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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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Rahman SU, Ali HS, Jafari B, Zaib S, Hameed A, Al-Kahraman YMSA, Langer P, Iqbal J. Structure-based virtual screening of dipeptidyl peptidase 4 inhibitors and their in vitro analysis. Comput Biol Chem 2020; 91:107326. [PMID: 32739275 DOI: 10.1016/j.compbiolchem.2020.107326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 10/24/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is one of the most widely prevalent metabolic disorders with no cure to date thus remains the most challenging task in the current drug discovery. Therefore, the only strategy to control diabetes prevalence is to develop novel efficacious therapeutics. Dipeptidyl Peptidase 4 (DPP-4) inhibitors are currently used as anti-diabetic drugs for the inhibition of incretins. This study aims to construct the chemical feature based on pharmacophore models for dipeptidyl peptidase IV. The structure-based pharmacophore modeling has been employed to evaluate new inhibitors of DPP-4. A four-featured pharmacophore model was developed from crystal structure of DPP-4 enzyme with 4-(2-aminoethyl) benzenesulfonyl fluoride in its active site via pharmacophore constructing tool of Molecular Operating Environment (MOE) consisting F1 Hyd (hydrophobic region), F2 Hyd|Cat|Don (hydrophobic cationic and donor region), F3 Acc (acceptor region) and F4 Hyd (hydrophobic region). The generated pharmacophore model was used for virtual screening of in-house compound library (the available compounds which were used for initial screening to get the few compounds for the current studies). The resultant selected compounds, after virtual screening were further validated using in vitro assay. Furthermore, structure-activity relationship was carried out for the compounds possessing significant inhibition potential after docking studies. The binding free energy of analogs was evaluated via molecular mechanics generalized Born surface area (MM-GBSA) and Poisson-Boltzmann surface area (MM-PBSA) methods using AMBER 16 as a molecular dynamics (MD) simulation package. Based on potential findings, we report that selected candidates are more likely to be used as DPP-4 inhibitors or as starting leads for the development of novel and potent DPP-4 inhibitors.
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Affiliation(s)
- Shafiq Ur Rahman
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Hafiz Saqib Ali
- Department of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Behzad Jafari
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Sumera Zaib
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Abdul Hameed
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Yasser M S A Al-Kahraman
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Peter Langer
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany; Leibniz Institut für Katalyse an der Universität Rostock e.V. (LIKAT), Albert-Einstein-Str. 29a, 18059 Rostock, Germany
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
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3
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Yeo J, Jung G, Tarakanova A, Martín-Martínez FJ, Qin Z, Cheng Y, Zhang YW, Buehler MJ. Multiscale modeling of keratin, collagen, elastin and related human diseases: Perspectives from atomistic to coarse-grained molecular dynamics simulations. EXTREME MECHANICS LETTERS 2018; 20:112-124. [PMID: 33344740 PMCID: PMC7745951 DOI: 10.1016/j.eml.2018.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Scleroproteins are an important category of proteins within the human body that adopt filamentous, elongated conformations in contrast with typical globular proteins. These include keratin, collagen, and elastin, which often serve a common mechanical function in structural support of cells and tissues. Genetic mutations alter these proteins, disrupting their functions and causing diseases. Computational characterization of these mutations has proven to be extremely valuable in identifying the intricate structure-function relationships of scleroproteins from the molecular scale up, especially if combined with multiscale experimental analysis and the synthesis of model proteins to test specific structure-function relationships. In this work, we review numerous critical diseases that are related to keratin, collagen, and elastin, and through several case studies, we propose ways of extensively utilizing multiscale modeling, from atomistic to coarse-grained molecular dynamics simulations, to uncover the molecular origins for some of these diseases and to aid in the development of novel cures and therapies. As case studies, we examine the effects of the genetic disease Epidermolytic Hyperkeratosis (EHK) on the structure and aggregation of keratins 1 and 10; we propose models to understand the diseases of Osteogenesis Imperfecta (OI) and Alport syndrome (AS) that affect the mechanical and aggregation properties of collagen; and we develop atomistic molecular dynamics and elastic network models of elastin to determine the role of mutations in diseases such as Cutis Laxa and Supravalvular Aortic Stenosis on elastin's structure and molecular conformational motions and implications for assembly.
