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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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GUPTA S, UNDALE VR, LAKHADIVE K. Novel Targets for Antimicrobials. Turk J Pharm Sci 2020; 17:565-575. [PMID: 33177939 PMCID: PMC7650728 DOI: 10.4274/tjps.galenos.2020.90197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/21/2020] [Indexed: 12/01/2022]
Abstract
Antimicrobial resistance (AMR) is the phenomenon developed by microorganism on exposure to antimicrobial agents, making them unresponsive. Development of microbial confrontation is a severe rising risk to global community well-being as treatment in addition, management of such resistant microbial infections is difficult and challenging. The situation requires action across all government sectors and society. The change in the molecular target on which antimicrobial drugs act is one of the key mechanisms behind AMR. One of the approaches to battle with AMR can be exploring newer molecular targets in microbes and discovering new molecules accordingly. There are various examples of novel targets such as biomolecules involving in biosynthesis of cell wall, biosynthesis of aromatic amino acid, cell disunion, biosynthesis of fatty acid, and isoprenoid biosynthesis and tRNA synthetases. Fatty acid biosynthesis (FAB) and their enzymes among all the above is the more appealing target for the advancement of new antimicrobial agents. Number of promising inhibitors have been developed for bacterial fatty acid synthesis (FAS) and also few of them are clinically used. Some of these potential inhibitors are found to be used in development of new antibacterial as a lead compound and have been discovered from high throughput screening processes like Platencimycin and their analogue, Platencin. The review majorly encompasses bacterial FAB in type II FAS system and potential inhibitors with respective targets of novel antibacterial.
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Affiliation(s)
- Suchita GUPTA
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
| | | | - Kedar LAKHADIVE
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
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Sun J, He W, Liu HY, Qin J, Ye CL. Design, synthesis and molecular docking of 1,4-benzodioxane thiazolidinedione piperazine derivatives as FabH inhibitors. Bioorg Chem 2019; 88:102958. [PMID: 31054434 DOI: 10.1016/j.bioorg.2019.102958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/17/2019] [Accepted: 04/28/2019] [Indexed: 10/26/2022]
Abstract
A series of novel 1,4-benzodioxane thiazolidinedione piperazine derivatives targeting FabH were designed and synthesized. The compounds exhibited better inhibitory activity against Gram-negative bacteria by computer-assisted screening, antibacterial activity test and E. coli FabH inhibitory activity test, wherein compound 6j exhibited the most significant inhibitory activity (MIC = 1.80 μΜ for P. aeruginosa, MIC = 1.56 μΜ for E. coli). Besides, compound 6j still showed the best E. coli FabH inhibitory activity (IC50 = 0.06 μΜ). Moreover, the antibacterial activities of all compounds were strongly correlated with the inhibitory ability of FabH, with a correlation coefficient of 0.954. Computational docking studies also showed that compound 6j has interacting with FabH key residues in the active site.
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Affiliation(s)
- Juan Sun
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China
| | - Wen He
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China
| | - Han-Yu Liu
- School of Life Science, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Jie Qin
- School of Life Science, Shandong University of Technology, Zibo 255049, People's Republic of China
| | - Chun-Lin Ye
- School of Biological & Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou 310023, People's Republic of China.
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Zhou S, Tan S, Fang D, Zhang R, Lin W, Wu W, Zheng K. Computational analysis of binding between benzamide-based derivatives and Abl wt and T315I mutant kinases. RSC Adv 2016. [DOI: 10.1039/c6ra19494j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An integrated computational study was performed to identify the binding mechanisms of benzamide-based derivatives with Abl_wt/Abl_T315I kinases for designing Abl inhibitors.
