1
|
Identification of Novel Inhibitor of Enoyl-Acyl Carrier Protein Reductase (InhA) Enzyme in Mycobacterium tuberculosis from Plant-Derived Metabolites: An In Silico Study. Antibiotics (Basel) 2022; 11:antibiotics11081038. [PMID: 36009907 PMCID: PMC9405319 DOI: 10.3390/antibiotics11081038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb.) enoyl-acyl carrier protein (ACP) reductase (InhA) is validated as a useful target for tuberculosis therapy and is considered an attractive enzyme to drug discovery. This study aimed to identify the novel inhibitor of the InhA enzyme, a potential target of M.tb. involved in the type II fatty acid biosynthesis pathway that controls mycobacterial cell envelope synthesis. We compiled 80 active compounds from Ruta graveolens and citrus plants belonging to the Rutaceae family for pharmacokinetics and molecular docking analyses. The chemical structures of the 80 phytochemicals and the 3D structure of the target protein were retrieved from the PubChem database and RCSB Protein Data Bank, respectively. The evaluation of druglikeness was performed based on Lipinski’s Rule of Five, while the computed phytochemical properties and molecular descriptors were used to predict the ADMET of the compounds. Amongst these, 11 pharmacokinetically-screened compounds were further examined by performing molecular docking analysis with an InhA target using AutoDock 4.2. The docking results showed that gravacridonediol, a major glycosylated natural alkaloid from Ruta graveolens, might possess a promising inhibitory potential against InhA, with a binding energy (B.E.) of −10.80 kcal/mole and inhibition constant (Ki) of 600.24 nM. These contrast those of the known inhibitor triclosan, which has a B.E. of −6.69 kcal/mole and Ki of 12.43 µM. The binding efficiency of gravacridonediol was higher than that of the well-known inhibitor triclosan against the InhA target. The present study shows that the identified natural compound gravacridonediol possesses drug-like properties and also holds promise in inhibiting InhA, a key target enzyme of M.tb.
Collapse
|
2
|
Kumar V, Jhamb SS, Sobhia ME. Cell wall permeability assisted virtual screening to identify potential direct InhA inhibitors of Mycobacterium tuberculosis and their biological evaluation. J Biomol Struct Dyn 2017; 36:3274-3290. [PMID: 28974157 DOI: 10.1080/07391102.2017.1387176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The arising cases of isoniazid-resistance have motivated research interests toward new class of molecules known as direct InhA inhibitors. Here, a combine approach of shape-based pharmacophore and descriptor-based 2D QSAR was used to identify the potential direct InhA inhibitors. The approach is duly assisted with in vitro testing and molecular dynamics simulations. A combination of empirical parameters was derived to use as a filter for cell wall permeability while 2D QSAR was used as another filter to predict the biological activity. Both filters were applied to prioritize the molecules for biological evaluation against anti-TB activity. It led to 6 potential molecules which showed > 90% inhibition of H37Rv strain of Mycobacterium tuberculosis in BACTEC assay. Further, MMGBSA binding free energy of identified molecules was compared with available highly potent molecule, 5-hexyl-2-(2-methylphenoxy) phenol (IC50 = 5nM) using molecular dynamics simulations. It showed two molecules with comparatively higher affinity toward InhA as compared to potent molecule. It indicated the candidature of identified molecules to be further considered in anti-TB drug development pipeline.
