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Chen W, Li A, Wang J, Zhong H, Yuan J, Luo Y, Ou J, Chen J, Li L. A Combined approach of QSAR study, molecular docking and pharmacokinetics prediction of promising Amide-Ac6-aminoacetonitriles Cathepsin K inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Wang J, Chen W, Zhong H, Luo Y, Zhang L, He L, Wu C, Li L. Identify of promising isoquinolone JNK1 inhibitors by combined application of 3D-QSAR, molecular docking and molecular dynamics simulation approaches. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Wang J, Peng W, Li X, Fan W, Wei D, Wu B, Fan L, Wu C, Li L. Towards to potential 2-cyano-pyrimidines cathepsin-K inhibitors: An in silico design and screening research based on comprehensive application of quantitative structure–activity relationships, molecular docking and ADMET prediction. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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4
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Wang JL, Li L, Hu MB, Wu B, Fan WX, Peng W, Wei DN, Wu CJ. In silico drug design of inhibitor of nuclear factor kappa B kinase subunit beta inhibitors from 2-acylamino-3-aminothienopyridines based on quantitative structure–activity relationships and molecular docking. Comput Biol Chem 2019; 78:297-305. [DOI: 10.1016/j.compbiolchem.2018.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 11/17/2022]
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5
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Nandi S, Ahmed S, Saxena AK. Combinatorial design and virtual screening of potent anti-tubercular fluoroquinolone and isothiazoloquinolone compounds utilizing QSAR and pharmacophore modelling. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:151-170. [PMID: 29347843 DOI: 10.1080/1062936x.2017.1419375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/16/2017] [Indexed: 05/19/2023]
Abstract
The virulence of tuberculosis infections resistant to conventional combination drug regimens cries for the design of potent fluoroquinolone compounds to be used as second line antimycobacterial chemotherapeutics. One of the most effective in silico methods is combinatorial design and high throughput screening by a ligand-based pharmacophore prior to experiment. The combinatorial design of a series of 3850 fluoroquinolone and isothiazoloquinolone compounds was then screened virtually by applying a topological descriptor based quantitative structure activity relationship (QSAR) for predicting highly active congeneric quinolone leads against Mycobacterium fortuitum and Mycobacterium smegmatis. The predicted highly active congeneric hits were then subjected to a comparative study between existing lead sparfloxacin with fluoroquinolone FQ hits as well as ACH-702 with predicted active isothiazoloquinolones, utilizing pharmacophore modelling to focus on the mechanism of drug binding against mycobacterial DNA gyrase. Finally, 68 compounds including 34 FQ and 34 isothiazoloquinolones were screened through high throughput screening comprising QSAR, the Lipinski rule of five and ligand-based pharmacophore modelling.
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Affiliation(s)
- S Nandi
- a Division of Pharmaceutical Chemistry , Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University , Kashipur , India
| | - S Ahmed
- a Division of Pharmaceutical Chemistry , Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University , Kashipur , India
| | - A K Saxena
- b Division of Medicinal and Process Chemistry , CSIR-Central Drug Research Institute , Lucknow , India
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Chitre TS, Asgaonkar KD, Patil SM, Kumar S, Khedkar VM, Garud DR. QSAR, docking studies of 1,3-thiazinan-3-yl isonicotinamide derivatives for antitubercular activity. Comput Biol Chem 2017; 68:211-218. [PMID: 28411471 DOI: 10.1016/j.compbiolchem.2017.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/17/2017] [Accepted: 03/28/2017] [Indexed: 11/24/2022]
Abstract
The enzyme - enoyl acyl carrier protein reductase (enoyl ACP reductase) is a validated target for antitubercular activity. Inhibition of this enzyme interferes with mycolic acid synthesis which is crucial for Mycobacterium tuberculosis cell growth. In the present work 2D and 3D quantitative structure activity relationship (QSAR) studies were carried out on a series of thiazinan-Isoniazid pharmacophore to design newer analogues. For 2D QSAR, the best statistical model was generated using SA-MLR method (r2=0.958, q2=0.922) while 3D QSAR model was derived using the SA KNN method (q2=0.8498). These studies could guide the topological, electrostatic, steric, hydrophobic substitutions around the nucleus based on which the NCEs were designed. Furthermore, molecular docking was performed to gauze the binding affinity of the designed analogues for enoyl ACP reductase enzyme. Amongst all the designed analogues the binding energies of SKS 01 and SKS 05 were found to be -5.267kcal/mol and -5.237kcal/mol respectively which was comparable with the binding energy of the standard Isoniazid (-6.254kcal/mol).