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Affiliation(s)
- Shengfu Zhou
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Shepei Tan
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Danqing Fang
- Department of Cardiothoracic Surgery
- Affiliated Second Hospital of Guangzhou Medical University
- Guangzhou 510260
- PR China
| | - Rong Zhang
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Weicong Lin
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Wenjuan Wu
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Kangcheng Zheng
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- PR China
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Design, synthesis and molecular modeling of pyrazole–quinoline–pyridine hybrids as a new class of antimicrobial and anticancer agents. Eur J Med Chem 2014; 76:549-57. [DOI: 10.1016/j.ejmech.2014.01.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 01/16/2023]
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Makawana JA, Sun J, Zhu HL. Schiff’s base derivatives bearing nitroimidazole moiety: New class of antibacterial, anticancer agents and potential EGFR tyrosine kinase inhibitors. Bioorg Med Chem Lett 2013; 23:6264-8. [DOI: 10.1016/j.bmcl.2013.09.086] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/29/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
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Zhou Y, Du QR, Sun J, Li JR, Fang F, Li DD, Qian Y, Gong HB, Zhao J, Zhu HL. Novel Schiff-base-derived FabH inhibitors with dioxygenated rings as antibiotic agents. ChemMedChem 2013; 8:433-41. [PMID: 23401291 DOI: 10.1002/cmdc.201200587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Indexed: 11/10/2022]
Abstract
Fatty acid biosynthesis plays a vital role in bacterial survival and several key enzymes involved in this biosynthetic pathway have been identified as attractive targets for the development of new antibacterial agents. Of these promising targets, β-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) is the most attractive target that could trigger the initiation of fatty acid biosynthesis and is highly conserved among Gram-positive and -negative bacteria. Designing small molecules with FabH inhibitory activity displays great significance for developing antibiotic agents, which should be highly selective, nontoxic and broad-spectrum. In this manuscript, a series of novel Schiff base compounds were designed and synthesized, and their biological activities were evaluated as potential inhibitors. Among these 21 new compounds, (E)-N-((3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)methylene)hexadecan-1-amine (10) showed the most potent antibacterial activity with a MIC value of 3.89-7.81 μM(-1) against the tested bacterial strains and exhibited the most potent E. coli FabH inhibitory activity with an IC(50) value of 1.6 μM. Docking simulation was performed to position compound 10 into the E. coli FabH active site to determine the probable binding conformation.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Hankou Road, Nanjing 210093, PR China
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Wang XL, Zhang YB, Tang JF, Yang YS, Chen RQ, Zhang F, Zhu HL. Design, synthesis and antibacterial activities of vanillic acylhydrazone derivatives as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Eur J Med Chem 2012; 57:373-82. [DOI: 10.1016/j.ejmech.2012.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/24/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
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Luo Y, Yang YS, Fu J, Zhu HL. Novel FabH inhibitors: a patent and article literature review (2000--2012). Expert Opin Ther Pat 2012; 22:1325-36. [PMID: 22998551 DOI: 10.1517/13543776.2012.727798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The traditional antimicrobial chemotherapy drugs play their effects mostly via bacterial interference with in vivo amino acids, nucleotides, amino sugars and other small molecule synthesis, or interfering the biochemical processes of these small molecules to synthesize nucleic acids, peptidoglycan and other biological macromolecules. In recent years, enzymes with single function in bacterial fatty acid synthetase system have become the genome-driven novel antibacterial drug targets. Among inhibitors of these targets, FabH inhibitors are distinguished, for their target is different from that of existing antibiotics. Therefore, discovery of FabH inhibitors might be a potential orientation to overcome bacterial resistance. AREAS COVERED This review summarized new patents and articles published on FabH inhibitors from 2000 to 2012. EXPERT OPINION The review gives a brief understanding about the background and development in the area of FabH inhibitors that aims to solve the bacterial resistance problem. This review puts emphasis on some typical small molecules, which participate in the process of FabH inhibition. Overall, the research scopes of antibacterial agents are getting broad. Fatty acid synthase (FAS) pathway has been proved to be a promising target for the therapy. However, claim of novel antibacterial agents with more active and higher specificity is still continued.
