i) importance of hydrophobic cavity, and (ii) introduction of polar groups similar to the guanidine group.
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Affiliation(s)
- Ruige Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
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4
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Issahaku AR, Aljoundi A, Soliman ME. Establishing the mutational effect on the binding susceptibility of AMG510 to KRAS switch II binding pocket: Computational insights. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100952] [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] Open
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5
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Rana N, Singh AK, Shuaib M, Gupta S, Habiballah MM, Alkhanani MF, Haque S, Reshi MS, Kumar S. Drug Resistance Mechanism of M46I-Mutation-Induced Saquinavir Resistance in HIV-1 Protease Using Molecular Dynamics Simulation and Binding Energy Calculation. Viruses 2022; 14:v14040697. [PMID: 35458427 PMCID: PMC9031992 DOI: 10.3390/v14040697] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
Drug-resistance-associated mutation in essential proteins of the viral life cycle is a major concern in anti-retroviral therapy. M46I, a non-active site mutation in HIV-1 protease has been clinically associated with saquinavir resistance in HIV patients. A 100 ns molecular dynamics (MD) simulation and MM-PBSA calculations were performed to study the molecular mechanism of M46I-mutation-based saquinavir resistance. In order to acquire deeper insight into the drug-resistance mechanism, the flap curling, closed/semi-open/open conformations, and active site compactness were studied. The M46I mutation significantly affects the energetics and conformational stability of HIV-1 protease in terms of RMSD, RMSF, Rg, SASA, and hydrogen formation potential. This mutation significantly decreased van der Waals interaction and binding free energy (∆G) in the M46I–saquinavir complex and induced inward flap curling and a wider opening of the flaps for most of the MD simulation period. The predominant open conformation was reduced, but inward flap curling/active site compactness was increased in the presence of saquinavir in M46I HIV-1 protease. In conclusion, the M46I mutation induced structural dynamics changes that weaken the protease grip on saquinavir without distorting the active site of the protein. The produced information may be utilized for the discovery of inhibitor(s) against drug-resistant HIV-1 protease.
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Affiliation(s)
- Nilottam Rana
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
| | - Sanjay Gupta
- Department of Urology, Pharmacology and Pathology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Mahmoud M. Habiballah
- Medical Laboratory Technology Department, Jazan University, Jazan 45142, Saudi Arabia;
- SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan 45142, Saudi Arabia
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
| | - Mohd Salim Reshi
- Toxicology and Pharmacology Lab., Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu & Kashmir, India;
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda 151401, Punjab, India; (N.R.); (A.K.S.); (M.S.)
- Correspondence:
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6
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13817-13832. [PMID: 33175558 DOI: 10.1021/acs.langmuir.0c02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease is regarded as a fascinating target for drug development against HIV infection. However, mutations causing drug resistance severely limit the efficiency of the recently marketed drugs in the treatment of HIV replication. To elucidate the binding mechanism of HIV-1 protease with promising inhibitor GRL-02031 and further to probe the resistance mechanism associated with mutations (I47V, L76V, V82A, and N88D) to the inhibitor, we applied multiple molecular dynamics (MMD) simulations along with energy analysis by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and solvated interaction energy (SIE) methodology on specific HIV-1 protease with GRL-0231 complexes. On the basis of detail analysis of the simulations, we revealed key characteristics that constitute the drug resistance of four mutation HIV-1 proteases toward GRL-02031: substitution of the side chain in these four mutation residues leads to a change in the distances between the flaps and catalytic sites, thereby reducing the affinity for GRL-02031 with these four mutation proteases, even though the L76V and N88D residues cannot directly contact GRL-02031. The results of energy analysis according to the MM-PBSA and SIE methods further indicated that hydrophobic interaction was considered to be the prime driving force for inhibitor GRL-02031 binding to protease and the decrease in van der Waals interactions between inhibitor GRL-02031 and mutant proteases as the primary cause of the drug resistance. Analyses of the hydrogen bonds and atomic interactions further provided detailed explanations for the resistance of these four mutation proteases toward inhibitor GRL-02031. The present study provides potential guidance on the structure-based inhibitors' design targeting HIV-1 protease.