Collapse
Affiliation(s)
- Vivek Kumar
- a Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Sarbjit Singh Jhamb
- b Common Biological Testing Lab (CBTL), Department of Pharmaceuticals , National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - M Elizabeth Sobhia
- a Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| |
Collapse
|
3
|
Lone MY, Manhas A, Athar M, Jha PC. Identification of InhA inhibitors: A combination of virtual screening, molecular dynamics simulations and quantum chemical studies. J Biomol Struct Dyn 2017; 36:2951-2965. [DOI: 10.1080/07391102.2017.1372313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Mohd. Athar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| |
Collapse
|
4
|
Lone MY, Athar M, Gupta VK, Jha PC. Identification of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase inhibitors: A combined in-silico and in-vitro analysis. J Mol Graph Model 2017; 76:172-180. [DOI: 10.1016/j.jmgm.2017.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 01/20/2023]
|
5
|
Gomes MN, Braga RC, Grzelak EM, Neves BJ, Muratov E, Ma R, Klein LL, Cho S, Oliveira GR, Franzblau SG, Andrade CH. QSAR-driven design, synthesis and discovery of potent chalcone derivatives with antitubercular activity. Eur J Med Chem 2017; 137:126-138. [PMID: 28582669 DOI: 10.1016/j.ejmech.2017.05.026] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
New anti-tuberculosis (anti-TB) drugs are urgently needed to battle drug-resistant Mycobacterium tuberculosis strains and to shorten the current 6-12-month treatment regimen. In this work, we have continued the efforts to develop chalcone-based anti-TB compounds by using an in silico design and QSAR-driven approach. Initially, we developed SAR rules and binary QSAR models using literature data for targeted design of new heteroaryl chalcone compounds with anti-TB activity. Using these models, we prioritized 33 compounds for synthesis and biological evaluation. As a result, 10 heteroaryl chalcone compounds (4, 8, 9, 11, 13, 17-20, and 23) were found to exhibit nanomolar activity against replicating mycobacteria, low micromolar activity against nonreplicating bacteria, and nanomolar and micromolar against rifampin (RMP) and isoniazid (INH) monoresistant strains (rRMP and rINH) (<1 μM and <10 μM, respectively). The series also show low activity against commensal bacteria and generally show good selectivity toward M. tuberculosis, with very low cytotoxicity against Vero cells (SI = 11-545). Our results suggest that our designed heteroaryl chalcone compounds, due to their high potency and selectivity, are promising anti-TB agents.
Collapse
Affiliation(s)
- Marcelo N Gomes
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Edyta M Grzelak
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil; Postgraduate Program of Society, Technology and Environment, University Center of Anápolis/UniEVANGELICA, Anápolis, Goiás, 75083-515, Brazil
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27955-7568, United States; Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Larry L Klein
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | | | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States.
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil.
| |
Collapse
|
6
|
Ahamad S, Rahman S, Khan FI, Dwivedi N, Ali S, Kim J, Imtaiyaz Hassan M. QSAR based therapeutic management of M. tuberculosis. Arch Pharm Res 2017; 40:676-694. [PMID: 28456911 DOI: 10.1007/s12272-017-0914-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/06/2017] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is responsible for severe mortality and morbidity worldwide but, under-developed and developing countries are more prone to infection. In search of effective and wide-spectrum anti-tubercular agents, interdisciplinary approaches are being explored. Of the several approaches used, computer based quantitative structure activity relationship (QSAR) have gained momentum. Structure-based drug design and discovery implies a combined knowledge of accurate prediction of ligand poses with the good prediction and interpretation of statistically validated models derived from the 3D-QSAR approach. The validated models are generally used to screen a small combinatorial library of potential synthetic candidates to identify hits which further subjected to docking to filter out compounds as novel potential emerging drug molecules to address multidrug-resistant tuberculosis. Several newer models are integrated to QSAR methods which include different types of chemical and biological data, and simultaneous prediction of pharmacological activities including toxicities and/or other safety profiles to get new compounds with desired activity. In the process, several newer molecules have been identified which are now being assessed for their clinical efficacy. Present review deals with the advances made in the field highlighting overall future prospects of the development of anti-tuberculosis drugs.
Collapse
Affiliation(s)
- Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, 450001, China.,Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa
| | - Neeraja Dwivedi
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India.
| |
Collapse
|
7
|
Morales-Bayuelo A. Analyzing the substitution effect on the CoMFA results within the framework of density functional theory (DFT). J Mol Model 2016; 22:164. [PMID: 27329189 DOI: 10.1007/s00894-016-3036-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
Though QSAR was originally developed in the context of physical organic chemistry, it has been applied very extensively to chemicals (drugs) which act on biological systems, in this idea one of the most important QSAR methods is the 3D QSAR model. However, due to the complexity of understanding the results it is necessary to postulate new methodologies to highlight their physical-chemical meaning. In this sense, this work postulates new insights to understand the CoMFA results using molecular quantum similarity and chemical reactivity descriptors within the framework of density functional theory. To obtain these insights a simple theoretical scheme involving quantum similarity (overlap, coulomb operators, their euclidean distances) and chemical reactivity descriptors such as chemical potential (μ), hardness (ɳ), softness (S), electrophilicity (ω), and the Fukui functions, was used to understand the substitution effect. In this sense, this methodology can be applied to analyze the biological activity and the stabilization process in the non-covalent interactions on a particular molecular set taking a reference compound.