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Affiliation(s)
- Jingjie Yeo
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - GangSeob Jung
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francisco J. Martín-Martínez
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuan Cheng
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Yong-Wei Zhang
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore 138632
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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Huang YMM, Raymundo MAV, Chen W, Chang CEA. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease. Biochemistry 2017; 56:1311-1323. [PMID: 28060481 DOI: 10.1021/acs.biochem.6b01112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Equilibrium constants, together with kinetic rate constants of binding, are key factors in the efficacy and safety of drug compounds, informing drug design. However, the association pathways of protein-ligand binding, which contribute to their kinetic behaviors, are little understood. In this work, we used unbiased all-atom molecular dynamics (MD) simulations with an explicit solvent model to study the association processes of protein-ligand binding. Using the HIV protease (HIVp)-xk263 and HIVp-ritonavir protein-ligand systems as cases, we observed that ligand association is a multistep process involving diffusion, localization, and conformational rearrangements of the protein, ligand, and water molecules. Moreover, these two ligands preferred different routes of binding, which reflect two well-known binding mechanisms: induced-fit and conformation selection models. Our study shows that xk263 has a stronger capacity for desolvating surrounding water molecules, thereby inducing a semiopen conformation of the HIVp flaps (induced-fit model). In contrast, the slow dehydration characteristic of ritonavir allows for gradual association with the binding pocket of HIVp when the protein's flap conformation is fully open (conformation selection model). By studying the mechanism of ligand association and understanding the role of solvent molecules during the binding event, we can obtain a different perspective on the mechanism of macromolecule recognition, providing insights into drug discovery.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Mark Anthony V Raymundo
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Wei Chen
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States.,ChemConsulting LLC , Frederick, Maryland 21704, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
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5
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Meng XM, Hu WJ, Mu YG, Sheng XH. Effect of allosteric molecules on structure and drug affinity of HIV-1 protease by molecular dynamics simulations. J Mol Graph Model 2016; 70:153-162. [PMID: 27723563 DOI: 10.1016/j.jmgm.2016.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 11/16/2022]
Abstract
Recent experiments show that small molecules can bind onto the allosteric sites of HIV-1 protease (PR), which provides a starting point for developing allosteric inhibitors. However, the knowledge of the effect of such binding on the structural dynamics and binding free energy of the active site inhibitor and PR is still lacking. Here, we report 200ns long molecular dynamics simulation results to gain insight into the influences of two allosteric molecules (1H-indole-6-carboxylic acid, 1F1 and 2-methylcyclohexano, 4D9). The simulations demonstrate that both allosteric molecules change the PR conformation and stabilize the structures of PR and the inhibitor; the residues of the flaps are sensitive to the allosteric molecules and the flexibility of the residues is pronouncedly suppressed; the additions of the small molecules to the allosteric sites strengthen the binding affinities of 3TL-PR by about 12-15kal/mol in the binding free energy, which mainly arises from electrostatic term. Interestingly, it is found that the action mechanisms of 1F1 and 4D9 are different, the former behaviors like a doorman that keeps the inhibitor from escape and makes the flaps (door) partially open; the latter is like a wedge that expands the allosteric space and meanwhile closes the flaps. Our data provide a theoretical support for designing the allosteric inhibitor.