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Affiliation(s)
- Yin Luo
- Nanjing University, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing 210093, People's Republic of China
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10
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Luo Y, Zhang LR, Hu Y, Zhang S, Fu J, Wang XM, Zhu HL. Synthesis and Antimicrobial Activities of Oximes Derived from O-Benzylhydroxylamine as FabH Inhibitors. ChemMedChem 2012; 7:1587-93. [DOI: 10.1002/cmdc.201200225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/12/2012] [Indexed: 11/07/2022]
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Yang YS, Zhang F, Gao C, Zhang YB, Wang XL, Tang JF, Sun J, Gong HB, Zhu HL. Discovery and modification of sulfur-containing heterocyclic pyrazoline derivatives as potential novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Bioorg Med Chem Lett 2012; 22:4619-24. [DOI: 10.1016/j.bmcl.2012.05.091] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/14/2012] [Accepted: 05/28/2012] [Indexed: 01/18/2023]
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Zeng GH, Wu WJ, Zhang R, Sun J, Xie WG, Shen Y. 3D-QSAR and Docking Studies of Pyrido[2,3-d]pyrimidine Derivatives as Wee1 Inhibitors. CHINESE J CHEM PHYS 2012. [DOI: 10.1088/1674-0068/25/03/297-307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Discovery of novel selective inhibitors of Staphylococcus aureus β-ketoacyl acyl carrier protein synthase III. Eur J Med Chem 2011; 47:261-9. [PMID: 22104972 DOI: 10.1016/j.ejmech.2011.10.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/22/2011] [Accepted: 10/28/2011] [Indexed: 11/22/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase III (KAS III) is a condensing enzyme in bacterial fatty acid synthesis and a potential target while designing novel antibiotics. In our previous report, we discovered the lead compound YKAs3003, which serves as an inhibitor of Escherichia coli KAS III (ecKAS III), and determined a reliable pharmacophore map from in silico screening. In this study, we determined two pharmacophore maps from receptor-oriented pharmacophore-based in silico screening of the x-ray structure of Staphylococcus aureus KAS III (saKAS III) to identify potent saKAS III inhibitors. We discovered a new potential inhibitor (6) with broad-spectrum antimicrobial activity and 0.8 nM binding affinity for saKAS III, proving the reliability of our pharmacophore map. Using optimization procedures, we identified three new antimicrobial saKAS III inhibitors: 6c (2,4-dichloro-benzoic acid (2,3,4-trihydroxy-benzylidene)-hydrazide), 6e (4-[(3-chloro-pyrazin-2-yl)-hydrazonomethyl]-benzene-1,3-diol), and 6 (4-[(5-trifluoromethyl-pyridin-2-yl)-hydrazonomethyl]-benzene-1,3-diol). All three inhibitors have a novel 4-hydrazonomethyl-benzene-1,3-diol core structure. These inhibitors exhibited high binding affinity to saKAS III and highly selective antimicrobial activities against S. aureus and methicillin-resistant S. aureus, with minimal inhibitory concentration values of 1-2 μg/mL.
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Sridhar J, Foroozesh M, Stevens CK. QSAR models of cytochrome P450 enzyme 1A2 inhibitors using CoMFA, CoMSIA and HQSAR. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:681-697. [PMID: 22004550 PMCID: PMC3371641 DOI: 10.1080/1062936x.2011.623320] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Quantitative structure-activity relationship (QSAR) studies were conducted on an in-house database of cytochrome P450 enzyme 1A2 inhibitors using the comparative molecular field analysis (CoMFA), comparative molecular similarity analysis (CoMSIA) and hologram QSAR (HQSAR) approaches. The database consisted of 36 active molecules featuring varied core structures. The model based on the naphthalene substructure alignment incorporating 19 molecules yielded the best model with a CoMFA cross validation value q(2) of 0.667 and a Pearson correlation coefficient r(2) of 0.976; a CoMSIA q(2) value of 0.616 and r(2) value of 0.985; and a HQSAR q(2) value of 0.652 and r(2) value of 0.917. A second model incorporating 34 molecules aligned using the benzene substructure yielded an acceptable CoMFA model with q(2) value of 0.5 and r(2) value of 0.991. Depending on the core structure of the molecule under consideration, new CYP1A2 inhibitors will be designed based on the results from these models.