Collapse
Affiliation(s)
- Alejandro Morales-Bayuelo
- Grupo de Química Cuántica y Teórica de la Universidad de Cartagena, Facultad de Ciencias, Programa de Química, Cartagena de Indias, Colombia. .,FONDECYT Postdoctoral Project N0 3150035, Universidad de Talca, Talca, Chile.
| |
Collapse
|
8
|
Shah P, Saquib M, Sharma S, Husain I, Sharma SK, Singh V, Srivastava R, Shaw AK, Siddiqi MI. 3D-QSAR and molecular modeling studies on 2,3-dideoxy hexenopyranosid-4-uloses as anti-tubercular agents targeting alpha-mannosidase. Bioorg Chem 2015; 59:91-6. [PMID: 25727263 DOI: 10.1016/j.bioorg.2015.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 11/18/2022]
Abstract
Ligand-based and structure-based methods were applied in combination to exploit the physicochemical properties of 2,3-dideoxy hex-2-enopyranosid-4-uloses against Mycobacterium tuberculosis H37Rv. Statistically valid 3D-QSAR models with good correlation and predictive power were obtained with CoMFA steric and electrostatic fields (r(2) = 0.797, q(2) = 0.589) and CoMSIA with combined steric, electrostatic, hydrophobic and hydrogen bond acceptor fields (r(2) = 0.867, q(2) = 0.570) based on training set of 33 molecules with predictive r(2) of 0.808 and 0.890 for CoMFA and CoMSIA respectively. The results illustrate the requirement of optimal alkyl chain length at C-1 position and acceptor groups along hydroxy methyl substituent of C-6 to enhance the anti-tubercular activity of the 2,3-dideoxy hex-2-enopyranosid-4-uloses while any substitution at C-3 position exert diminishing effect on anti-tubercular activity of these enulosides. Further, homology modeling of M. tuberculosis alpha-mannosidase followed by molecular docking and molecular dynamics simulations on co-complexed models were performed to gain insight into the rationale for binding affinity of selected inhibitors with the target of interest. The comprehensive information obtained from this study will help to better understand the structural basis of biological activity of this class of molecules and guide further design of more potent analogues as anti-tubercular agents.
Collapse
Affiliation(s)
- Priyanka Shah
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Mohammad Saquib
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Smriti Sharma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Irfan Husain
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Sandeep K Sharma
- Microbiology Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Vinayak Singh
- Microbiology Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Ranjana Srivastava
- Microbiology Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Arun K Shaw
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India.
| |
Collapse
|
9
|
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: 1.4] [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
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Pauli I, dos Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LFSM, Basso LA, Santos DS, Guido RVC, Andricopulo AD, Norberto de Souza O. Discovery of new inhibitors of Mycobacterium tuberculosis InhA enzyme using virtual screening and a 3D-pharmacophore-based approach. J Chem Inf Model 2013; 53:2390-401. [PMID: 23889525 DOI: 10.1021/ci400202t] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis InhA (MtInhA) is an attractive enzyme to drug discovery efforts due to its validation as an effective biological target for tuberculosis therapy. In this work, two different virtual-ligand-screening approaches were applied in order to identify new InhA inhibitors' candidates from a library of ligands selected from the ZINC database. First, a 3-D pharmacophore model was built based on 36 available MtInhA crystal structures. By combining structure-based and ligand-based information, four pharmacophoric points were designed to select molecules able to satisfy the binding features of MtInhA substrate-binding cavity. The second approach consisted of using four well established docking programs, with different search algorithms, to compare the binding mode and score of the selected molecules from the aforementioned library. After detailed analyses of the results, six ligands were selected for in vitro analysis. Three of these molecules presented a satisfactory inhibitory activity with IC50 values ranging from 24 (±2) μM to 83 (±5) μM. The best compound presented an uncompetitive inhibition mode to NADH and 2-trans-dodecenoyl-CoA substrates, with Ki values of 24 (±3) μM and 20 (±2) μM, respectively. These molecules were not yet described as antituberculars or as InhA inhibitors, making its novelty interesting to start efforts on ligand optimization in order to identify new effective drugs against tuberculosis having InhA as a target. More studies are underway to dissect the discovered uncompetitive inhibitor interactions with MtInhA.