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Affiliation(s)
- Ruige Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130023, People's Republic of China
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7
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Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 2020; 17:13. [PMID: 32430025 PMCID: PMC7236880 DOI: 10.1186/s12977-020-00520-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. Results Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ effect on \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease’s active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, University of Saarland, 66123, Saarbrücken, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Hauke Walter
- Medizinisches Labor Stendal, 39576, Stendal, Germany
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. .,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany. .,Faculty of Medicine, Saarland University, 66421, Homburg, Germany.
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8
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Wong-Sam A, Wang YF, Zhang Y, Ghosh AK, Harrison RW, Weber IT. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. ACS OMEGA 2018; 3:12132-12140. [PMID: 30288468 PMCID: PMC6167001 DOI: 10.1021/acsomega.8b01683] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5, were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PRL76V). Compound 5 exhibited the best K i value of 1.9 nM for PRL76V, whereas the other three inhibitors had K i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PRL76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PRL76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.
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Affiliation(s)
- Andres Wong-Sam
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ying Zhang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- RNA Therapeutics Institute and Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts
Medical School, Worcester, Massachusetts 01605, United States
| | - Arun K. Ghosh
- Department of Chemistry and Department
of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robert W. Harrison
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Irene T. Weber
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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9
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Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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10
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Romeo I, Marascio N, Pavia G, Talarico C, Costa G, Alcaro S, Artese A, Torti C, Liberto MC, Focà A. Structural Modeling of New Polymorphism Clusters of HCV Polymerase Isolated from Direct‐Acting Antiviral Naïve Patients: Focus on Dasabuvir and Setrobuvir Binding Affinity. ChemistrySelect 2018. [DOI: 10.1002/slct.201800649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Isabella Romeo
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Nadia Marascio
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Grazia Pavia
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Carmine Talarico
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Giosuè Costa
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Stefano Alcaro
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Anna Artese
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Carlo Torti
- Department of Medical and Surgical SciencesUnit of Infectious and Tropical DiseasesSchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy)
| | - Maria Carla Liberto
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Alfredo Focà
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
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11
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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12
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Chen J, Wang X, Zhu T, Zhang Q, Zhang JZH. A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. J Chem Inf Model 2015; 55:1903-13. [DOI: 10.1021/acs.jcim.5b00173] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jianzhong Chen
- School
of Science, Shandong Jiaotong University, Jinan 250357 China
| | - Xingyu Wang
- NYU−ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Tong Zhu
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
| | - Qinggang Zhang
- Collage
of Physics and Electronic Science, Shandong Normal University, Jinan 250014, China
| | - John Z. H. Zhang
- NYU−ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- State
Key Laboratory of Precision Spectroscopy, Institute of Theoretical
and Computational Science, East China Normal University, Shanghai 200062, China
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13
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Tzoupis H, Leonis G, Avramopoulos A, Mavromoustakos T, Papadopoulos MG. Systematic molecular dynamics, MM-PBSA, and ab initio approaches to the saquinavir resistance mechanism in HIV-1 PR due to 11 double and multiple mutations. J Phys Chem B 2014; 118:9538-52. [PMID: 25036111 DOI: 10.1021/jp502687q] [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
Mutations in the human immunodeficiency virus (HIV) enable virus replication even when appropriate antiretroviral therapy is followed, thus leading to the emergence of drug resistance. In a previous work, we systematically examined seven single mutations that are associated with saquinavir (SQV) resistance in HIV-1 protease (Tzoupis, H.; Leonis, G.; Mavromoustakos, T.; Papadopoulos, M. G. J. Chem. Theory Comput. 2013, 9, 1754-1764). Herein, we extend our analysis, which includes seven double (G48V-V82A, L10I-G48V, G48V-L90M, I84V-L90M, L10I-V82A, L10I-L63P, A71V-G73S) and four multiple (L10I-L63P-A71V, L10I-G48V-V82A, G73S-I84V-L90M, L10I-L63P-A71V-G73S-I84V-L90M) SQV-HIV-1 PR mutant complexes, in an attempt to generalize our findings and formulate the main elements of the SQV resistance mechanism in the protease. On the basis of molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and ab initio computational approaches, we identified specific features that constitute the HIV-1 PR mechanism of resistance at the molecular level: the low flexibility of SQV in the binding cavity and the preservation of hydrogen bonding (HB) and van der Waals interactions between SQV and several active-site (Gly27/27', Asp29/29'/30/30', especially Asp25/25') and flap (Ile50/50', Gly48/48') residues of the protease contribute significantly to efficient binding. The total enthalpy loss in all mutants is mostly due to the loss in enthalpy of the active-site region. Furthermore, it was observed that mutation accumulation may induce stabilization to SQV and to the flaps through enhanced HB interactions that lead to improved inhibition (e.g., accumulation of mutations in complexes containing L10I, G48V, L63P, I84V, or L90M single mutations). It was also concluded that permanent flap closure is obtained independently of mutations and SQV binding is mostly driven by van der Waals, nonpolar, and exchange-energy contributions. Importantly, it was indicated that the optimal positioning of SQV and the structure of the binding cavity are tightly coupled, since small changes in geometry may affect the binding energy greatly. The results of our theoretical approaches are in agreement with experimental evidence and provide a reliable description of SQV resistance in HIV-1 PR.