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Zhang HJ, Qin X, Liu K, Zhu DD, Wang XM, Zhu HL. Synthesis, antibacterial activities and molecular docking studies of Schiff bases derived from N-(2/4-benzaldehyde-amino) phenyl-N′-phenyl-thiourea. Bioorg Med Chem 2011; 19:5708-15. [DOI: 10.1016/j.bmc.2011.06.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/24/2011] [Accepted: 06/25/2011] [Indexed: 10/17/2022]
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Zhang HJ, Zhu DD, Li ZL, Sun J, Zhu HL. Synthesis, molecular modeling and biological evaluation of β-ketoacyl-acyl carrier protein synthase III (FabH) as novel antibacterial agents. Bioorg Med Chem 2011; 19:4513-9. [DOI: 10.1016/j.bmc.2011.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/05/2011] [Accepted: 06/08/2011] [Indexed: 11/29/2022]
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Li HQ, Luo Y, Zhu HL. Discovery of vinylogous carbamates as a novel class of β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. Bioorg Med Chem 2011; 19:4454-9. [DOI: 10.1016/j.bmc.2011.06.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/13/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
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Li ZL, Li QS, Zhang HJ, Hu Y, Zhu DD, Zhu HL. Design, synthesis and biological evaluation of urea derivatives from o-hydroxybenzylamines and phenylisocyanate as potential FabH inhibitors. Bioorg Med Chem 2011; 19:4413-20. [DOI: 10.1016/j.bmc.2011.06.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/16/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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Liu J, Li Y, Zhang HX, Zhang SW, Yang L. Studies of H4R antagonists using 3D-QSAR, molecular docking and molecular dynamics. J Mol Model 2011; 18:991-1001. [PMID: 21647664 DOI: 10.1007/s00894-011-1137-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 05/23/2011] [Indexed: 12/15/2022]
Abstract
Three-dimensional quantitative structure-activity relationship studies were performed on a series of 88 histamine receptor 4 (H4R) antagonists in an attempt to elucidate the 3D structural features required for activity. Several in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), molecular docking, and molecular dynamics (MD), were carried out. The results show that both the ligand-based CoMFA model (Q (2) = 0.548, R (ncv) (2) = 0.870, R (pre) (2) = 0.879, SEE = 0.410, SEP = 0.386) and the CoMSIA model (Q (2) = 0.526, R (ncv) (2) =0.866, R (pre) (2) = 0.848, SEE = 0.416, SEP = 0.413) are acceptable, as they show good predictive capabilities. Furthermore, a combined analysis incorporating CoMFA, CoMSIA contour maps and MD results shows that (1) compounds with bulky or hydrophobic substituents at positions 4-6 in ring A (R2 substituent), positively charged or hydrogen-bonding (HB) donor groups in the R1 substituent, and hydrophilic or HB acceptor groups in ring C show enhanced biological activities, and (2) the key amino acids in the binding pocket are TRP67, LEU71, ASP94, TYR95, PHE263 and GLN266. To our best knowledge, this work is the first to report the 3D-QSAR modeling of these H4R antagonists. The conclusions of this work may lead to a better understanding of the mechanism of antagonism and aid in the design of new, more potent H4R antagonists.
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Affiliation(s)
- Jing Liu
- Department of Materials Science and Chemical Engineering, Dalian University of Technology, Dalian 116012, Liaoning, China
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Liu J, Li Y, Zhang S, Xiao Z, Ai C. Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics. Int J Mol Sci 2011; 12:1196-221. [PMID: 21541053 PMCID: PMC3083700 DOI: 10.3390/ijms12021196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/25/2011] [Accepted: 02/09/2011] [Indexed: 12/26/2022] Open
Abstract
In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q(2) = 0.603, R(2) (ncv) = 0.829, R(2) (pre) = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q(2) = 0.506, R(2) (ncv) =0.838, R(2) (pre) = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R(3) substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R(1) substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists.
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Affiliation(s)
- Jing Liu
- School of Chemical Engineering, Dalian University of Technology, Dalian, 116012, Liaoning, China; E-Mails: (J.L.); (S.Z.)
