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De Paris R, Vahl Quevedo C, Ruiz DD, Gargano F, de Souza ON. A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model. BMC Bioinformatics 2018; 19:235. [PMID: 29929475 PMCID: PMC6013854 DOI: 10.1186/s12859-018-2222-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/29/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor (FFR) models predict realistic binding energy accurately and improve scoring to enhance selectiveness. At the same time, methods have been proposed to reduce the high computational costs involved in considering the explicit flexibility of proteins in receptor-ligand docking. This study introduces a novel method to optimize ensemble docking-based experiments by reducing the size of an InhA FFR model at docking runtime and scaling docking workflow invocations on cloud virtual machines. RESULTS First, in order to find the most affordable cost-benefit pool of virtual machines, we evaluated the performance of the docking workflow invocations in different configurations of Azure instances. Second, we validated the gains obtained by the proposed method based on the quality of the Reduced Fully-Flexible Receptor (RFFR) models produced using AutoDock4.2. The analyses show that the proposed method reduced the model size by approximately 50% while covering at least 86% of the best docking results from the 74 ligands tested. Third, we tested our novel method using AutoDock Vina, a different docking software, and showed the positive accuracy achieved in the resulting RFFR models. Finally, our results demonstrated that the method proposed optimized ensemble docking experiments and is applicable to different docking software. In addition, it detected new binding modes, which would be unreachable if employing only the rigid structure used to generate the InhA FFR model. CONCLUSIONS Our results showed that the selective method is a valuable strategy for optimizing ensemble docking-based experiments using different docking software. The RFFR models produced by discarding non-promising snapshots from the original model are accurately shaped for a larger number of ligands, and the elapsed time spent in the ensemble docking experiments are considerably reduced.
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Affiliation(s)
- Renata De Paris
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Christian Vahl Quevedo
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Duncan D. Ruiz
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Furia Gargano
- Bioinformatics and Biossystems Modeling and Simulation Lab—LABIO, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 602, Porto Alegre, RS, Brazil
| | - Osmar Norberto de Souza
- Bioinformatics and Biossystems Modeling and Simulation Lab—LABIO, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 602, Porto Alegre, RS, Brazil
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52
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Modi P, Patel S, Chhabria MT. Identification of some novel pyrazolo[1,5-a]pyrimidine derivatives as InhA inhibitors through pharmacophore-based virtual screening and molecular docking. J Biomol Struct Dyn 2018; 37:1736-1749. [PMID: 29663870 DOI: 10.1080/07391102.2018.1465852] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The InhA inhibitors play key role in mycolic acid synthesis by preventing the fatty acid biosynthesis pathway. In this present article, Pharmacophore modelling and molecular docking study followed by in silico virtual screening could be considered as effective strategy to identify newer enoyl-ACP reductase inhibitors. Pyrrolidine carboxamide derivatives were opted to generate pharmacophore models using HypoGen algorithm in Discovery studio 2.1. Further it was employed to screen Zinc and Minimaybridge databases to identify and design newer potent hit molecules. The retrieved newer hits were further evaluated for their drug likeliness and docked against enoyl acyl carrier protein reductase. Here, novel pyrazolo[1,5-a]pyrimidine analogues were designed and synthesized with good yields. Structural elucidation of synthesized final molecules was perform through IR, MASS, 1H-NMR, 13C-NMR spectroscopy and further tested for its in vitro anti-tubercular activity against H37Rv strain using Microplate Alamar blue assay (MABA) method. Most of the synthesized compounds displayed strong anti-tubercular activities. Further, these potent compounds were gauged for MDR-TB, XDR-TB and cytotoxic study.
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Affiliation(s)
- Palmi Modi
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,b Department of Pharmacy , Dharmsinh Desai University , Nadiad 387001 , Gujarat , India
| | - Shivani Patel
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,c Division of Biological and Life Sciences , Ahmedabad University , Ahmedabad 380009 , Gujarat , India
| | - Mahesh T Chhabria
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India
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53
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Prati F, Zuccotto F, Fletcher D, Convery MA, Fernandez‐Menendez R, Bates R, Encinas L, Zeng J, Chung C, De Dios Anton P, Mendoza‐Losana A, Mackenzie C, Green SR, Huggett M, Barros D, Wyatt PG, Ray PC. Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. ChemMedChem 2018; 13:672-677. [PMID: 29399991 PMCID: PMC5915743 DOI: 10.1002/cmdc.201700774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 11/17/2022]
Abstract
Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization.
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Affiliation(s)
- Federica Prati
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Fabio Zuccotto
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Daniel Fletcher
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Maire A. Convery
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Raquel Fernandez‐Menendez
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Robert Bates
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Lourdes Encinas
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Jingkun Zeng
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Chun‐wa Chung
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Paco De Dios Anton
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Alfonso Mendoza‐Losana
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Claire Mackenzie
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Simon R. Green
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Margaret Huggett
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - David Barros
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Paul G. Wyatt
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Peter C. Ray
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
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54
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AlMatar M, Makky EA, Var I, Kayar B, Köksal F. Novel compounds targeting InhA for TB therapy. Pharmacol Rep 2018; 70:217-226. [DOI: 10.1016/j.pharep.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/26/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023]
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55
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Tatum NJ, Liebeschuetz JW, Cole JC, Frita R, Herledan A, Baulard AR, Willand N, Pohl E. New active leads for tuberculosis booster drugs by structure-based drug discovery. Org Biomol Chem 2018; 15:10245-10255. [PMID: 29182187 DOI: 10.1039/c7ob00910k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The transcriptional repressor EthR from Mycobacterium tuberculosis, a member of the TetR family of prokaryotic homo-dimeric transcription factors, controls the expression of the mycobacterial mono-oxygenase EthA. EthA is responsible for the bio-activation of the second-line tuberculosis pro-drug ethionamide, and consequently EthR inhibitors boost drug efficacy. Here, we present a comprehensive in silico structure-based screening protocol that led to the identification of a number of novel scaffolds of EthR inhibitors in subsequent biophysical screening by thermal shift assay. Growth inhibition assays demonstrated that five of the twenty biophysical hits were capable of boosting ethionamide activity in vitro, with the best novel scaffold displaying an EC50 of 34 μM. In addition, the co-crystal structures of EthR with four new ligands at resolution ranging from 2.1 to 1.4 Å confirm the binding and inactivation mode, and will enable future lead development.
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Affiliation(s)
- Natalie J Tatum
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK.
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56
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An overview on crystal structures of InhA protein: Apo-form, in complex with its natural ligands and inhibitors. Eur J Med Chem 2018; 146:318-343. [PMID: 29407960 DOI: 10.1016/j.ejmech.2018.01.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 11/23/2022]
Abstract
The enoyl-ACP reductase InhA from the mycobacterial fatty acid biosynthesis pathway has become a target of interest for the development of new anti-tubercular drugs. This protein has been identified as essential for the survival of Mycobacterium tuberculosis, the causative agent of tuberculosis, and as the main target of two pro-drugs: isoniazid, the frontline anti-tubercular drug, and ethionamide, a second-line medicine. Since most cases of resistance to isoniazid and ethionamide result from mutations in the mycobacterial activating enzyme (KatG for isoniazid and EthA for ethionamide), research of direct InhA inhibitors, avoiding the activation step, has emerged as a promising strategy for combating tuberculosis. Thereby, InhA is drawing much attention and its three-dimensional structure has been particularly studied. A better understanding of key sites of interactions responsible for InhA inhibition arises thus as an essential tool for the rational design of new potent inhibitors. In this paper, we propose an overview of the 80 available crystal structures of wild-type and mutant InhA, in its apo form, in complex with its cofactor, with an analogue of its natural ligands (C16 fatty acid and/or NADH) or with inhibitors. We will first discuss structural and mechanistic aspects in order to highlight key features of the protein before delivering thorough inventory of structures of InhA in the presence of synthetic ligands to underline the key interactions implicated in high affinity inhibition.