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Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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14
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Xue W, Jiao P, Liu H, Yao X. Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598. Antiviral Res 2014; 104:40-51. [PMID: 24462692 DOI: 10.1016/j.antiviral.2014.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/09/2023]
Abstract
Hepatitis C virus (HCV) NS5B protein is an RNA-dependent RNA polymerase (RdRp) with essential functions in viral genome replication and represents a promising therapeutic target to develop direct-acting antivirals (DAAs). Multiple nonnucleoside inhibitors (NNIs) binding sites have been identified within the polymerase. VX-222 and ANA598 are two NNIs targeting thumb II site and palm I site of HCV NS5B polymerase, respectively. These two molecules have been shown to be very effective in phase II clinical trials. However, the emergence of resistant HCV replicon variants (L419M, M423T, I482L mutants to VX-222 and M414T, M414L, G554D mutants to ANA598) has significantly decreased their efficacy. To elucidate the molecular mechanism about how these mutations influenced the drug binding mode and decreased drug efficacy, we studied the binding modes of VX-222 and ANA598 to wild-type and mutant polymerase by molecular modeling approach. Molecular dynamics (MD) simulations results combined with binding free energy calculations indicated that the mutations significantly altered the binding free energy and the interaction for the drugs to polymerase. The further per-residue binding free energy decomposition analysis revealed that the mutations decreased the interactions with several key residues, such as L419, M423, L474, S476, I482, L497, for VX-222 and L384, N411, M414, Y415, Q446, S556, G557 for ANA598. These were the major origins for the resistance to these two drugs. In addition, by analyzing the residue interaction network (RIN) of the complexes between the drugs with wild-type and the mutant polymerase, we found that the mutation residues in the networks involved in the drug resistance possessed a relatively lower size of topology centralities. The shift of betweenness and closeness values of binding site residues in the mutant polymerase is relevant to the mechanism of drug resistance of VX-222 and ANA598. These results can provide an atomic-level understanding about the mechanisms of drug resistance conferred by the studied mutations and will be helpful to design more potent inhibitors which could effectively overcome drug resistance of antivirus agents.
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Affiliation(s)
- Weiwei Xue
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Pingzu Jiao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.
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15
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Tinago W, O'Halloran JA, O'Halloran RM, Macken A, Lambert JS, Sheehan GJ, Mallon PWG. Characterization of associations and development of atazanavir resistance after unplanned treatment interruptions. HIV Med 2013; 15:224-32. [DOI: 10.1111/hiv.12107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 12/30/2022]
Affiliation(s)
- W Tinago
- HIV Molecular Research Group; School of Medicine and Medical Science; University College Dublin; Dublin Ireland
- Department of Community Medicine; College of Health Sciences; University of Zimbabwe; Harare Zimbabwe
| | - JA O'Halloran
- Department of Infectious Diseases; Mater Misericordiae University Hospital; Dublin Ireland
| | - RM O'Halloran
- Department of Infectious Diseases; Mater Misericordiae University Hospital; Dublin Ireland
| | - A Macken
- HIV Molecular Research Group; School of Medicine and Medical Science; University College Dublin; Dublin Ireland
| | - JS Lambert
- Department of Infectious Diseases; Mater Misericordiae University Hospital; Dublin Ireland
| | - GJ Sheehan
- Department of Infectious Diseases; Mater Misericordiae University Hospital; Dublin Ireland
| | - PWG Mallon
- HIV Molecular Research Group; School of Medicine and Medical Science; University College Dublin; Dublin Ireland
- Department of Infectious Diseases; Mater Misericordiae University Hospital; Dublin Ireland
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16