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Lv PC, Sun J, Luo Y, Yang Y, Zhu HL. Design, synthesis, and structure-activity relationships of pyrazole derivatives as potential FabH inhibitors. Bioorg Med Chem Lett 2010; 20:4657-60. [PMID: 20594840 DOI: 10.1016/j.bmcl.2010.05.105] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/24/2010] [Accepted: 05/29/2010] [Indexed: 10/19/2022]
Abstract
Fatty acid biosynthesis is essential for bacterial survival. FabH, beta-ketoacyl-acyl carrier protein (ACP) synthase III, is a particularly attractive target, since it is central to the initiation of fatty acid biosynthesis and is highly conserved among Gram-positive and -negative bacteria. Fifty-six 1-acetyl-3,5-diphenyl-4,5-dihydro-(1H)-pyrazole derivatives were synthesized and developed as potent inhibitors of FabH. This inhibitor class demonstrates strong antibacterial activity. Escherichia coli FabH inhibitory assay and docking simulation indicated that the compounds 1-(5-(4-fluorophenyl)-3-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)ethanone (12) and 1-(5-(4-chlorophenyl)-3-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)ethanone (13) were potent inhibitors of E. coli FabH.
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Affiliation(s)
- Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People's Republic of China
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Soung MG, Hwang TY, Sung ND. Synthesis and 3D-QSARs Analyses of Herbicidal O,O-Dialkyl-1-phenoxyacetoxy-1-methylphosphonate Analogues as a New Class of Potent Inhibitors of Pyruvate Dehydrogenase. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.5.1361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Garg A, Tewari R, Raghava GPS. KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. BMC Bioinformatics 2010; 11:125. [PMID: 20222969 PMCID: PMC2841597 DOI: 10.1186/1471-2105-11-125] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 03/11/2010] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Identification of novel drug targets and their inhibitors is a major challenge in the field of drug designing and development. Diaminopimelic acid (DAP) pathway is a unique lysine biosynthetic pathway present in bacteria, however absent in mammals. This pathway is vital for bacteria due to its critical role in cell wall biosynthesis. One of the essential enzymes of this pathway is dihydrodipicolinate synthase (DHDPS), considered to be crucial for the bacterial survival. In view of its importance, the development and prediction of potent inhibitors against DHDPS may be valuable to design effective drugs against bacteria, in general. RESULTS This paper describes a methodology for predicting novel/potent inhibitors against DHDPS. Here, quantitative structure activity relationship (QSAR) models were trained and tested on experimentally verified 23 enzyme's inhibitors having inhibitory value (Ki) in the range of 0.005-22(mM). These inhibitors were docked at the active site of DHDPS (1YXD) using AutoDock software, which resulted in 11 energy-based descriptors. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using best four energy-based descriptors yielding correlation values R/q2 of 0.82/0.67 and MAE of 2.43. Additionally, Support Vector Machine (SVM) based model was developed with three crucial descriptors selected using F-stepping remove-one approach, which enhanced the performance by attaining R/q2 values of 0.93/0.80 and MAE of 1.89. To validate the performance of QSAR models, external cross-validation procedure was adopted which accomplished high training/testing correlation values (q2/r2) in the range of 0.78-0.83/0.93-0.95. CONCLUSIONS Our results suggests that ligand-receptor binding interactions for DHDPS employing QSAR modeling seems to be a promising approach for prediction of antibacterial agents. To serve the experimentalist to develop novel/potent inhibitors, a webserver "KiDoQ" has been developed http://crdd.osdd.net/raghava/kidoq, which allows the prediction of Ki value of a new ligand molecule against DHDPS.