Collapse
Affiliation(s)
- Ivani Pauli
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO, Faculdade de Informática, PUCRS , Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Gurdal EE, Durmaz I, Cetin-Atalay R, Yarim M. Synthesis and cytotoxicity studies of novel benzhydrylpiperazine carboxamide and thioamide derivatives. J Enzyme Inhib Med Chem 2013; 29:205-14. [DOI: 10.3109/14756366.2013.765416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Enise Ece Gurdal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University
Kayisdagi, IstanbulTurkey
| | - Irem Durmaz
- Department of Molecular Biology and Genetics, BilGen, Genetics and Biotechnology Research Center, Faculty of Science, Bilkent University
Bilkent, AnkaraTurkey
| | - Rengul Cetin-Atalay
- Department of Molecular Biology and Genetics, BilGen, Genetics and Biotechnology Research Center, Faculty of Science, Bilkent University
Bilkent, AnkaraTurkey
| | - Mine Yarim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University
Kayisdagi, IstanbulTurkey
| |
Collapse
|
13
|
Abstract
The search for small molecules with activity against Mycobacterium tuberculosis increasingly uses -high-throughput screening and computational methods. Previously, we have analyzed recent studies in which computational tools were used for cheminformatics. We have now updated this analysis to illustrate how they may assist in finding desirable leads for tuberculosis drug discovery. We provide our thoughts on strategies for drug discovery efforts for neglected diseases.
Collapse
Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay Varina, NC, USA
| | | |
Collapse
|
14
|
Binding site analysis, 3D-QSAR studies, and molecular design of flavonoids derivatives as potent neuraminidase inhibitors. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0054-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
15
|
Ekins S, Freundlich JS, Choi I, Sarker M, Talcott C. Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery. Trends Microbiol 2011; 19:65-74. [PMID: 21129975 PMCID: PMC3034835 DOI: 10.1016/j.tim.2010.10.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/15/2010] [Accepted: 10/29/2010] [Indexed: 01/31/2023]
Abstract
We are witnessing the growing menace of both increasing cases of drug-sensitive and drug-resistant Mycobacterium tuberculosis strains and the challenge to produce the first new tuberculosis (TB) drug in well over 40 years. The TB community, having invested in extensive high-throughput screening efforts, is faced with the question of how to optimally leverage these data to move from a hit to a lead to a clinical candidate and potentially, a new drug. Complementing this approach, yet conducted on a much smaller scale, cheminformatic techniques have been leveraged and are examined in this review. We suggest that these computational approaches should be optimally integrated within a workflow with experimental approaches to accelerate TB drug discovery.
Collapse
Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 601 Runnymede Avenue, Jenkintown, PA 19046, USA.