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Affiliation(s)
- Xian-Mei Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Wei-Jun Hu
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
| | - Yu-Guang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 639815, Singapore.
| | - Xie-Huang Sheng
- School of Chemistry, Shandong Normal University, Jinan 250014, China
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6
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Persico M, Di Dato A, Orteca N, Cimino P, Novellino E, Fattorusso C. Use of Integrated Computational Approaches in the Search for New Therapeutic Agents. Mol Inform 2016; 35:309-25. [DOI: 10.1002/minf.201501028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Marco Persico
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Antonio Di Dato
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Nausicaa Orteca
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Paola Cimino
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano, Salerno Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
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7
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Kumar R, Gupta D. Identification of CYP1B1-specific candidate inhibitors using combination ofin silicoscreening, integrated knowledge-based filtering, and molecular dynamics simulations. Chem Biol Drug Des 2016; 88:730-739. [DOI: 10.1111/cbdd.12803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/09/2016] [Accepted: 06/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Rakesh Kumar
- Translational Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); New Delhi Delhi India
| | - Dinesh Gupta
- Translational Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); New Delhi Delhi India
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8
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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9
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Huang YMM, Kang M, Chang CEA. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J Mol Recognit 2015; 27:537-48. [PMID: 25042708 DOI: 10.1002/jmr.2377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/05/2022]
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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10
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Chuang YC, Chang CH, Lin JT, Yang CN. Molecular modelling studies of sirtuin 2 inhibitors using three-dimensional structure-activity relationship analysis and molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2014; 11:723-33. [PMID: 25502412 DOI: 10.1039/c4mb00620h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sirtuin 2 (SIRT2) is a nicotinamide-adenine-dinucleotide-dependent histone deacetylase that plays a vital role in various biological processes related to DNA regulation, metabolism, and longevity. Recent studies on SIRT2 have indicated its therapeutic potential for neurodegenerative diseases such as Parkinson's disease. In this study, a series of SIRT2 inhibitors with a 2-anilinobenzamide core was analysed using a combination of molecular modelling techniques. A three-dimensional structure-activity relationship (3D-QSAR) model adopting a comparative molecular field analysis (CoMFA) method with a non-cross-validated correlation coefficient R(2) = 0.992 (for training set) and a correlation coefficient Rtest(2) = 0.804 (for test set) was generated to determine the structural requirements for inhibitory activity. Furthermore, we employed molecular dynamics (MD) simulations and the molecular mechanics/generalized Born surface area (MM/GBSA) method to compare the binding modes of a potent and selective compound interacting with SIRT1, SIRT2, and SIRT3 and also their binding free energies to shed light on the selectivity of the footing of structural and energetic investigations. The steric and electrostatic contour maps from the 3D-QSAR analysis identified several key interactions also observed in the MD simulations. According to these results, we provide guidelines for developing novel potent and selective SIRT2 inhibitors.
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Affiliation(s)
- Yu-Chung Chuang
- Department of Life Sciences, National University of Kaohsiung, 700, Kaohsiung University Road, Nan-Tzu District 811, Kaohsiung, Taiwan.
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11
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Sokkar P, Choi SM, Rhee YM. Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems. J Chem Theory Comput 2013; 9:3728-39. [DOI: 10.1021/ct400091a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pandian Sokkar
- Center for
Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
| | - Sun Mi Choi
- Center for
Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784,
Korea
| | - Young Min Rhee
- Center for
Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784,
Korea
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12
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Chang HW, Chung FS, Yang CN. Molecular modeling of p38α mitogen-activated protein kinase inhibitors through 3D-QSAR and molecular dynamics simulations. J Chem Inf Model 2013; 53:1775-86. [PMID: 23808966 DOI: 10.1021/ci4000085] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The p38 mitogen-activated protein kinase (MAPK) signaling pathway plays an essential role in inflammation and other physiological processes. Because specific inhibitors of p38α and p38β MAPK block the production of the major inflammatory cytokines and other proteins, p38α and p38β MAPK represent promising targets for the treatment of inflammation. In this work, a series of p38α inhibitors based on the structural scaffold of 4-benzoyl-5-aminopyrazole were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for p38 MAPK inhibition. Furthermore, we employed molecular dynamics (MD) simulations and the MM/GBSA method to compare the binding modes and binding free energies of a potent and selective compound interacting with p38α, p38β, p38γ, and p38δ MAPK in detail. Contour maps generated via 3D-QSAR analysis identified several key interactions that were also indicated through MD simulations. The binding free energies calculated via the MM/GBSA method were strongly correlated with experimentally observed biological activities and explained the selective inhibition of p38α and p38β, but not p38γ and p38δ detected here. On the basis of the obtained results, we provide insights regarding the development of novel potent p38α MAPK inhibitors.