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Xue W, Ban Y, Liu H, Yao X. Computational study on the drug resistance mechanism against HCV NS3/4A protease inhibitors vaniprevir and MK-5172 by the combination use of molecular dynamics simulation, residue interaction network, and substrate envelope analysis. J Chem Inf Model 2013; 54:621-33. [PMID: 23745769 DOI: 10.1021/ci400060j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hepatitis C virus (HCV) NS3/4A protease is an important and attractive target for anti-HCV drug development and discovery. Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease. However, the emergence of resistance to these two inhibitors reduced the effectiveness of vaniprevir and MK-5172 against viral replication. Among the drug resistance mutations, three single-site mutations at residues Arg155, Ala156, and Asp168 in NS3/4A protease are especially important due to their resistance to nearly all inhibitors in clinical development. A detailed understanding of drug resistance mechanism to vaniprevir and MK-5172 is therefore very crucial for the design of novel potent agents targeting viral variants. In this work, molecular dynamics (MD) simulation, binding free energy calculation, free energy decomposition, residue interaction network (RIN), and substrate envelope analysis were used to study the detailed drug resistance mechanism of the three mutants R155K, A156T, and D168A to vaniprevir and MK-5172. MD simulation was used to investigate the binding mode for these two inhibitors to wild-type and resistant mutants of HCV NS3/4A protease. Binding free energy calculation and free energy decomposition analysis reveal that drug resistance mutations reduced the interactions between the active site residues and substituent in the P2 to P4 linker of vaniprevir and MK-5172. Furthermore, RIN and substrate envelope analysis indicate that the studied mutations of the residues are located outside the substrate (4B5A) binding site and selectively decrease the affinity of inhibitors but not the activity of the enzyme and consequently help NS3/4A protease escape from the effect of the inhibitors without influencing the affinity of substrate binding. These findings can provide useful information for understanding the drug resistance mechanism against vaniprevir and MK-5172. The results can also provide some potential clues for further design of novel inhibitors that are less susceptible to drug resistance.
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Affiliation(s)
- Weiwei Xue
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
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17
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State-of-the-art and dissemination of computational tools for drug-design purposes: a survey among Italian academics and industrial institutions. Future Med Chem 2013; 5:907-27. [PMID: 23682568 DOI: 10.4155/fmc.13.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During the first edition of the Computationally Driven Drug Discovery meeting, held in November 2011 at Dompé Pharma (L'Aquila, Italy), a questionnaire regarding the diffusion and the use of computational tools for drug-design purposes in both academia and industry was distributed among all participants. This is a follow-up of a previously reported investigation carried out among a few companies in 2007. The new questionnaire implemented five sections dedicated to: research group identification and classification; 18 different computational techniques; software information; hardware data; and economical business considerations. In this article, together with a detailed history of the different computational methods, a statistical analysis of the survey results that enabled the identification of the prevalent computational techniques adopted in drug-design projects is reported and a profile of the computational medicinal chemist currently working in academia and pharmaceutical companies in Italy is highlighted.
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18
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Srivastava HK, Sastry GN. Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches. J Chem Inf Model 2012; 52:3088-98. [PMID: 23121465 DOI: 10.1021/ci300385h] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The binding free energies (ΔG(Bind)) obtained from molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface area (MM-GBSA) calculations using molecular dynamics (MD) trajectories are the most popular procedures to measure the strength of interactions between a ligand and its receptor. Several attempts have been made to correlate the ΔG(Bind) and experimental IC(50) values in order to observe the relationship between binding strength of a ligand (with its receptor) and its inhibitory activity. The duration of MD simulations seems very important for getting acceptable correlation. Here, we are presenting a systematic study to estimate the reasonable MD simulation time for acceptable correlation between ΔG(Bind) and experimental IC(50) values. A comparison between MM-PBSA and MM-GBSA approaches is also presented at various time scales. MD simulations (10 ns) for 14 HIV protease inhibitors have been carried out by using the Amber program. MM-PBSA/GBSA based ΔG(Bind) have been calculated and correlated with experimental IC(50) values at different time scales (0-1 to 0-10 ns). This study clearly demonstrates that the MM-PBSA based ΔG(Bind) (ΔG(Bind)-PB) values provide very good correlation with experimental IC(50) values (quantitative and qualitative) when MD simulation is carried out for a longer time; however, MM-GBSA based ΔG(Bind) (ΔG(Bind)-GB) values show acceptable correlation for shorter time of simulation also. The accuracy of ΔG(Bind)-PB increases and ΔG(Bind)-GB remains almost constant with the increasing time of simulation.