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Affiliation(s)
- Trupti S Chitre
- Department of Pharmaceutical Chemistry, All India Shri Shivaji Memorial Society's College of Pharmacy, Kennedy Road, Near R.T.O., Pune 411001, M.S., India.
| | - Kalyani D Asgaonkar
- Department of Pharmaceutical Chemistry, All India Shri Shivaji Memorial Society's College of Pharmacy, Kennedy Road, Near R.T.O., Pune 411001, M.S., India
| | - Shital M Patil
- Department of Pharmaceutical Chemistry, All India Shri Shivaji Memorial Society's College of Pharmacy, Kennedy Road, Near R.T.O., Pune 411001, M.S., India
| | - Shiva Kumar
- Department of Pharmaceutical Chemistry, All India Shri Shivaji Memorial Society's College of Pharmacy, Kennedy Road, Near R.T.O., Pune 411001, M.S., India
| | - Vijay M Khedkar
- Paris Saclay University, U892 INRA, 78350 Jouy en Josas, France
| | - Dinesh R Garud
- Department of Chemistry, Sir Parashurambhau College, Affiliated to Savitribai Phule Pune University, Tilak Road, Pune 411030, India
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Sharma MC. A Structure-Activity Relationship Study of Naphthoquinone Derivatives as Antitubercular Agents Using Molecular Modeling Techniques. Interdiscip Sci 2015; 7:346-56. [PMID: 26159131 DOI: 10.1007/s12539-015-0011-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 11/25/2022]
Abstract
Tuberculosis (TB) is one of the major causes of death worldwide. Mycobacterium tuberculosis, the leading causative agent of TB, is responsible for the morbidity and mortality of a large population worldwide. In view of above and as a part of our effort to develop new and potent anti-TB agents, a series of substituted naphthoquinone derivatives were subjected to molecular modeling using various feature selection methods. The statistically significant best 2D-QSAR model having correlation coefficient [Formula: see text] and cross-validated squared correlation coefficient [Formula: see text] with external predictive ability of [Formula: see text] was developed by SA-PLS, and group-based QSAR model having [Formula: see text] and [Formula: see text] with [Formula: see text] was developed by SA-PLS. Further analysis using three-dimensional QSAR technique identifies a suitable model obtained by SA-partial least square method leading to antitubercular activity prediction. k-nearest neighbor molecular field analysis was used to construct the best 3D-QSAR model using SA-PLS method, showing good correlative and predictive capabilities in terms of [Formula: see text] and [Formula: see text]. The pharmacophore analysis results obtained from this study show that the distance between the aromatic/hydrophobic and the naphthoquinone moiety sites to the aliphatic and acceptor groups should be connected with almost the same distance for significant antitubercular activity. The information rendered by QSAR models may lead to a better understanding of structural requirements of antitubercular activity and also can help in the design of novel potent antitubercular activity.
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Affiliation(s)
- Mukesh C Sharma
- Drug Research Laboratory, School of Pharmacy, Devi Ahilya University, Takshila Campus, Khandwa Road, Indore, 452 001, India.
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Minovski N, Novic M, Solmajer T. The impact of Mycobacterium tuberculosis gyrB point mutations on 6-fluoroquinolones resistance profile: in silico mutagenesis and structure-based assessment. RSC Adv 2015. [DOI: 10.1039/c4ra16031b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The latest confirmedM. tuberculosis gyrBpoint mutations assembling thegyrBhot spot region strongly involved in 6-fluoroquinolones resistance for the first time enabled thein silicoconstruction and structure-based assays ongyrBmutant models.
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Affiliation(s)
- Nikola Minovski
- Laboratory for Chemometrics
- National Institute of Chemistry
- 1001 Ljubljana
- Slovenia
| | - Marjana Novic
- Laboratory for Chemometrics
- National Institute of Chemistry
- 1001 Ljubljana
- Slovenia
| | - Tom Solmajer
- Laboratory for Molecular Modeling
- National Institute of Chemistry
- 1001 Ljubljana
- Slovenia
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Minovski N, Perdih A, Novic M, Solmajer T. Cluster-based molecular docking study forin silicoidentification of novel 6-fluoroquinolones as potential inhibitors againstMycobacterium tuberculosis. J Comput Chem 2012; 34:790-801. [DOI: 10.1002/jcc.23205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/22/2012] [Accepted: 11/30/2012] [Indexed: 01/15/2023]
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Agrawal KM, Talele GS. Synthesis and antibacterial, antimycobacterial and docking studies of novel N-piperazinyl fluoroquinolones. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0074-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Aboul-Fadl T, Abdel-Aziz HA, Abdel-Hamid MK, Elsaman T, Thanassi J, Pucci MJ. Schiff bases of indoline-2,3-dione: potential novel inhibitors of Mycobacterium tuberculosis (Mtb) DNA gyrase. Molecules 2011; 16:7864-79. [PMID: 22143547 PMCID: PMC6264139 DOI: 10.3390/molecules16097864] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 08/23/2011] [Accepted: 09/07/2011] [Indexed: 11/19/2022] Open
Abstract
In the present study a series of Schiff bases of indoline-2,3-dione were synthesized and investigated for their Mtb gyrase inhibitory activity. Promising inhibitory activity was demonstrated with some of these derivatives, which exhibited IC50 values ranging from 50–157 μM. The orientation and the ligand-receptor interactions of such molecules within the Mtb DNA gyrase A subunit active site were investigated applying a multi-step docking protocol using Molecular Operating Environment (MOE) and Autodock4 docking software. The results revealed the importance of the isatin moiety and the connecting side chain for strong interactions with the enzyme active site. Among the tested compounds the terminal aromatic ring benzofuran showed the best activity. Promising new leads for developing a novel class of Mtb gyrase inhibitors were obtained from Schiff bases of indoline-2,3-dione.
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Affiliation(s)
- Tarek Aboul-Fadl
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
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