| | | | | | | | | |
Collapse
|
16
|
Rational questing for potential novel inhibitors of FabK from Streptococcus pneumoniae by combining FMO calculation, CoMFA 3D-QSAR modeling and virtual screening. J Mol Model 2010; 17:1483-92. [DOI: 10.1007/s00894-010-0847-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 09/02/2010] [Indexed: 01/04/2023]
|
17
|
Insight into crucial inhibitor–enzyme interaction of arylamides as novel direct inhibitors of the enoyl ACP reductase (InhA) from Mycobacterium tuberculosis: computer-aided molecular design. MONATSHEFTE FUR CHEMIE 2010. [DOI: 10.1007/s00706-010-0359-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Sun J, Cai S, Mei H, Li J, Yan N, Wang Q, Lin Z, Huo D. Molecular Docking and QSAR Studies on Substituted Acyl(thio)urea and Thiadiazolo [2,3-α] Pyrimidine Derivatives as Potent Inhibitors of Influenza Virus Neuraminidase. Chem Biol Drug Des 2010; 76:245-54. [DOI: 10.1111/j.1747-0285.2010.01006.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
19
|
Stoddard SV, Yu X, Potter PM, Wadkins RM. In Silico Design and Evaluation of Carboxylesterase Inhibitors. JOURNAL OF PEST SCIENCE 2010; 35:240-249. [PMID: 23487487 PMCID: PMC3593733 DOI: 10.1584/jpestics.r10-06] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Carboxylesterases (CEs) are important enzymes that catalyze biological detoxification, hydrolysis of certain pesticides, and metabolism of many esterified drugs. The development of inhibitors for CE has many potential uses, including increasing drug lifetime and altering biodistrubution; reducing or abrogating toxicity of metabolized drugs; and reducing pest resistance to insecticides. In this review, we discuss the major classes of known mammalian CE inhibitors and describe our computational efforts to design new scaffolds for development of novel, selective inhibitors. We discuss several strategies for in silico inhibitor development, including structure docking, database searching, multidimensional quantitative structure activity analysis (QSAR), and a newly-used approach that uses QSAR combined with de novo drug design. While our research is focused on design of specific inhibitors for human intestinal carboxylesterase (hiCE), the methods described are generally applicable to inhibitors of other enzymes, including CE from other tissues and organisms.
Collapse
Affiliation(s)
- Shana V. Stoddard
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Xiaozhen Yu
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Philip M. Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| |
Collapse
|
20
|
Lu XY, Chen YD, You QD. 3D-QSAR studies of arylcarboxamides with inhibitory activity on InhA using pharmacophore-based alignment. Chem Biol Drug Des 2009; 75:195-203. [PMID: 20028393 DOI: 10.1111/j.1747-0285.2009.00926.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enoyl acyl carrier protein reductase (InhA) is a promising target for the development of antituberculosis drugs. The InhA-bound conformation of an indole-5-amide inhibitor (Genz 10850) (PDB code: IP44) was used to build a pharmacophore model by LigandScout. This model was then successfully used to identify the bioactive conformation and align 40 structurally diverse arylcarboxamide derivatives. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on arylcarboxamides-based InhA inhibitors based on pharmacophore alignment. The best prediction was obtained with CoMSIA model combining steric and electrostatic fields (, r(2) = 0.972). The model was validated by an external test set, which gave a good predictive value (). Graphical interpretation of the results revealed important structural features of the zarylcarboxamides related to the active site of InhA. The results may be exploited for further design and virtual screening for some novel InhA inhibitors.
Collapse
Affiliation(s)
- Xiao-Yun Lu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | | | | |
Collapse
|
21
|
Lu XY, Chen YD, Jiang YJ, You QD. Discovery of potential new InhA direct inhibitors based on pharmacophore and 3D-QSAR analysis followed by in silico screening. Eur J Med Chem 2009; 44:3718-30. [PMID: 19428156 DOI: 10.1016/j.ejmech.2009.03.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Revised: 03/28/2009] [Accepted: 03/30/2009] [Indexed: 11/25/2022]
Abstract
This study develops an efficient approach for discovering new InhA direct inhibitors in theory. The InhA-bound conformation of a pyrrolidine carboxamide inhibitor was used to build a pharmacophore model. This model with feature-shape query was successfully used to identify and align the bioactive conformations of pyrrolidine carboxamide analogues and screen SPECS database. A statistically valid 3D-QSAR with good results (r(2)(cv)=0.660 and r(2)=0.962) was obtained. From database screening, 30 hits were selected and identified as potential leads, which exhibit good estimated activities by 3D-QSAR model. Docking studies were carried out on two representative hits to analyze their interactions with InhA. Also, the interactions between existing pyrazole inhibitors and InhA were explored based on the pharmacophore model.
Collapse
Affiliation(s)
- Xiao-Yun Lu
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | | | | | | |
Collapse
|