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Panda SK, Saxena S, Guruprasad L. Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III. J Biomol Struct Dyn 2019; 38:1887-1902. [PMID: 31179839 DOI: 10.1080/07391102.2019.1624296] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative opportunistic pathogen commonly associated with hospital-acquired infections that are often resistant even to antibiotics. Heptosyltransferase (HEP) belongs to the family of glycosyltransferase-B (GT-B) and plays an important in the synthesis of lipopolysaccharides (LPS) essential for the formation of bacterial cell membrane. HEP-III participates in the transfer of heptose sugar to the outer surface of bacteria to synthesize LPS. LPS truncation increases the bacterial sensitivity to hydrophobic antibiotics and detergents, making the HEP as a novel drug target. In the present study, we report the 3D homology model of K. pneumoniae HEP-III and its structure validation. Active site was identified based on similarities with known structures using Dali server, and structure-based pharmacophore model was developed for the active site substrate ADP. The generated pharmacophore model was used as a 3D search query for virtual screening of the ASINEX database. The hit compounds were further filtered based on fit value, molecular docking, docking scores, molecular dynamics (MD) simulations of HEP-III complexed with hit molecules, followed by binding free energy calculations using Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA). The insights obtained in this work provide the rationale for design of novel inhibitors targeting K. pneumoniae HEP-III and the mechanistic aspects of their binding. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Shalini Saxena
- School of Chemistry, University of Hyderabad, Hyderabad, India
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Pandey P, Lynn AM, Bandyopadhyay P. Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach. Bioinformation 2017; 13:144-148. [PMID: 28690380 PMCID: PMC5498780 DOI: 10.6026/97320630013144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/23/2022] Open
Abstract
α-Isopropylmalate Synthase (α-IPMS) encoded by leuA in Mycobacterium tuberculosis (M.tb) is involved in the leucine biosynthesis pathway and is extremely critical for the synthesis of branched-chain amino acids (leucine, isoleucine and valine). α-IPMS activity is required not only for the proliferation of M.tb but is also indispensable for its survival during the latent phase of infection. It is absent in humans and is widely regarded as one of the validated drug targets against Tuberculosis (TB). Despite its essentiality, any study on designing of potential chemical inhibitors against α-IPMS has not been reported so far. In the present study, in silico identification of putative inhibitors against α-IPMS exploring three chemical databases i.e. NCI, DrugBank and ChEMBL is reported through structurebased drug design and filtering of ligands based on the pharmacophore feature of the actives. In the absence of experimental results of any inhibitor against α-IPMS, a stringent validation of docking results is done by comparing with molecular mechanics/Poisson- Boltzmann surface area (MM/PBSA) calculations by investigating two more proteins for which experimental results are known.
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Affiliation(s)
- Preeti Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067
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Abstract
It has long been reported that Mycobacterium tuberculosis is capable of synthesizing the α-glucan glycogen. However, what makes this bacterium stand out is that it coats itself in a capsule that mainly consists of a glycogen-like α-glucan. This polymer helps the pathogen evade immune responses. In 2010, the biosynthesis of α-glucans has been shown to not only involve the classical enzymes of glycogen metabolism but also a distinct GlgE pathway. Since then, this pathway has attracted attention not least in terms of the quest for new inhibitors that could be developed into new treatments for tuberculosis. Some lines of recent inquiry have shed a lot of light on to how GlgE catalyses the polymerization of α-glucan, using α-maltose 1-phosphate (M1P) as a building block and how the pathways are regulated. Nevertheless, many unanswered questions remain regarding the synthesis and role of α-glucans in mycobacteria and the numerous other bacteria that possess the GlgE pathway.