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57
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de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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58
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Laborde J, Deraeve C, Bernardes-Génisson V. Update of Antitubercular Prodrugs from a Molecular Perspective: Mechanisms of Action, Bioactivation Pathways, and Associated Resistance. ChemMedChem 2017; 12:1657-1676. [DOI: 10.1002/cmdc.201700424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/12/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Julie Laborde
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Céline Deraeve
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Vania Bernardes-Génisson
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
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59
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Khedr MA, Pillay M, Chandrashekharappa S, Chopra D, Aldhubiab BE, Attimarad M, Alwassil OI, Mlisana K, Odhav B, Venugopala KN. Molecular modeling studies and anti-TB activity of trisubstituted indolizine analogues; molecular docking and dynamic inputs. J Biomol Struct Dyn 2017; 36:2163-2178. [PMID: 28657441 DOI: 10.1080/07391102.2017.1345325] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of trisubstituted indolizine analogues has been designed as a result of a fragment-based approach to target the inhibition of mycobacterial enoyl-acyl carrier protein reductase. Anti-tuberculosis (TB) screening of the characterized compounds by a resazurin microplate assay method revealed that ethyl group at second position of indolizine nucleus exhibited activity against susceptible and multidrug-resistant strains of Mycobacterium tuberculosis at concentration of 5.5 and 11.3 μg/mL, respectively. A molecular docking study was also conducted to evaluate the stability of the active compounds, and compound with ethyl substitution at second position of indolizine nucleus showed the highest free binding energy of ΔG -24.11 (kcal/mol), a low clash score of 3.04, and high lipo score of -13.33. Indolizine analog with ethyl substitution at second position demonstrated Molecular Mechanics/Generalized Born Surface Area (-23.85 kcal/mol). Two molecular dynamics studies were computed (100 ps and 50 ns) to calculate the relationship between the potential and kinetic energies of the active anti-TB compound with time and temperature. The discovery of this lead may have a positive impact on anti-TB drug discovery.
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Affiliation(s)
- Mohammed A Khedr
- a Department of Pharmaceutical Sciences , College of Clinical Pharmacy, King Faisal University , Al-Ahsa 31982 , Kingdom of Saudi Arabia
| | - Melendhran Pillay
- b Department of Microbiology, National Health Laboratory Services , KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001 , South Africa
| | - Sandeep Chandrashekharappa
- c Institute for Stem Cell Biology and Regenerative Medicine , NCBS, TIFR, GKVK, Bellary Road, Bangalore 560 065 , India
| | - Deepak Chopra
- d Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066 , India
| | - Bandar E Aldhubiab
- a Department of Pharmaceutical Sciences , College of Clinical Pharmacy, King Faisal University , Al-Ahsa 31982 , Kingdom of Saudi Arabia
| | - Mahesh Attimarad
- a Department of Pharmaceutical Sciences , College of Clinical Pharmacy, King Faisal University , Al-Ahsa 31982 , Kingdom of Saudi Arabia
| | - Osama Ibrahim Alwassil
- a Department of Pharmaceutical Sciences , College of Clinical Pharmacy, King Faisal University , Al-Ahsa 31982 , Kingdom of Saudi Arabia
| | - Koleka Mlisana
- b Department of Microbiology, National Health Laboratory Services , KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001 , South Africa
| | - Bharti Odhav
- e Department of Biotechnology and Food Technology , Durban University of Technology , Durban 4001 , South Africa
| | - Katharigatta N Venugopala
- a Department of Pharmaceutical Sciences , College of Clinical Pharmacy, King Faisal University , Al-Ahsa 31982 , Kingdom of Saudi Arabia.,e Department of Biotechnology and Food Technology , Durban University of Technology , Durban 4001 , South Africa
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60
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Disruption of key NADH-binding pocket residues of the Mycobacterium tuberculosis InhA affects DD-CoA binding ability. Sci Rep 2017; 7:4714. [PMID: 28680153 PMCID: PMC5498604 DOI: 10.1038/s41598-017-05042-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 05/24/2017] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB) is a global health problem that affects over 10 million people. There is an urgent need to develop novel antimicrobial therapies to combat TB. To achieve this, a thorough understanding of key validated drug targets is required. The enoyl reductase InhA, responsible for synthesis of essential mycolic acids in the mycobacterial cell wall, is the target for the frontline anti-TB drug isoniazid. To better understand the activity of this protein a series of mutants, targeted to the NADH co-factor binding pocket were created. Residues P193 and W222 comprise a series of hydrophobic residues surrounding the cofactor binding site and mutation of both residues negatively affect InhA function. Construction of an M155A mutant of InhA results in increased affinity for NADH and DD-CoA turnover but with a reduction in Vmax for DD-CoA, impairing overall activity. This suggests that NADH-binding geometry of InhA likely permits long-range interactions between residues in the NADH-binding pocket to facilitate substrate turnover in the DD-CoA binding region of the protein. Understanding the precise details of substrate binding and turnover in InhA and how this may affect protein-protein interactions may facilitate the development of improved inhibitors enabling the development of novel anti-TB drugs.
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61
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Ang MLT, Zainul Rahim SZ, de Sessions PF, Lin W, Koh V, Pethe K, Hibberd ML, Alonso S. EthA/R-Independent Killing of Mycobacterium tuberculosis by Ethionamide. Front Microbiol 2017; 8:710. [PMID: 28487681 PMCID: PMC5403819 DOI: 10.3389/fmicb.2017.00710] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/06/2017] [Indexed: 11/13/2022] Open
Abstract
Ethionamide (ETH) is part of the drug arsenal available to treat multi-drug resistant tuberculosis. The current paradigm of this pro-drug activation involves the mycobacterial enzyme EthA and the transcriptional repressor, EthR. However, several lines of evidence suggest the involvement of additional players. The ethA/R locus was deleted in Mycobacterium bovis BCG and three Mycobacterium tuberculosis (MTB) strains. While complete resistance to ETH was observed with BCG ethA/R KO, drug susceptibility and dose-dependent killing were retained in the ethA/R KO MTB mutants, suggesting the existence of an alternative pathway of ETH bio-activation in MTB. We further demonstrated that this alternative pathway is EthR-independent, whereby re-introduction of ethR in ethA/R KO MTB did not lead to increased resistance to ETH. Consistently, ethA KO MTB (with intact ethR expression) displayed similar ETH susceptibility profile as their ethA/R KO counterparts. To identify the alternative ETH bio-activator, spontaneous ETH-resistant mutants were obtained from ethA/R KO MTB and whole genome sequencing identified single nucleotide polymorphisms in mshA, involved in mycothiol biosynthesis and previously linked to ETH resistance. Deletion of mshA in ethA/R KO MTB led to complete ETH resistance, supporting that the role of MshA in ETH killing is EthA/R-independent. Furthermore mshA single KO MTB displayed levels of ETH resistance similar or greater than those obtained with ethA/R KO strains, supporting that mshA is as critical as ethA/R for ETH killing efficacy.