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Affiliation(s)
- Aarti Garg
- Bioinformatics Centre, Institute of Microbial Technology, Sector-39A, Chandigarh, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Rupinder Tewari
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gajendra PS Raghava
- Bioinformatics Centre, Institute of Microbial Technology, Sector-39A, Chandigarh, India
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Li HQ, Luo Y, Lv PC, Shi L, Liu CH, Zhu HL. Design and synthesis of novel deoxybenzoin derivatives as FabH inhibitors and anti-inflammatory agents. Bioorg Med Chem Lett 2010; 20:2025-8. [DOI: 10.1016/j.bmcl.2010.01.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 12/10/2009] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
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Lv PC, Wang KR, Yang Y, Mao WJ, Chen J, Xiong J, Zhu HL. Design, synthesis and biological evaluation of novel thiazole derivatives as potent FabH inhibitors. Bioorg Med Chem Lett 2009; 19:6750-4. [DOI: 10.1016/j.bmcl.2009.09.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/23/2009] [Accepted: 09/26/2009] [Indexed: 10/20/2022]
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Lee PJ, Bhonsle JB, Gaona HW, Huddler DP, Heady TN, Kreishman-Deitrick M, Bhattacharjee A, McCalmont WF, Gerena L, Lopez-Sanchez M, Roncal NE, Hudson TH, Johnson JD, Prigge ST, Waters NC. Targeting the fatty acid biosynthesis enzyme, beta-ketoacyl-acyl carrier protein synthase III (PfKASIII), in the identification of novel antimalarial agents. J Med Chem 2009; 52:952-63. [PMID: 19191586 DOI: 10.1021/jm8008103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of fatty acids to the human malaria parasite, Plasmodium falciparum, and differences due to a type I fatty acid synthesis (FAS) pathway in the parasite, make it an attractive drug target. In the present study, we developed and a utilized a pharmacophore to select compounds for testing against PfKASIII, the initiating enzyme of FAS. This effort identified several PfKASIII inhibitors that grouped into various chemical classes of sulfides, sulfonamides, and sulfonyls. Approximately 60% of the submicromolar inhibitors of PfKASIII inhibited in vitro growth of the malaria parasite. These compounds inhibited both drug sensitive and resistant parasites and testing against a mammalian cell line revealed an encouraging in vitro therapeutic index for the most active compounds. Docking studies into the active site of PfKASIII suggest a potential binding mode that exploits amino acid residues at the mouth of the substrate tunnel.
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Affiliation(s)
- Patricia J Lee
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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Al-Balas Q, Anthony NG, Al-Jaidi B, Alnimr A, Abbott G, Brown AK, Taylor RC, Besra GS, McHugh TD, Gillespie SH, Johnston BF, Mackay SP, Coxon GD. Identification of 2-aminothiazole-4-carboxylate derivatives active against Mycobacterium tuberculosis H37Rv and the beta-ketoacyl-ACP synthase mtFabH. PLoS One 2009; 4:e5617. [PMID: 19440303 PMCID: PMC2680598 DOI: 10.1371/journal.pone.0005617] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/21/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a disease which kills two million people every year and infects approximately over one-third of the world's population. The difficulty in managing tuberculosis is the prolonged treatment duration, the emergence of drug resistance and co-infection with HIV/AIDS. Tuberculosis control requires new drugs that act at novel drug targets to help combat resistant forms of Mycobacterium tuberculosis and reduce treatment duration. METHODOLOGY/PRINCIPAL FINDINGS Our approach was to modify the naturally occurring and synthetically challenging antibiotic thiolactomycin (TLM) to the more tractable 2-aminothiazole-4-carboxylate scaffold to generate compounds that mimic TLM's novel mode of action. We report here the identification of a series of compounds possessing excellent activity against M. tuberculosis H(37)R(v) and, dissociatively, against the beta-ketoacyl synthase enzyme mtFabH which is targeted by TLM. Specifically, methyl 2-amino-5-benzylthiazole-4-carboxylate was found to inhibit M. tuberculosis H(37)R(v) with an MIC of 0.06 microg/ml (240 nM), but showed no activity against mtFabH, whereas methyl 2-(2-bromoacetamido)-5-(3-chlorophenyl)thiazole-4-carboxylate inhibited mtFabH with an IC(50) of 0.95+/-0.05 microg/ml (2.43+/-0.13 microM) but was not active against the whole cell organism. CONCLUSIONS/SIGNIFICANCE These findings clearly identify the 2-aminothiazole-4-carboxylate scaffold as a promising new template towards the discovery of a new class of anti-tubercular agents.