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Syson K, Stevenson CEM, Miah F, Barclay JE, Tang M, Gorelik A, Rashid AM, Lawson DM, Bornemann S. Ligand-bound Structures and Site-directed Mutagenesis Identify the Acceptor and Secondary Binding Sites of Streptomyces coelicolor Maltosyltransferase GlgE. J Biol Chem 2016; 291:21531-21540. [PMID: 27531751 PMCID: PMC5076824 DOI: 10.1074/jbc.m116.748160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
GlgE is a maltosyltransferase involved in α-glucan biosynthesis in bacteria that has been genetically validated as a target for tuberculosis therapies. Crystals of the Mycobacterium tuberculosis enzyme diffract at low resolution so most structural studies have been with the very similar Streptomyces coelicolor GlgE isoform 1. Although the donor binding site for α-maltose 1-phosphate had been previously structurally defined, the acceptor site had not. Using mutagenesis, kinetics, and protein crystallography of the S. coelicolor enzyme, we have now identified the +1 to +6 subsites of the acceptor/product, which overlap with the known cyclodextrin binding site. The sugar residues in the acceptor subsites +1 to +5 are oriented such that they disfavor the binding of malto-oligosaccharides that bear branches at their 6-positions, consistent with the known acceptor chain specificity of GlgE. A secondary binding site remote from the catalytic center was identified that is distinct from one reported for the M. tuberculosis enzyme. This new site is capable of binding a branched α-glucan and is most likely involved in guiding acceptors toward the donor site because its disruption kinetically compromises the ability of GlgE to extend polymeric substrates. However, disruption of this site, which is conserved in the Streptomyces venezuelae GlgE enzyme, did not affect the growth of S. venezuelae or the structure of the polymeric product. The acceptor subsites +1 to +4 in the S. coelicolor enzyme are well conserved in the M. tuberculosis enzyme so their identification could help inform the design of inhibitors with therapeutic potential.
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Affiliation(s)
- Karl Syson
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Farzana Miah
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - J Elaine Barclay
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Minhong Tang
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Andrii Gorelik
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abdul M Rashid
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M Lawson
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Stephen Bornemann
- From the Biological Chemistry Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Kumar V, Singh HN, Tomar AK, Dantham S, Yadav S. Searching new targets to counter drug resistance – GTPase-Obg mRNA expression analysis in Mycobacterium under stress and in silico docking with GTPase inhibitors. J Biomol Struct Dyn 2016; 35:1804-1812. [DOI: 10.1080/07391102.2016.1195284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Vikrant Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | | | - Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Subrahamanyam Dantham
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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Sharma V, Wakode S. Structural insight into selective phosphodiesterase 4B inhibitors: pharmacophore-based virtual screening, docking, and molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:1339-1349. [DOI: 10.1080/07391102.2016.1183520] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Vidushi Sharma
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), University of Delhi, Mehrauli-Badarpur Road, Pushp Vihar, Sector-3, New Delhi 110017, India
| | - Sharad Wakode
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), University of Delhi, Mehrauli-Badarpur Road, Pushp Vihar, Sector-3, New Delhi 110017, India
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John A, Sivashanmugam M, Umashankar V, Natarajan SK. Virtual screening, molecular dynamics, and binding free energy calculations on human carbonic anhydrase IX catalytic domain for deciphering potential leads. J Biomol Struct Dyn 2016; 35:2155-2168. [DOI: 10.1080/07391102.2016.1207565] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arun John
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, Tamil Nadu, India
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Muthukumaran Sivashanmugam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, Tamil Nadu, India
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Vetrivel Umashankar
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, Tamil Nadu, India
| | - Sulochana Konerirajapuram Natarajan
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai 600006, Tamil Nadu, India
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Kitaoka M. Diversity of phosphorylases in glycoside hydrolase families. Appl Microbiol Biotechnol 2015; 99:8377-90. [PMID: 26293338 DOI: 10.1007/s00253-015-6927-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/05/2015] [Indexed: 01/02/2023]
Abstract
Phosphorylases are useful catalysts for the practical preparation of various sugars. The number of known specificities was 13 in 2002 and is now 30. The drastic increase in available genome sequences has facilitated the discovery of novel activities. Most of these novel phosphorylase activities have been identified through the investigations of glycoside hydrolase families containing known phosphorylases. Here, the diversity of phosphorylases in each family is described in detail.
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Affiliation(s)
- Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan.
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