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Affiliation(s)
- Michelle L T Ang
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Siti Z Zainul Rahim
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | | | - Wenwei Lin
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Vanessa Koh
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
| | - Kevin Pethe
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
| | - Martin L Hibberd
- Genome Institute of SingaporeSingapore, Singapore.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical MedicineLondon, UK
| | - Sylvie Alonso
- Department of Microbiology and Immunology, Yong Loo Lin School of MedicineSingapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of SingaporeSingapore, Singapore
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62
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Bengtson HN, Homolka S, Niemann S, Reis AJ, da Silva PE, Gerasimova YV, Kolpashchikov DM, Rohde KH. Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors. Biosens Bioelectron 2017; 94:176-183. [PMID: 28284077 DOI: 10.1016/j.bios.2017.02.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/21/2017] [Accepted: 02/28/2017] [Indexed: 02/07/2023]
Abstract
Current diagnostic tools for Mycobacterium tuberculosis (Mtb) have many disadvantages including low sensitivity, slow turnaround times, or high cost. Accurate, easy to use, and inexpensive point of care molecular diagnostic tests are urgently needed for the analysis of multidrug resistant (MDR) and extensively drug resistant (XDR) Mtb strains that emerge globally as a public health threat. In this study, we established proof-of-concept for a novel diagnostic platform (TB-DzT) for Mtb detection and the identification of drug resistant mutants using binary deoxyribozyme sensors (BiDz). TB-DzT combines a multiplex PCR with single nucleotide polymorphism (SNP) detection using highly selective BiDz sensors targeting loci associated with species typing and resistance to rifampin, isoniazid and fluoroquinolone antibiotics. Using the TB-DzT assay, we demonstrated accurate detection of Mtb and 5 mutations associated with resistance to three anti-TB drugs in clinical isolates. The assay also enables detection of a minority population of drug resistant Mtb, a clinically relevant scenario referred to as heteroresistance. Additionally, we show that TB-DzT can detect the presence of unknown mutations at target loci using combinatorial BiDz sensors. This diagnostic platform provides the foundation for the development of cost-effective, accurate and sensitive alternatives for molecular diagnostics of MDR- and XDR-TB.
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Affiliation(s)
- Hillary N Bengtson
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Borstel, Germany
| | - Ana Júlia Reis
- Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | | | - Yulia V Gerasimova
- Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA; Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
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63
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Spagnuolo LA, Eltschkner S, Yu W, Daryaee F, Davoodi S, Knudson SE, Allen EKH, Merino J, Pschibul A, Moree B, Thivalapill N, Truglio JJ, Salafsky J, Slayden RA, Kisker C, Tonge PJ. Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors. J Am Chem Soc 2017; 139:3417-3429. [PMID: 28151657 DOI: 10.1021/jacs.6b11148] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition-state destabilization rather than ground-state stabilization. In the present work, we evaluate the inhibition of InhA by 14 triazole-based diphenyl ethers and use a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to 3 orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min, which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.
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Affiliation(s)
- Lauren A Spagnuolo
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Sandra Eltschkner
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Weixuan Yu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Fereidoon Daryaee
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Shabnam Davoodi
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Susan E Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | - Eleanor K H Allen
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Jonathan Merino
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Annica Pschibul
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Ben Moree
- Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Neil Thivalapill
- Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States
| | - James J Truglio
- Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States
| | - Joshua Salafsky
- Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Richard A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
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Discovery of cofactor-specific, bactericidal Mycobacterium tuberculosis InhA inhibitors using DNA-encoded library technology. Proc Natl Acad Sci U S A 2016; 113:E7880-E7889. [PMID: 27864515 DOI: 10.1073/pnas.1610978113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current frontline therapies include the drug isoniazid, which inhibits the essential NADH-dependent enoyl-acyl-carrier protein (ACP) reductase, InhA. To inhibit InhA, isoniazid must be activated by the catalase-peroxidase KatG. Isoniazid resistance is linked primarily to mutations in the katG gene. Discovery of InhA inhibitors that do not require KatG activation is crucial to combat MDR TB. Multiple discovery efforts have been made against InhA in recent years. Until recently, despite achieving high potency against the enzyme, these efforts have been thwarted by lack of cellular activity. We describe here the use of DNA-encoded X-Chem (DEX) screening, combined with selection of appropriate physical properties, to identify multiple classes of InhA inhibitors with cell-based activity. The utilization of DEX screening allowed the interrogation of very large compound libraries (1011 unique small molecules) against multiple forms of the InhA enzyme in a multiplexed format. Comparison of the enriched library members across various screening conditions allowed the identification of cofactor-specific inhibitors of InhA that do not require activation by KatG, many of which had bactericidal activity in cell-based assays.
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Overview on mechanisms of isoniazid action and resistance in Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2016; 45:474-492. [DOI: 10.1016/j.meegid.2016.09.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/02/2016] [Accepted: 09/03/2016] [Indexed: 12/17/2022]
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A new strategy for strain improvement of Aurantiochytrium sp. based on heavy-ions mutagenesis and synergistic effects of cold stress and inhibitors of enoyl-ACP reductase. Enzyme Microb Technol 2016; 93-94:182-190. [DOI: 10.1016/j.enzmictec.2016.08.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/30/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022]
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Saraav I, Pandey K, Misra R, Singh S, Sharma M, Sharma S. Characterization of MymA protein as a flavin-containing monooxygenase and as a target of isoniazid. Chem Biol Drug Des 2016; 89:152-160. [DOI: 10.1111/cbdd.12840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/12/2016] [Accepted: 08/06/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Iti Saraav
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Kirti Pandey
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Richa Misra
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Swati Singh
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Monika Sharma
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Sadhna Sharma
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
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69
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Rožman K, Sosič I, Fernandez R, Young RJ, Mendoza A, Gobec S, Encinas L. A new 'golden age' for the antitubercular target InhA. Drug Discov Today 2016; 22:492-502. [PMID: 27663094 DOI: 10.1016/j.drudis.2016.09.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
Abstract
The increasing prevalence of multidrug-resistant strains of Mycobacterium tuberculosis is the main contributing factor in unfavorable outcomes in the treatment of tuberculosis. Studies suggest that direct inhibitors of InhA, an enoyl-ACP-reductase, might yield promising clinical candidates that can be developed into new antitubercular drugs. In this review, we describe the application of different hit-identification strategies to InhA, which clearly illustrate the druggability of its active site through distinct binding mechanisms. We further characterize four classes of InhA inhibitors that show novel binding modes, and provide evidence of their successful target engagement as well as their in vivo activity.
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Affiliation(s)
- Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Raquel Fernandez
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Robert J Young
- GlaxoSmithKline Medicines Research Centre, Stevenage, Herfordshire SG1 2NY, UK
| | - Alfonso Mendoza
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Lourdes Encinas
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain.
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70
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Quémard A. New Insights into the Mycolate-Containing Compound Biosynthesis and Transport in Mycobacteria. Trends Microbiol 2016; 24:725-738. [DOI: 10.1016/j.tim.2016.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/14/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022]
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71
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Bommineni GR, Kapilashrami K, Cummings JE, Lu Y, Knudson SE, Gu C, Walker SG, Slayden RA, Tonge PJ. Thiolactomycin-Based Inhibitors of Bacterial β-Ketoacyl-ACP Synthases with in Vivo Activity. J Med Chem 2016; 59:5377-90. [PMID: 27187871 DOI: 10.1021/acs.jmedchem.6b00236] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
β-Ketoacyl-ACP synthases (KAS) are key enzymes involved in the type II bacterial fatty acid biosynthesis (FASII) pathway and are putative targets for antibacterial discovery. Several natural product KAS inhibitors have previously been reported, including thiolactomycin (TLM), which is produced by Nocardia spp. Here we describe the synthesis and characterization of optically pure 5R-thiolactomycin (TLM) analogues that show improved whole cell activity against bacterial strains including methicillin-resistant Staphylococcus aureus (MRSA) and priority pathogens such as Francisella tularensis and Burkholderia pseudomallei. In addition, we identify TLM analogues with in vivo efficacy against MRSA and Klebsiella pneumoniae in animal models of infection.