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Affiliation(s)
- Hsin-Wen Chang
- Institute of Biotechnology, National University of Kaohsiung, Taiwan
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13
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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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14
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Oehme DP, Brownlee RTC, Wilson DJD. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease. J Comput Chem 2012; 33:2566-80. [DOI: 10.1002/jcc.23095] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/27/2012] [Accepted: 07/25/2012] [Indexed: 11/05/2022]
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15
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Li D, Liu MS, Ji B, Hwang KC, Huang Y. Identifying the molecular mechanics and binding dynamics characteristics of potent inhibitors to HIV-1 protease. Chem Biol Drug Des 2012; 80:440-54. [PMID: 22621379 DOI: 10.1111/j.1747-0285.2012.01417.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the primary inhibition targets for chemotherapy of AIDS because of its critical role in the replication cycle of the HIV. In this work, a combinatory coarse-grained and atomistic simulation method was developed for dissecting molecular mechanisms and binding process of inhibitors to the active site of HIV-1 PR, in which 35 typical inhibitors were trialed. We found that the molecular size and stiffness of the inhibitors and the binding energy between the inhibitors and PR play important roles in regulating the binding process. Comparatively, the smaller and more flexible inhibitors have larger binding energy and higher binding rates; they even bind into PR without opening the flaps. In contrast, the larger and stiffer inhibitors have lower binding energy and lower binding rate, and their binding is subjected to the opening and gating of the PR flaps. Furthermore, the components of binding free energy were quantified and analyzed by their dependence on the molecular size, structures, and hydrogen bond networks of inhibitors. Our results also deduce significant dynamics descriptors for determining the quantitative structure and property relationship in potent drug ligands for HIV-1 PR inhibition.
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Affiliation(s)
- Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, China
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16
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Mao Y. Dynamical basis for drug resistance of HIV-1 protease. BMC STRUCTURAL BIOLOGY 2011; 11:31. [PMID: 21740562 PMCID: PMC3149572 DOI: 10.1186/1472-6807-11-31] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 07/08/2011] [Indexed: 11/30/2022]
Abstract
Background Protease inhibitors designed to bind to protease have become major anti-AIDS drugs. Unfortunately, the emergence of viral mutations severely limits the long-term efficiency of the inhibitors. The resistance mechanism of these diversely located mutations remains unclear. Results Here I use an elastic network model to probe the connection between the global dynamics of HIV-1 protease and the structural distribution of drug-resistance mutations. The models for study are the crystal structures of unbounded and bound (with the substrate and nine FDA approved inhibitors) forms of HIV-1 protease. Coarse-grained modeling uncovers two groups that couple either with the active site or the flap. These two groups constitute a majority of the drug-resistance residues. In addition, the significance of residues is found to be correlated with their dynamical changes in binding and the results agree well with the complete mutagenesis experiment of HIV-1 protease. Conclusions The dynamic study of HIV-1 protease elucidates the functional importance of common drug-resistance mutations and suggests a unifying mechanism for drug-resistance residues based on their dynamical properties. The results support the robustness of the elastic network model as a potential predictive tool for drug resistance.
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Affiliation(s)
- Yi Mao
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN 37996, USA.