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Affiliation(s)
- Hemant Kumar Srivastava
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India
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19
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Meher BR, Wang Y. Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism. J Mol Graph Model 2012; 38:430-45. [PMID: 23142620 DOI: 10.1016/j.jmgm.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/31/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
Abstract
Most of the currently treated HIV-1 protease (HIV-PR) inhibitors have been prone to suffer from the mutations associated drug resistance. Therefore, it is necessary to search for potent alternatives against the drug resistance. In the current study we have tested the single-walled carbon nanotube (SWCNT) as an inhibitor in wild type (WT) as well as in three primary mutants (I50V(PR), V82A(PR) and I84V(PR)) of the HIV-1-PR through docking the SWCNT in the active site region, and then performed all-atom MD simulations for the complexes. The conformational dynamics of HIV-PR with a 20 ns trajectory reveals that the SWCNT can effectively bind to the HIV-1-PR active site and regulate the flap dynamics such as maintaining the flap-flap closed. To gain an insight into the binding affinity, we also performed the MM-PBSA based binding free energy calculations for the four HIV-PR/SWCNT complexes. It was observed that, although the binding between the SWCNT and the HIV-PR decreases due to the mutations, the SWCNTs bind to the HIV-PRs 3-5 folds stronger than the most potent HIV-1-PR inhibitor, TMC114. Remarkably, the significant interactions with binding energy higher than 1kcal/mol focus on the flap and active regions, which favors closing flap-flap and deactivating the active residues of the HIV-PR. The flap dynamics and binding strength information for HIV-PR and SWCNTs can help design SWCNT-based HIV-1-PR inhibitors.
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Affiliation(s)
- Biswa Ranjan Meher
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA
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20
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Beier C, Zacharias M. Tackling the challenges posed by target flexibility in drug design. Expert Opin Drug Discov 2012; 5:347-59. [PMID: 22823087 DOI: 10.1517/17460441003713462] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD Current computational docking methods are often effective in predicting accurate drug-binding geometries in cases of relatively rigid target structures. However, binding of drug-like ligands to protein receptor molecules frequently involves or even requires conformational adaptation. Realistic prediction of ligand-receptor binding geometries and complex stability needs in many cases an appropriate inclusion of conformational changes, not only for the ligand, but also for the receptor molecule. AREAS COVERED IN THIS REVIEW Recent approaches to efficiently account for target receptor flexibility during docking simulations are reviewed. WHAT THE READER WILL GAIN The reader will gain insights into methods to efficiently treat protein side-chain flexibility and approaches for continuous adaptation of backbone conformations in pre-calculated essential or soft collective degrees of freedom. In addition, molecular dynamics or Monte Carlo based methods providing simultaneous inclusion of receptor and ligand flexibility are discussed as well as promising new developments to generate conformationally diverse ensembles of a protein structure. The large variety of possible conformational changes in proteins on ligand binding is illustrated for the enzyme reverse transcriptase of HIV-1, which is an important drug target. TAKE HOME MESSAGE If the backbone conformation of the binding site does not change, current docking programs can perform well by taking side-chain reorientations into account only. Future progress to account for full target flexibility in docking requires both accurate prediction of the essential modes of backbone motion and improvements in scoring to enhance selectivity. Thus, the scoring function should realistically cover energetic and particularly entropic contributions to binding, which would allow more realistic estimates of binding free energies.
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Affiliation(s)
- Christian Beier
- Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, D-28759 Bremen, Germany
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21
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Wright DW, Wan S, Shublaq N, Zasada SJ, Coveney PV. From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:585-98. [PMID: 22899636 DOI: 10.1002/wsbm.1186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the promises made that genomic sequencing would transform therapy by introducing a new era of personalized medicine, relatively few tangible breakthroughs have been made. This has led to the recognition that complex interactions at multiple spatial, temporal, and organizational levels may often combine to produce disease. Understanding this complexity requires that existing and future models are used and interpreted within a framework that incorporates knowledge derived from investigations at multiple levels of biological function. It also requires a computational infrastructure capable of dealing with the vast quantities of data generated by genomic approaches. In this review, we discuss the use of molecular modeling to generate quantitative and qualitative insights at the smallest scales of the systems biology hierarchy, how it can play an important role in the development of a systems understanding of disease and in the application of such knowledge to help discover new therapies and target existing ones on a personal level.