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Affiliation(s)
| | | | - Jason E Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | | | - Susan E Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | | | | | - Richard A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
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72
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Guardia A, Gulten G, Fernandez R, Gómez J, Wang F, Convery M, Blanco D, Martínez M, Pérez-Herrán E, Alonso M, Ortega F, Rullás J, Calvo D, Mata L, Young R, Sacchettini JC, Mendoza-Losana A, Remuiñán M, Ballell Pages L, Castro-Pichel J. N-Benzyl-4-((heteroaryl)methyl)benzamides: A New Class of Direct NADH-Dependent 2-trans Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors with Antitubercular Activity. ChemMedChem 2016; 11:687-701. [PMID: 26934341 DOI: 10.1002/cmdc.201600020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/12/2016] [Indexed: 12/14/2022]
Abstract
Isoniazid (INH) remains one of the cornerstones of antitubercular chemotherapy for drug-sensitive strains of M. tuberculosis bacteria. However, the increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains containing mutations in the KatG enzyme, which is responsible for the activation of INH into its antitubercular form, have rendered this drug of little or no use in many cases of drug-resistant tuberculosis. Presented herein is a novel family of antitubercular direct NADH-dependent 2-trans enoyl-acyl carrier protein reductase (InhA) inhibitors based on an N-benzyl-4-((heteroaryl)methyl)benzamide template; unlike INH, these do not require prior activation by KatG. Given their direct InhA target engagement, these compounds should be able to circumvent KatG-related resistance in the clinic. The lead molecules were shown to be potent inhibitors of InhA and showed activity against M. tuberculosis bacteria. This new family of inhibitors was found to be chemically tractable, as exemplified by the facile synthesis of analogues and the establishment of structure-activity relationships. Furthermore, a co-crystal structure of the initial hit with the enzyme is disclosed, providing valuable information toward the design of new InhA inhibitors for the treatment of MDR/XDR tuberculosis.
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Affiliation(s)
- Ana Guardia
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain.
| | - Gulcin Gulten
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard College Station, TX, 77843-2128, USA
| | - Raquel Fernandez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Jesus Gómez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Maire Convery
- Molecular Discovery Research, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Delia Blanco
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - María Martínez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Esther Pérez-Herrán
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Marta Alonso
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Fátima Ortega
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joaquín Rullás
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - David Calvo
- Centro de Investigación Básica, Platform Technologies and Science, GlaxoSmithKline, Parque Tecnológico de Madrid, 28760 Tres Cantos, Madrid, Spain
| | - Lydia Mata
- Centro de Investigación Básica, Platform Technologies and Science, GlaxoSmithKline, Parque Tecnológico de Madrid, 28760 Tres Cantos, Madrid, Spain
| | - Robert Young
- Molecular Discovery Research, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard College Station, TX, 77843-2128, USA
| | - Alfonso Mendoza-Losana
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Modesto Remuiñán
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluís Ballell Pages
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Julia Castro-Pichel
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
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Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis: Genes, Mutations, and Causalities. Microbiol Spectr 2016; 2:MGM2-0014-2013. [PMID: 26104204 DOI: 10.1128/microbiolspec.mgm2-0014-2013] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoniazid (INH) is the cornerstone of tuberculosis (TB) chemotherapy, used for both treatment and prophylaxis of TB. The antimycobacterial activity of INH was discovered in 1952, and almost as soon as its activity was published, the first INH-resistant Mycobacterium tuberculosis strains were reported. INH and its structural analog and second-line anti-TB drug ethionamide (ETH) are pro-drugs. INH is activated by the catalase-peroxidase KatG, while ETH is activated by the monooxygenase EthA. The resulting active species reacts with NAD+ to form an INH-NAD or ETH-NAD adduct, which inhibits the enoyl ACP reductase InhA, leading to mycolic acid biosynthesis inhibition and mycobacterial cell death. The major mechanism of INH resistance is mutation in katG, encoding the activator of INH. One specific KatG variant, S315T, is found in 94% of INH-resistant clinical isolates. The second mechanism of INH resistance is a mutation in the promoter region of inhA (c-15t), which results in inhA overexpression and leads to titration of the drug. Mutations in the inhA open reading frame and promoter region are also the major mechanism of resistance to ETH, found more often in ETH-resistant clinical isolates than mutations in the activator of ETH. Other mechanisms of resistance to INH and ETH include expression changes of the drugs' activators, redox alteration, drug inactivation, and efflux pump activation. In this article, we describe each known mechanism of resistance to INH and ETH and its importance in M. tuberculosis clinical isolates.
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74
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Abstract
In this chapter we review the molecular mechanisms of drug resistance to the major first- and second-line antibiotics used to treat tuberculosis.
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75
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Kumar V, Sobhia ME. Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA. PLoS One 2015; 10:e0144635. [PMID: 26658674 PMCID: PMC4682841 DOI: 10.1371/journal.pone.0144635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/21/2015] [Indexed: 12/20/2022] Open
Abstract
Examination of InhA mutants I16T, I21V, I47T, S94A, and I95P showed that direct and water mediated H-bond interactions between NADH and binding site residues reduced drastically. It allowed conformational flexibility to NADH, particularly at the pyrophosphate region, leading to weakening of its binding at dinucleotide binding site. The highly scattered distribution of pyrophosphate dihedral angles and chi1 side chain dihedral angles of corresponding active site residues therein confirmed weak bonding between InhA and NADH. The average direct and water mediated bridged H-bond interactions between NADH and mutants were observed weaker as compared to wild type. Further, estimated NADH binding free energy in mutants supported the observed weakening of InhA-NADH interactions. Similarly, per residue contribution to NADH binding was also found little less as compared to corresponding residues in wild type. This investigation clearly depicted and supported the effect of mutations on NADH binding and can be accounted for isoniazid resistance as suggested by previous biochemical and mutagenic studies. Further, structural analysis of InhA provided the crucial points to enhance the NADH binding affinity towards InhA mutants in the presence of direct InhA inhibitors to combat isoniazid drug resistance. This combination could be a potential alternative for treatment of drug resistant tuberculosis.