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Affiliation(s)
- Qosay Al-Balas
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Nahoum G. Anthony
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Bilal Al-Jaidi
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Amani Alnimr
- Department of Infection, University College London, London, United Kingdom
| | - Grainne Abbott
- Strathclyde Innovations in Drug Research, Glasgow, United Kingdom
| | - Alistair K. Brown
- School of Biosciences, University of Birmingham, Edgebaston, Birmingham, United Kingdom
| | - Rebecca C. Taylor
- School of Biosciences, University of Birmingham, Edgebaston, Birmingham, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgebaston, Birmingham, United Kingdom
| | - Timothy D. McHugh
- Department of Infection, University College London, London, United Kingdom
| | | | - Blair F. Johnston
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Simon P. Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Geoffrey D. Coxon
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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Pasha FA, Muddassar M, Joo Cho S. Molecular Docking and 3D QSAR Studies of Chk2 Inhibitors. Chem Biol Drug Des 2009; 73:292-300. [DOI: 10.1111/j.1747-0285.2009.00773.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ashek A, San Juan AA, Cho SJ. HQSAR study of β-ketoacyl‐acyl carrier protein synthase III (FabH) inhibitors. J Enzyme Inhib Med Chem 2008; 22:7-14. [PMID: 17373541 DOI: 10.1080/14756360600920149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The enzyme FabH catalyzes the initial step of fatty acid biosynthesis via a type II fatty acid synthase. The pivotal role of this essential enzyme combined with its unique structural features and ubiquitous occurrence in bacteria has made it an attractive new target for the development of antibacterial and antiparasitic compounds. Predictive hologram quantitative structure activity relationship (HQSAR) model was developed for a series of benzoylamino benzoic acid derivatives acting as FabH inhibitor. The best HQSAR model was generated using atoms and bond types as fragment distinction and 4-7 as fragment size showing cross-validated q2 value of 0.678 and conventional r2 value of 0.920. The predictive ability of the model was validated by an external test set of 6 compounds giving satisfactory predictive r2 value of 0.82. The contribution maps obtained from this model were used to explain the individual atomic contributions to the overall activity. It was confirmed from the contribution map that both ring A and ring C play a vital role for activity. Moreover hydroxyl substitution in the ortho position of ring A is favorable for better inhibitory activity. Therefore the information derived from the contribution map can be used to design potent FabH inhibitors.
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Affiliation(s)
- Ali Ashek
- Korea Institute of Science and Technology, Biochemicals Research Center, Cheongryang, Seoul 130-650, South Korea
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Pasha FA, Muddassar M, Lee C, Cho SJ. Mechanism based QSAR studies of N-phenylbenzamides as antimicrobial agents. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2008; 26:128-135. [PMID: 21783900 DOI: 10.1016/j.etap.2008.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 05/31/2023]
Abstract
N-Phenyl benzamides are potent antibacterial agents. They are active against both Gram-positive and Gram-negative bacteria. The Gram-positive bacteria have strong and thick cell wall while the Gram-negative bacterial have thin and permeable cell wall. The DFT based QSAR reveals that molecular weight and total energy significantly contribute to activity against both kinds of target. The electrophilicity index involved in QSAR models derived with anti-Gram-positive activity indicates the dominance of electrostatic interaction. The molar refractivity and logP is involved in QSAR model derived with anti-Gram-negative activity shows steric and hydrophobic interaction. The CoMFA and CoMSIA results also indicate that anti-Gram-positive bacterial activity is a function of electrostatic field effect but the anti-Gram-negative activity depends on hydrophobicity and steric field effect. The CoMFA and CoMSIA contour maps give an indication, the electropositive group around benzene "X" and an electronegative group around carbonyl oxygen is desirable for better anti-Gram-positive bacterial activity. A hydrophobic group around meta position of ring "X" with bulky group at ortho position and a small group at para position are desirable for better activity against Gram-negative target. The findings are reasonable and the mechanism might be different due to difference in composition of cell wall. The cell wall of Gram-positive target does not allow the permeability and only external electrostatic interaction is possible while the cell wall of Gram-negative target allows the permeability of molecules inside the cell for possible hydrophobic and steric bulk interaction.