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Deng NJ, Zheng W, Gallicchio E, Levy RM. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc 2011; 133:9387-94. [PMID: 21561098 DOI: 10.1021/ja2008032] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding. We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR. To overcome the time scale limitation of conventional molecular dynamics (MD) simulations, our method combines replica exchange MD with transition path theory (TPT) to study the diversity and temperature dependence of the pathways connecting functionally important states of the protease. At low temperatures the large-scale flap opening is dominated by a small number of paths; at elevated temperatures the transition occurs through many structurally heterogeneous routes. The expanded conformation in the crystal structure 1TW7 is found to closely mimic a key intermediate in the flap-opening pathways at low temperature. We investigated the different transition mechanisms between the semi-open and closed forms. The calculated relaxation times reveal fast semi-open ↔ closed transitions, and infrequently the flaps fully open. The ligand binding rate predicted from this kinetic model increases by 38-fold from 285 to 309 K, which is in general agreement with experiments. To our knowledge, this is the first application of a network model constructed from atomistic simulations together with TPT to analyze conformational changes between different functional states of a natively folded protein.
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Affiliation(s)
- Nan-jie Deng
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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Li D, Ji B, Hwang KC, Huang Y. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket. PLoS One 2011; 6:e19268. [PMID: 21559397 PMCID: PMC3084818 DOI: 10.1371/journal.pone.0019268] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.
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Affiliation(s)
- Dechang Li
- School of Aerospace, Department of Engineering Mechanics, Tsinghua University, Beijing, China
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19
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Peters MH. Langevin dynamics for the transport of flexible biological macromolecules in confined geometries. J Chem Phys 2011; 134:025105. [DOI: 10.1063/1.3525381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pandey RB, Farmer BL. Globular structure of a human immunodeficiency virus-1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation. J Chem Phys 2010; 132:125101. [PMID: 20370150 DOI: 10.1063/1.3358340] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.
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Affiliation(s)
- R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406-5046, USA.
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21
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Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: atomistic and coarse-grained simulations. J Mol Graph Model 2010; 29:171-7. [PMID: 20580296 DOI: 10.1016/j.jmgm.2010.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 05/20/2010] [Accepted: 05/20/2010] [Indexed: 11/24/2022]
Abstract
Nanoparticles such as fullerenes and carbon nanotubes have been extensively studied for biomedical applications. In this paper, we report the design of carbon nanotubes as HIV-1 protease inhibitors. Docking and molecular dynamics calculations are performed using an atomistic model to explore the optimal interaction structure and free energy between the nanotube and HIV-1 protease. A coarse-grained model is then developed based on the atomistic model, allowing us to investigate the dynamic behaviors of the protease in the bound and unbound states. The dynamic process reveals that the carbon nanotube is able to bind to the active site of the protease and prevent the active flaps from opening up, thus blocking the function of the protease. This process is strongly influenced by the size of the nanotube. The binding of carbon nanotubes to an alternative binding site other than the active site is also explored. Therefore, carbon nanotube-based inhibitors have great potential for application as HIV-1 protease inhibitors.
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Li D, Ji B, Hwang K, Huang Y. Crucial roles of the subnanosecond local dynamics of the flap tips in the global conformational changes of HIV-1 protease. J Phys Chem B 2010; 114:3060-9. [PMID: 20143801 DOI: 10.1021/jp1005549] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To understand the underlying mechanisms of the open and closed conformational change of HIV-1 protease (HIV-1 PR) at multiple time scales, we performed serial fully unrestrained, extremely long time molecular dynamics simulations with an explicit solvent model. Spontaneous semiopen to closed conformational transition and inhibitor-collision-induced opening of the flaps were simulated in a real time scale. We found that the rapid, local subnanosecond fluctuations of the flap tips might be the mechanisms triggering the global open and close conformational transitions at the 100-ns time scale. The subnanosecond fluctuation is induced by the Phi-Psi rotations of the residues at the flap tips, mainly Psi of Gly49 and Phi of Ile50, disturbing the interactions between the two tips and then their stability. We further showed that the water molecule W301 is helpful for the stability of the PR-inhibitor complex by acting as a collision buffer for the dynamic interaction between flap tips and the inhibitor. These results might help gain a better insight into the dynamics of HIV-1 PR, especially the local dynamics of the flap tips, which may provide important guidelines for design of novel potent inhibitors.
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Affiliation(s)
- Dechang Li
- Department of Engineering Mechanics, School of Aerospace, Tsinghua University, Beijing 100084, China
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