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Affiliation(s)
- Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
- * E-mail:
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Kouassi AF, Kone M, Keita M, Esmel A, Megnassan E, N'Guessan YT, Frecer V, Miertus S. Computer-Aided Design of Orally Bioavailable Pyrrolidine Carboxamide Inhibitors of Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Pharmacokinetic Profiles. Int J Mol Sci 2015; 16:29744-71. [PMID: 26703572 PMCID: PMC4691139 DOI: 10.3390/ijms161226196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 11/16/2022] Open
Abstract
We have carried out a computational structure-based design of new potent pyrrolidine carboxamide (PCAMs) inhibitors of enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (MTb). Three-dimensional (3D) models of InhA-PCAMx complexes were prepared by in situ modification of the crystal structure of InhA-PCAM1 (Protein Data Bank (PDB) entry code: 4U0J), the reference compound of a training set of 20 PCAMs with known experimental inhibitory potencies (IC50(exp)). First, we built a gas phase quantitative structure-activity relationships (QSAR) model, linearly correlating the computed enthalpy of the InhA-PCAM complex formation and the IC50(exp). Further, taking into account the solvent effect and loss of inhibitor entropy upon enzyme binding led to a QSAR model with a superior linear correlation between computed Gibbs free energies (ΔΔGcom) of InhA-PCAM complex formation and IC50(exp) (pIC50(exp) = -0.1552·ΔΔGcom + 5.0448, R² = 0.94), which was further validated with a 3D-QSAR pharmacophore model generation (PH4). Structural information from the models guided us in designing of a virtual combinatorial library (VL) of more than 17 million PCAMs. The VL was adsorption, distribution, metabolism and excretion (ADME) focused and reduced down to 1.6 million drug like orally bioavailable analogues and PH4 in silico screened to identify new potent PCAMs with predicted IC50(pre) reaching up to 5 nM. Combining molecular modeling and PH4 in silico screening of the VL resulted in the proposed novel potent antituberculotic agent candidates with favorable pharmacokinetic profiles.
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Affiliation(s)
- Affiba Florance Kouassi
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
| | - Mawa Kone
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Akori Esmel
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Yao Thomas N'Guessan
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
| | - Vladimir Frecer
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
- Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia.
- International Centre for Applied Research and Sustainable Technology, Bratislava SK-84104, Slovakia.
| | - Stanislav Miertus
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
- International Centre for Applied Research and Sustainable Technology, Bratislava SK-84104, Slovakia.
- Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava SK-91701, Slovakia.
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Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae. J Bacteriol 2015; 198:463-76. [PMID: 26553852 DOI: 10.1128/jb.00360-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/03/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED β-Ketoacyl-(acyl carrier protein) reductase (FabG) catalyzes the key reductive reaction in the elongation cycle of fatty acid synthesis (FAS), which is a vital metabolic pathway in bacteria and a promising target for new antibiotic development. The activation of the enzyme is usually linked to the formation of a catalytic triad and cofactor binding, and crystal structures of FabG from different organisms have been captured in either the active or inactive conformation. However, the structural elements which enable activation of FabG require further exploration. Here we report the findings of structural, enzymatic, and binding studies of the FabG protein found in the causative agent of cholera, Vibrio cholerae (vcFabG). vcFabG exists predominantly as a dimer in solution and is able to self-associate to form tetramers, which is the state seen in the crystal structure. The formation of the tetramer may be promoted by the presence of the cofactor NADP(H). The transition between the dimeric and tetrameric states of vcFabG is related to changes in the conformations of the α4/α5 helices on the dimer-dimer interface. Two glycine residues adjacent to the dimer interface (G92 and G141) are identified to be the hinge for the conformational changes, while the catalytic tyrosine (Y155) and a glutamine residue that forms hydrogen bonds to both loop β4-α4 and loop β5-α5 (Q152) stabilize the active conformation. The functions of the aforementioned residues were confirmed by binding and enzymatic assays for the corresponding mutants. IMPORTANCE This paper describes the results of structural, enzymatic, and binding studies of FabG from Vibrio cholerae (vcFabG). In this work, we dissected the structural elements responsible for the activation of vcFabG. The structural information provided here is essential for the development of antibiotics specifically targeting bacterial FabG, especially for the multidrug-resistant strains of V. cholerae.
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78
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A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis. J Mol Model 2015; 21:252. [PMID: 26361768 DOI: 10.1007/s00894-015-2799-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
Abstract
Initiation of the Tuberculosis Structural Consortium has resulted in the expansion of the Mycobacterium tuberculosis (MTB) protein structural database. Currently, 969 experimentally solved structures are available for 354 MTB proteins. This includes multiple crystal structures for a given protein under different functional conditions, such as the presence of different ligands or mutations. In depth analysis of the multiple structures reveal that subtle differences exist in conformations of a given protein under varied conditions. Therefore, it is immensely important to understand the conformational differences between the multiple structures of a given protein in order to select the most suitable structure for molecular docking and structure-based drug designing. Here, we introduce a web portal ( http://bmi.icmr.org.in/mtbsd/torsion.php ) that we developed to provide comparative data on the ensemble of available structures of MTB proteins, such as Cα root means square deviation (RMSD), sequence identity, presence of mutations and torsion angles. Additionally, torsion angles were used to perform principal component analysis (PCA) to identify the conformational differences between the structures. Additionally, we present a few case studies to demonstrate this database. Graphical Abstract Conformational changes seen in the structures of the enoyl-ACP reductase protein encoded by the Mycobacterial gene inhA.
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79
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Rajkhowa S, Jha AN, Deka RC. Anti-tubercular drug development: computational strategies to identify potential compounds. J Mol Graph Model 2015; 62:56-68. [PMID: 26386453 DOI: 10.1016/j.jmgm.2015.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/13/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
InhA is an attractive target to combat tuberculosis (TB), which is targeted by many pro-drugs (isoniazid, etc.) and drugs such as triclosan. However, triclosan is less useful as an antitubercular drug due to its low bioavailability and therefore, in order to overcome this difficulty, many derivatives of triclosan were prepared. Here, we have combined various computational techniques to virtually screen out four potential triclosan derivatives. Molecular docking methods have been employed to screen out 32 out of 62 triclosan derivatives considering the mode of binding and the top re-rank scores. A comparative study on the chemical properties of triclosan and some of its derivatives has been performed using density functional theory (DFT) calculations. DFT based global reactivity descriptors (GRD), such as hardness, chemical potential, chemical softness, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries were used to investigate the usefulness of these descriptors for understanding the reactive nature and sites of the molecules. QSAR equations were built using these descriptors considering these 32 compounds. Four common compounds showing the best correlation and the best docking scores were considered for the ADMET property calculations and their dynamical movements have been studied using molecular dynamics simulations. Our results showed that these four compounds are chemically more active than triclosan and have the potential to inhibit the Mycobacterium tuberculosis enoyl acyl carrier protein reductase. This work shows that combination of different computational techniques may help to screen out potential drug candidates from a list of possible ones.
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Affiliation(s)
- Sanchaita Rajkhowa
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology & Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur 784028, Assam, India.
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80
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De Paris R, Quevedo CV, Ruiz DDA, Norberto de Souza O. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features. PLoS One 2015. [PMID: 26218832 PMCID: PMC4517875 DOI: 10.1371/journal.pone.0133172] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill biologically relevant information from MD trajectories, especially for docking purposes.