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Affiliation(s)
- David W Wright
- Centre for Computational Science, University College London, London, UK
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22
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Yang Y, Shen Y, Li S, Jin N, Liu H, Yao X. Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity. MOLECULAR BIOSYSTEMS 2012; 8:3049-60. [DOI: 10.1039/c2mb25217a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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23
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Wiesmann F, Vachta J, Ehret R, Walter H, Kaiser R, Stürmer M, Tappe A, Däumer M, Berg T, Naeth G, Braun P, Knechten H. The L76V mutation in HIV-1 protease is potentially associated with hypersusceptibility to protease inhibitors Atazanavir and Saquinavir: is there a clinical advantage? AIDS Res Ther 2011; 8:7. [PMID: 21314993 PMCID: PMC3049128 DOI: 10.1186/1742-6405-8-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 02/13/2011] [Indexed: 11/15/2022] Open
Abstract
Background Although being considered as a rarely observed HIV-1 protease mutation in clinical isolates, the L76V-prevalence increased 1998-2008 in some European countries most likely due to the approval of Lopinavir, Amprenavir and Darunavir which can select L76V. Beside an enhancement of resistance, L76V is also discussed to confer hypersusceptibility to the drugs Atazanavir and Saquinavir which might enable new treatment strategies by trying to take advantage of particular mutations. Results Based on a cohort of 47 L76V-positive patients, we examined if there might exist a clinical advantage for L76V-positive patients concerning long-term success of PI-containing regimens in patients with limited therapy options. Genotypic- and phenotypic HIV-resistance tests from 47 mostly multi-resistant, L76V-positive patients throughout Germany were accomplished retrospectively 1999-2009. Five genotype-based drug-susceptibility predictions received from online interpretation-tools for Atazanavir, Saquinavir, Amprenavir and Lopinavir, were compared to phenotype-based predictions that were determined by using a recombinant virus assay along with a Virtual Phenotype™(Virco). The clinical outcome of the L76V-adapted follow-up therapy was determined by monitoring viral load for 96 weeks. Conclusions In this analysis, the mostly used interpretation systems overestimated the L76V-mutation concerning Atazanavir- and SQV resistance. In fact, a clear benefit in drug susceptibility for these drugs was observed in phenotype analysis after establishment of L76V. More importantly, long-term therapy success was significantly higher in patients receiving Atazanavir and/or Saquinavir plus one L76V-selecting drug compared to patients without L76V-selecting agents (p = 0.002). In case of L76V-occurrence ATV and/or SQV may represent encouraging options for patients in deep salvage situations.
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A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network. J Mol Model 2011; 17:2693-705. [PMID: 21279524 DOI: 10.1007/s00894-011-0971-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 01/11/2011] [Indexed: 12/14/2022]
Abstract
The two retroviruses human T-lymphotropic virus type I (HTLV-I) and human immunodeficiency virus type 1 (HIV-1) are the causative agents of severe and fatal diseases including adult T-cell leukemia and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease that is essential for replication and therefore represents a key target for drugs interfering with viral infection. The retroviral proteases from HIV-1 and HTLV-I share 31% sequence identity and high structural similarities. Yet, their substrate specificities and inhibition profiles differ substantially. In this study, we performed all-atom molecular dynamics (MD) simulations for both enzymes in their ligand-free states and in complex with model substrates in order to compare their dynamic behaviors and enhance our understanding of the correlation between sequence, structure, and dynamics in this protein family. We found extensive similarities in both local and overall protein dynamics, as well as in the energetics of their interactions with model substrates. Interestingly, those residues that are important for strong ligand binding are frequently not conserved in sequence, thereby offering an explanation for the differences in binding specificity. Moreover, we identified an interaction network of contacts between conserved residues that interconnects secondary structure elements and serves as a scaffold for the protein fold. This interaction network is conformationally stable over time and may provide an explanation for the highly similar dynamic behavior of the two retroviral proteases, even in the light of their rather low overall sequence identity.
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25
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Investigating the structural basis of arylamides to improve potency against M. tuberculosis strain through molecular dynamics simulations. Eur J Med Chem 2010; 45:5585-93. [DOI: 10.1016/j.ejmech.2010.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/13/2010] [Accepted: 09/04/2010] [Indexed: 11/18/2022]
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