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Arfeen M, Patel R, Khan T, Bharatam PV. Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: understanding the factors contributing to selectivity. J Biomol Struct Dyn 2015. [PMID: 26209183 DOI: 10.1080/07391102.2015.1063457] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glycogen synthase kinase-3 is a constitutively acting, multifunctional serine threonine kinase, the role of which has been implicated in several physiological pathways and has emerged as a promising target for the treatment of type-II diabetes and Alzheimer's disease. In order to provide a detailed understanding of the origin of selectivity determinants of ATP competitive inhibitors, molecular dynamics simulations in combination with MM-PBSA binding energy calculations were performed using crystal structures of GSK-3β and CDK-2 in complex with 12 ATP competitive inhibitors. Analysis of energy contributions indicate that electrostatic interaction energy dictates the selectivity of ATP competitive inhibitors against CDK-2. Key interactions as well as residues that potentially make a major contribution to the binding free energy were identified at the ATP binding site. This analysis stresses the need for the inhibitors to interact with Lys85, Thr138, and Arg141 in the binding site of GSK-3β to show selectivity. The residue-wise energy decomposition analysis further suggested the additional role of Gln185 in determining the selectivity of maleimides. The results obtained in this study can be utilized to design new selective GSK-3 ATP competitive inhibitors.
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Affiliation(s)
- Minhajul Arfeen
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Rahul Patel
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Tosif Khan
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Prasad V Bharatam
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
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Silva JRA, Bishai WR, Govender T, Lamichhane G, Maguire GEM, Kruger HG, Lameira J, Alves CN. Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2. J Biomol Struct Dyn 2015; 34:304-17. [PMID: 25762064 DOI: 10.1080/07391102.2015.1029000] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-LdtMt2 - residues 120-408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of Mycobacterium tuberculosis. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.
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Affiliation(s)
- José Rogério A Silva
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
| | - William R Bishai
- b Department of Medicine, Division of Infectious Diseases , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Thavendran Govender
- c Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Gyanu Lamichhane
- c Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- d Taskforce to study Resistance Emergence & Antimicrobial Development Technology , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- d Taskforce to study Resistance Emergence & Antimicrobial Development Technology , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Jeronimo Lameira
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
| | - Cláudio N Alves
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
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Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system. J Comput Aided Mol Des 2013; 27:479-90. [DOI: 10.1007/s10822-013-9657-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 06/02/2013] [Indexed: 01/21/2023]
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