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Affiliation(s)
- Renata De Paris
- Grupo de Pesquisa em Inteligência de Negócio—GPIN, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681-Prédio 32, sala 628, Porto Alegre, RS, Brasil
| | - Christian V. Quevedo
- Grupo de Pesquisa em Inteligência de Negócio—GPIN, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681-Prédio 32, sala 628, Porto Alegre, RS, Brasil
| | - Duncan D. A. Ruiz
- Grupo de Pesquisa em Inteligência de Negócio—GPIN, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681-Prédio 32, sala 628, Porto Alegre, RS, Brasil
- * E-mail: (DDAR); (ONS)
| | - Osmar Norberto de Souza
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas—LABIO, Faculdade de Informática, PUCRS, Av. Ipiranga, 6681- Building 32, Room 602, Porto Alegre, RS, Brasil
- * E-mail: (DDAR); (ONS)
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81
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Shaw DJ, Adamczyk K, Frederix PWJM, Simpson N, Robb K, Greetham GM, Towrie M, Parker AW, Hoskisson PA, Hunt NT. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid. J Chem Phys 2015; 142:212401. [DOI: 10.1063/1.4914097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Daniel J. Shaw
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Katrin Adamczyk
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Pim W. J. M. Frederix
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Niall Simpson
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Kirsty Robb
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Gregory M. Greetham
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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82
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Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach. J Struct Biol 2015; 190:328-37. [PMID: 25891098 DOI: 10.1016/j.jsb.2015.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/21/2022]
Abstract
InhA is an enoyl-ACP reductase of Mycobacterium tuberculosis implicated in the biosynthesis of mycolic acids, essential constituents of the mycobacterial cell wall. To date, this enzyme is considered as a promising target for the discovery of novel antitubercular drugs. In this work, we describe the first crystal structure of the apo form of the wild-type InhA at 1.80Å resolution as well as the crystal structure of InhA in complex with the synthetic metabolite of the antitubercular drug isoniazid refined to 1.40Å. This metabolite, synthesized in the absence of InhA, is able to displace and replace the cofactor NADH in the enzyme active site. This work provides a unique opportunity to enlighten the structural adaptation of apo-InhA to the binding of the NADH cofactor or of the isoniazid adduct. In addition, a differential scanning fluorimetry study of InhA, in the apo-form as well as in the presence of NAD(+), NADH and INH-NADH was performed showing that binding of the INH-NADH adduct had a strong stabilizing effect.
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83
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Chakraborty S, Rhee KY. Tuberculosis Drug Development: History and Evolution of the Mechanism-Based Paradigm. Cold Spring Harb Perspect Med 2015; 5:a021147. [PMID: 25877396 DOI: 10.1101/cshperspect.a021147] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Modern tuberculosis (TB) chemotherapy is widely viewed as a crowning triumph of anti-infectives research. However, only one new TB drug has entered clinical practice in the past 40 years while drug resistance threatens to further destabilize the pandemic. Here, we review a brief history of TB drug development, focusing on the evolution of mechanism(s)-of-action studies and key conceptual barriers to rational, mechanism-based drugs.
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Affiliation(s)
- Sumit Chakraborty
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10021 Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - Kyu Y Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10021 Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
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84
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Proteome-wide lysine acetylation profiling of the human pathogen Mycobacterium tuberculosis. Int J Biochem Cell Biol 2015; 59:193-202. [DOI: 10.1016/j.biocel.2014.11.010] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 10/05/2014] [Accepted: 11/21/2014] [Indexed: 12/15/2022]
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85
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Kamsri P, Punkvang A, Hannongbua S, Saparpakorn P, Pungpo P. Elucidating structural basis of benzofuran pyrrolidine pyrazole derivatives for enhancing potency against both the InhA enzyme and intact M. tuberculosis cells: a combined MD simulations and 3D-QSAR study. RSC Adv 2015. [DOI: 10.1039/c5ra08103c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structural concept for enhancing both IC50 and MIC90 activities summarized from MD simulations and CoMSIA results.
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Affiliation(s)
- Pharit Kamsri
- Department of Chemistry
- Faculty of Science
- Ubon Ratchathani University
- Thailand
| | | | - Supa Hannongbua
- Department of Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok
- Thailand
| | | | - Pornpan Pungpo
- Department of Chemistry
- Faculty of Science
- Ubon Ratchathani University
- Thailand
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86
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Šink R, Sosič I, Živec M, Fernandez-Menendez R, Turk S, Pajk S, Alvarez-Gomez D, Lopez-Roman EM, Gonzales-Cortez C, Rullas-Triconado J, Angulo-Barturen I, Barros D, Ballell-Pages L, Young RJ, Encinas L, Gobec S. Design, Synthesis, and Evaluation of New Thiadiazole-Based Direct Inhibitors of Enoyl Acyl Carrier Protein Reductase (InhA) for the Treatment of Tuberculosis. J Med Chem 2014; 58:613-24. [DOI: 10.1021/jm501029r] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Roman Šink
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Matej Živec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Raquel Fernandez-Menendez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Samo Turk
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Stane Pajk
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
| | - Daniel Alvarez-Gomez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Eva Maria Lopez-Roman
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carolina Gonzales-Cortez
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joaquin Rullas-Triconado
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Inigo Angulo-Barturen
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - David Barros
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluís Ballell-Pages
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Robert J. Young
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Lourdes Encinas
- Diseases
of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Stanislav Gobec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenija
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87
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Stec J, Vilchèze C, Lun S, Perryman AL, Wang X, Freundlich JS, Bishai W, Jacobs WR, Kozikowski AP. Biological evaluation of potent triclosan-derived inhibitors of the enoyl-acyl carrier protein reductase InhA in drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. ChemMedChem 2014; 9:2528-37. [PMID: 25165007 PMCID: PMC4213240 DOI: 10.1002/cmdc.201402255] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Indexed: 11/09/2022]
Abstract
New triclosan (TRC) analogues were evaluated for their activity against the enoyl-acyl carrier protein reductase InhA in Mycobacterium tuberculosis (Mtb). TRC is a well-known inhibitor of InhA, and specific modifications to its positions 5 and 4' afforded 27 derivatives; of these compounds, seven derivatives showed improved potency over that of TRC. These analogues were active against both drug-susceptible and drug-resistant Mtb strains. The most active compound in this series, 4-(n-butyl)-1,2,3-triazolyl TRC derivative 3, had an MIC value of 0.6 μg mL(-1) (1.5 μM) against wild-type Mtb. At a concentration equal to its MIC, this compound inhibited purified InhA by 98 %, and showed an IC50 value of 90 nM. Compound 3 and the 5-methylisoxazole-modified TRC 14 were able to inhibit the biosynthesis of mycolic acids. Furthermore, mc(2) 4914, an Mtb strain overexpressing inhA, was found to be less susceptible to compounds 3 and 14, supporting the notion that InhA is the likely molecular target of the TRC derivatives presented herein.
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Affiliation(s)
- Jozef Stec
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States, Fax: +1-312-996-7107
- Department of Pharmaceutical Sciences, College of Pharmacy, Chicago State University, 9501 S. King Drive, Chicago, Illinois 60628, United States
| | - Catherine Vilchèze
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD 21231-1044, United States
| | - Alexander L. Perryman
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - Xin Wang
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - Joel S. Freundlich
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
- Department of Pharmacology and Physiology, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - William Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD 21231-1044, United States
| | - William R. Jacobs
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Alan P. Kozikowski
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States, Fax: +1-312-996-7107
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88
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Punkvang A, Kamsri P, Saparpakorn P, Hannongbua S, Wolschann P, Irle S, Pungpo P. Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation. Chem Biol Drug Des 2014; 86:91-101. [PMID: 25354564 DOI: 10.1111/cbdd.12465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/03/2023]
Abstract
Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity.
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Affiliation(s)
- Auradee Punkvang
- Faculty of Science, Nakhon Phanom University, Muang, Nakhon Phanom, 48000, Thailand
| | - Pharit Kamsri
- Department of Chemistry, Ubon Ratchathani University, 85 Sthollmark Road, Warinchamrap, Ubonratchathani, 34190, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Peter Wolschann
- Institute for Theoretical Chemistry, University of Vienna, Vienna, A-1090, Austria.,Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Stephan Irle
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Pornpan Pungpo
- Department of Chemistry, Ubon Ratchathani University, 85 Sthollmark Road, Warinchamrap, Ubonratchathani, 34190, Thailand
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89
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Duan X, Xiang X, Xie J. Crucial components of mycobacterium type II fatty acid biosynthesis (Fas-II) and their inhibitors. FEMS Microbiol Lett 2014; 360:87-99. [DOI: 10.1111/1574-6968.12597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/27/2023] Open
Affiliation(s)
- Xiangke Duan
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
| | - Xiaohong Xiang
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals; State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area; Key Laboratory of Eco-Environments in Three Gorges Reservoir Region; Ministry of Education; School of Life Sciences; Southwest University; Beibei Chongqing China
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90
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Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study. J Mol Model 2014; 20:2319. [PMID: 24935113 DOI: 10.1007/s00894-014-2319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.