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Affiliation(s)
- F A Pasha
- Computational Science Center, Future Fusion Technology Division, Korea Institute of Science and Technology, P.O. Box 131, Seoul 130-650, South Korea
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Pasha FA, Muddassar M, Beg Y, Cho SJ. DFT-based de novo QSAR of Phenoloxidase Inhibitors. Chem Biol Drug Des 2008; 71:483-493. [PMID: 18402556 DOI: 10.1111/j.1747-0285.2008.00651.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: 11/29/2022]
Abstract
The phenoloxidase or tyrosinase is a key enzyme in insects, which is responsible for hydroxylation of tyrosine into o-quinones via o-diphenols. A series of benzaldehyde thiosemicarbazone, benzaldehyde and benzoic acid families were taken with their pragmatic pIC(50) values against phenoloxidase from pieris rapae (Lepidoptera) larvae. Density functional theory-based quantitative structure-activity relationship (QSAR) analyses were performed to speculate the key interaction. The most fitted four different QSAR models were identified and discussed. The softness, electrophilicity index, molar refractivity and log P were identified as best descriptors; however, the atomic values of softness and philicity obtained from Fukui function are more significant than global values. The study reveals that electrostatic and steric fields jointly contribute to activity. To gain further insight, the three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses were performed using two molecular field techniques: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The successful 3D-QSAR models were obtained from CoMFA (q(2)= 0.94, r(2)= 0.99, r(2)(pred)= 0.92) and CoMSIA (q(2)= 0.94, r(2)= 0.98, r(2)(pred)= 0/95). The CoMFA and CoMSIA results indicate that, a bulky and negative group around sulfur atom but a small and positive group around nitrogen atom might have good effects on activity. The ortho and meta positions of ring are favorable for small group. These QSAR models might be helpful to design the novel and potent inhibitors.
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Affiliation(s)
- Farhan Ahmad Pasha
- Computational Science Center, Future Fusion Technology Division, Korea Institute of Science and Technology, PO Box 131, Seoul 130-650, South KoreaDepartment of Chemistry, Bareilly College, Bareilly, IndiaCollege of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Korea
| | - Muhhammad Muddassar
- Computational Science Center, Future Fusion Technology Division, Korea Institute of Science and Technology, PO Box 131, Seoul 130-650, South KoreaDepartment of Chemistry, Bareilly College, Bareilly, IndiaCollege of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Korea
| | - Yakub Beg
- Computational Science Center, Future Fusion Technology Division, Korea Institute of Science and Technology, PO Box 131, Seoul 130-650, South KoreaDepartment of Chemistry, Bareilly College, Bareilly, IndiaCollege of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Korea
| | - Seung Joo Cho
- Computational Science Center, Future Fusion Technology Division, Korea Institute of Science and Technology, PO Box 131, Seoul 130-650, South KoreaDepartment of Chemistry, Bareilly College, Bareilly, IndiaCollege of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Korea
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Bandyopadhyaya AK, Tiwari R, Tjarks W. Comparative molecular field analysis and comparative molecular similarity indices analysis of boron-containing human thymidine kinase 1 substrates. Bioorg Med Chem 2006; 14:6924-32. [PMID: 16828556 DOI: 10.1016/j.bmc.2006.06.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 06/14/2006] [Accepted: 06/19/2006] [Indexed: 10/24/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) using CoMFA and CoMSIA techniques was applied to evaluate 56 pyrimidine nucleosides as substrates of human thymidine kinase 1 (hTK1), 27 of them containing a carborane substituent either at the 3-, 5-, or 3'-position of the 2'-deoxyuridine scaffold. This is the first report describing 3D-QSAR studies of compounds containing boron atoms. Both CoMFA and CoMSIA models were derived from a training set of 47 molecules and the predictive capacity of the CoMSIA model was successfully validated by accurately calculating known phosphorylation rates of both boronated and non-boron hTK1 substrates that were not included in the training set. The optimal CoMSIA model provided the following values: q(2) 0.622, r(2) 0.983, s 0.165, and F 187.5. Contour maps obtained from the CoMSIA model were in agreement with the experimentally determined biological data.
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Affiliation(s)
- Achintya K Bandyopadhyaya
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
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