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91
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Shahine A, Prasetyoputri A, Rossjohn J, Beddoe T. A structural characterization of the isoniazid Mycobacterium tuberculosis drug target, Rv2971, in its unliganded form. Acta Crystallogr F Struct Biol Commun 2014; 70:572-7. [PMID: 24817712 PMCID: PMC4014321 DOI: 10.1107/s2053230x14007158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 03/31/2014] [Indexed: 11/10/2022] Open
Abstract
Aldo-keto reductases (AKR) are a large superfamily of NADPH-dependent oxidoreductases and play a role in detoxification of toxic metabolites. Rv2971, an AKR in Mycobacterium tuberculosis, has recently been identified as a target of isoniazid, a key first-line drug against tuberculosis. Here, the cloning, expression, purification, crystallization and structural characterization of Rv2971 are described. To gain insight into its function, the crystal structure of Rv2971 was successfully determined to 1.60 Å resolution in its unliganded form. The structure exhibits a TIM-barrel fold typical of AKRs, revealing structural characteristics essential for function and substrate specificities, allowing a structural comparison between Rv2971 and other mycobacterial AKRs.
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Affiliation(s)
- Adam Shahine
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Anggia Prasetyoputri
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI), Indonesia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, Wales
| | - Travis Beddoe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Agriculture Sciences, La Trobe University, Bundoora, Victoria, Australia
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92
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Kamsri P, Koohatammakun N, Srisupan A, Meewong P, Punkvang A, Saparpakorn P, Hannongbua S, Wolschann P, Prueksaaroon S, Leartsakulpanich U, Pungpo P. Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:473-488. [PMID: 24785640 DOI: 10.1080/1062936x.2014.898690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor-enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.
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Affiliation(s)
- P Kamsri
- a Department of Chemistry, Faculty of Science , Ubon Ratchathani University , Ubonratchathani , Thailand
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93
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Schiebel J, Chang A, Shah S, Lu Y, Liu L, Pan P, Hirschbeck MW, Tareilus M, Eltschkner S, Yu W, Cummings JE, Knudson SE, Bommineni GR, Walker SG, Slayden RA, Sotriffer CA, Tonge PJ, Kisker C. Rational design of broad spectrum antibacterial activity based on a clinically relevant enoyl-acyl carrier protein (ACP) reductase inhibitor. J Biol Chem 2014; 289:15987-6005. [PMID: 24739388 DOI: 10.1074/jbc.m113.532804] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphylococcus-specific 2-pyridone compound that inhibits the enoyl-acyl carrier protein reductase (FabI), has recently been shown to possess human efficacy for the treatment of methicillin-resistant Staphylococcus aureus infections, which constitute a serious threat to human health. In this study, we solved the structures of three different FabI homologues in complex with several pyridone inhibitors, including CG400549. Based on these structures, we rationalize the 65-fold reduced affinity of CG400549 toward Escherichia coli versus S. aureus FabI and implement concepts to improve the spectrum of antibacterial activity. The identification of different conformational states along the reaction coordinate of the enzymatic hydride transfer provides an elegant visual depiction of the relationship between catalysis and inhibition, which facilitates rational inhibitor design. Ultimately, we developed the novel 4-pyridone-based FabI inhibitor PT166 that retained favorable pharmacokinetics and efficacy in a mouse model of S. aureus infection with extended activity against Gram-negative and mycobacterial organisms.
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Affiliation(s)
- Johannes Schiebel
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany, the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Andrew Chang
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Sonam Shah
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Yang Lu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Li Liu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Pan Pan
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Maria W Hirschbeck
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Mona Tareilus
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Sandra Eltschkner
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Weixuan Yu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Jason E Cummings
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Susan E Knudson
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Gopal R Bommineni
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Stephen G Walker
- School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Richard A Slayden
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Christoph A Sotriffer
- the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Peter J Tonge
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Caroline Kisker
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany,
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94
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Pan P, Knudson S, Bommineni GR, Li HJ, Lai CT, Liu N, Garcia-Diaz M, Simmerling C, Patil SS, Slayden RA, Tonge PJ. Time-dependent diaryl ether inhibitors of InhA: structure-activity relationship studies of enzyme inhibition, antibacterial activity, and in vivo efficacy. ChemMedChem 2014; 9:776-91. [PMID: 24616444 PMCID: PMC4126670 DOI: 10.1002/cmdc.201300429] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 11/07/2022]
Abstract
The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. In the present work, we demonstrate that two time-dependent B-ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug-target residence time in this system, we have explored the inhibition of InhA by a series of B-ring modified analogues. Seven ortho-substituted compounds were found to be time-dependent inhibitors of InhA, where the slow step leading to the final enzyme-inhibitor complex (EI*) is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.
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Affiliation(s)
- Pan Pan
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Susan Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-2025
| | - Gopal R. Bommineni
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Huei-Jiun Li
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Cheng-Tsung Lai
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
- Biochemistry and Structural Biology, Stony Brook, NY 11794-3400
| | - Nina Liu
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Miguel Garcia-Diaz
- Pharmacological Sciences Graduate Program, Stony Brook University, Stony Brook, NY 11794-3400
| | - Carlos Simmerling
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | | | - Richard A. Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-2025
| | - Peter J. Tonge
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
- Biochemistry and Structural Biology, Stony Brook, NY 11794-3400
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95
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Jiang L, Gao Z, Li Y, Wang S, Dong Y. Crystal structures and kinetic properties of enoyl-acyl carrier protein reductase I from Candidatus Liberibacter asiaticus. Protein Sci 2014; 23:366-77. [PMID: 24407918 PMCID: PMC3970888 DOI: 10.1002/pro.2418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/20/2013] [Accepted: 01/06/2014] [Indexed: 01/02/2023]
Abstract
Huanglongbing (HLB) is a destructive citrus disease. The leading cause of HLB is Candidatus Liberibacter asiaticus. Fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. Enoyl-acyl carrier protein reductase (also called ENR or FabI and a product of the fabI gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agents. We determined the crystal structures of FabI from Ca. L. asiaticus in its apoform as well as in complex with b-nicotinamide adenine dinucleotide (NAD) at 1.7 and 2.7 Å resolution, respectively, to facilitate the design and screening of small molecule inhibitors of FabI. The monomeric ClFabI is highly similar to other known FabI structures as expected; however, unlike the typical tetramer, ClFabI exists as a hexamer in crystal, whereas as dimer in solution, on the other hand, the substrate binding loop which always disordered in apoform FabI structures is ordered in apo-ClFabI. Interestingly, the structure of ClFabI undergoes remarkable conformational change in the substrate-binding loop in the presence of NAD. We conclude that the signature sequence motif of FabI can be considered as Gly-(Xaa)5-Ser-(Xaa)n-Val-Tyr-(Xaa)6-Lys-(Xaa)n-Thr instead of Tyr-(Xaa)6-Lys. We have further identified isoniazid as a competitive inhibitor with NADH.
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Affiliation(s)
- Ling Jiang
- Ministry of Education Key Laboratory of Plant Biology, Department of Horticulture and ForestryHuazhong Agricultural University, Wuhan 430070, China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of SciencesBeijing, 100049, China
| | - Yanhua Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of SciencesBeijing, 100049, China
| | - Shennan Wang
- Ministry of Education Key Laboratory of Plant Biology, Department of Horticulture and ForestryHuazhong Agricultural University, Wuhan 430070, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of SciencesBeijing, 100049, China
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96
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Rychtarčíková Z, Krátký M, Gazvoda M, Komlóová M, Polanc S, Kočevar M, Stolaříková J, Vinšová J. N-substituted 2-isonicotinoylhydrazinecarboxamides--new antimycobacterial active molecules. Molecules 2014; 19:3851-68. [PMID: 24686575 PMCID: PMC6271275 DOI: 10.3390/molecules19043851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/02/2022] Open
Abstract
This report presents a new modification of the isoniazid (INH) structure linked with different anilines via a carbonyl group obtained by two synthetic procedures and with N-substituted 5-(pyridine-4-yl)-1,3,4-oxadiazole-2-amines prepared by their cyclisation. All synthesised derivatives were characterised by IR, NMR, MS and elemental analyses and were evaluated in vitro for their antimycobacterial activity against Mycobacterium tuberculosis H37Rv, Mycobacterium avium 330/88, Mycobacterium kansasii 235/80 and one clinical isolated strain of M. kansasii 6509/96. 2-Isonicotinoyl-N-(4-octylphenyl)hydrazinecarboxamide displayed an in vitro efficacy comparable to that of INH for M. tuberculosis with minimum inhibitory concentrations (MICs) of 1–2 μM. Among the halogenated derivatives, the best anti-tuberculosis activity was found for 2-isonicotinoyl-N-(2,4,6-trichlorophenyl)hydrazinecarboxamide (MIC = 4 μM). In silico modelling on the enoyl-acyl carrier protein reductase InhA confirmed that longer alkyl substituents are advantageous for the interactions and affinity to InhA. Most of the hydrazinecarboxamides, especially those derived from 4-alkylanilines, exhibited significant activity against INH-resistant nontuberculous mycobacteria.
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Affiliation(s)
- Zuzana Rychtarčíková
- Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
| | - Martin Krátký
- Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia.
| | - Markéta Komlóová
- Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
| | - Slovenko Polanc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia.
| | - Marijan Kočevar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia.
| | - Jiřina Stolaříková
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health in Ostrava, Partyzánské náměstí 7, 702 00 Ostrava, Czech Republic.
| | - Jarmila Vinšová
- Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic.
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97
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Winck AT, Machado KS, de Souza ON, Ruiz DD. Context-based preprocessing of molecular docking data. BMC Genomics 2014; 14 Suppl 6:S6. [PMID: 24564276 PMCID: PMC3909228 DOI: 10.1186/1471-2164-14-s6-s6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Data preprocessing is a major step in data mining. In data preprocessing, several known techniques can be applied, or new ones developed, to improve data quality such that the mining results become more accurate and intelligible. Bioinformatics is one area with a high demand for generation of comprehensive models from large datasets. In this article, we propose a context-based data preprocessing approach to mine data from molecular docking simulation results. The test cases used a fully-flexible receptor (FFR) model of Mycobacterium tuberculosis InhA enzyme (FFR_InhA) and four different ligands. Results We generated an initial set of attributes as well as their respective instances. To improve this initial set, we applied two selection strategies. The first was based on our context-based approach while the second used the CFS (Correlation-based Feature Selection) machine learning algorithm. Additionally, we produced an extra dataset containing features selected by combining our context strategy and the CFS algorithm. To demonstrate the effectiveness of the proposed method, we evaluated its performance based on various predictive (RMSE, MAE, Correlation, and Nodes) and context (Precision, Recall and FScore) measures. Conclusions Statistical analysis of the results shows that the proposed context-based data preprocessing approach significantly improves predictive and context measures and outperforms the CFS algorithm. Context-based data preprocessing improves mining results by producing superior interpretable models, which makes it well-suited for practical applications in molecular docking simulations using FFR models.
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98
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Encinas L, O'Keefe H, Neu M, Remuiñán MJ, Patel AM, Guardia A, Davie CP, Pérez-Macías N, Yang H, Convery MA, Messer JA, Pérez-Herrán E, Centrella PA, Alvarez-Gómez D, Clark MA, Huss S, O'Donovan GK, Ortega-Muro F, McDowell W, Castañeda P, Arico-Muendel CC, Pajk S, Rullás J, Angulo-Barturen I, Alvarez-Ruíz E, Mendoza-Losana A, Ballell Pages L, Castro-Pichel J, Evindar G. Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA. J Med Chem 2014; 57:1276-88. [PMID: 24450589 DOI: 10.1021/jm401326j] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tuberculosis (TB) is one of the world's oldest and deadliest diseases, killing a person every 20 s. InhA, the enoyl-ACP reductase from Mycobacterium tuberculosis, is the target of the frontline antitubercular drug isoniazid (INH). Compounds that directly target InhA and do not require activation by mycobacterial catalase peroxidase KatG are promising candidates for treating infections caused by INH resistant strains. The application of the encoded library technology (ELT) to the discovery of direct InhA inhibitors yielded compound 7 endowed with good enzymatic potency but with low antitubercular potency. This work reports the hit identification, the selected strategy for potency optimization, the structure-activity relationships of a hundred analogues synthesized, and the results of the in vivo efficacy studies performed with the lead compound 65.
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Affiliation(s)
- Lourdes Encinas
- ELT Boston, Platform Technology & Science, GlaxoSmithKline , Waltham, Massachusetts 02451, United States
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99
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An altered Mycobacterium tuberculosis metabolome induced by katG mutations resulting in isoniazid resistance. Antimicrob Agents Chemother 2014; 58:2144-9. [PMID: 24468786 DOI: 10.1128/aac.02344-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The most common form of drug resistance found in tuberculosis (TB)-positive clinical samples is monoresistance to isoniazid. Various genomics and proteomics studies to date have investigated this phenomenon; however, the exact mechanisms relating to how this occurs, as well as the implications of this on the TB-causing organisms function and structure, are only partly understood. Considering this, we followed a metabolomics research approach to identify potential new metabolic pathways and metabolite markers, which when interpreted in context would give a holistic explanation for many of the phenotypic characteristics associated with a katG mutation and the resulting isoniazid resistance in Mycobacterium tuberculosis. In order to achieve these objectives, gas chromatography-time of flight mass spectrometry (GCxGC-TOFMS)-generated metabolite profiles from two isoniazid-resistant strains were compared to a wild-type parent strain. Principal component analyses showed clear differentiation between the groups, and the metabolites best describing the separation between these groups were identified. It is clear from the data that due to a mutation in the katG gene encoding catalase, the isoniazid-resistant strains experience increased susceptibility to oxidative stress and have consequently adapted to this by upregulating the synthesis of a number of compounds involved in (i) increased uptake and use of alkanes and fatty acids as a source of carbon and energy and (ii) the synthesis of a number of compounds directly involved in reducing oxidative stress, including an ascorbic acid degradation pathway, which to date hasn't been proposed to exist in these organisms.
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100
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Belardinelli JM, Morbidoni HR. Recycling and refurbishing old antitubercular drugs: the encouraging case of inhibitors of mycolic acid biosynthesis. Expert Rev Anti Infect Ther 2014; 11:429-40. [DOI: 10.1586/eri.13.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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