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Tabti K, Ahmad I, Zafar I, Sbai A, Maghat H, Bouachrine M, Lakhlifi T. Profiling the Structural determinants of pyrrolidine derivative as gelatinases (MMP-2 and MMP-9) inhibitors using in silico approaches. Comput Biol Chem 2023; 104:107855. [PMID: 37023640 DOI: 10.1016/j.compbiolchem.2023.107855] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/28/2023]
Abstract
Quantitative structure activity relationship (QSAR) studies on pyrrolidine derivatives have been established using CoMFA, CoMSIA, and Hologram QSAR analysis to estimate the values (pIC50) of gelatinase inhibitors. When the CoMFA cross-validation value, Q², was 0.625, the training set coefficient of determination, R² was 0.981. In CoMSIA, Q² was 0.749 and R² was 0.988. In the HQSAR, Q² was 0.84 and R² was 0.946. Visualization of these models was performed by contour maps showing favorable and unfavorable regions for activity, while visualization of HQSAR model was performed by a colored atomic contribution graph. Based on the results obtained of external validation, the CoMSIA model was statistically more significant and robust and was selected as the best model to predict new, more active inhibitors. To study the modes of interactions of the predicted compounds in the active site of MMP-2 and MMP-9, a simulation of molecular docking was realized. A combined study of MD simulations and calculation of free binding energy, were also carried out to validate the results obtained on the best predicted and most active compound in dataset and the compound NNGH as control compound. The results confirm the molecular docking results and indicate that the predicted ligands were stable in the binding site of MMP-2 and MMP-9.
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Baidya SK, Banerjee S, Adhikari N, Jha T. Selective Inhibitors of Medium-Size S1' Pocket Matrix Metalloproteinases: A Stepping Stone of Future Drug Discovery. J Med Chem 2022; 65:10709-10754. [PMID: 35969157 DOI: 10.1021/acs.jmedchem.1c01855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among various matrix metalloproteinases (MMPs), MMPs having medium-size S1' pockets are established as promising biomolecular targets for executing crucial roles in cancer, cardiovascular diseases, and neurodegenerative diseases. However, no such MMP inhibitors (MMPIs) are available to date as drug candidates despite a lot of continuous research work for more than three decades. Due to a high degree of structural resemblance among these MMPs, designing selective MMPIs is quite challenging. However, the variability and uniqueness of the S1' pockets of these MMPs make them promising targets for designing selective MMPIs. In this perspective, the overall structural aspects of medium-size S1' pocket MMPs including the unique binding patterns of enzyme-inhibitor interactions have been discussed in detail to acquire knowledge regarding selective inhibitor designing. This overall knowledge will surely be a curtain raiser for the designing of selective MMPIs as drug candidates in the future.
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Affiliation(s)
- Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Abstract
MMP2, a Zn2+-dependent metalloproteinase, is related to cancer and angiogenesis. Inhibition of this enzyme might result in a potential antimetastatic drug to leverage the anticancer drug armory. In silico or computer-aided ligand-based drug design is a method of rational drug design that takes multiple chemometrics (i.e., multi-quantitative structure-activity relationship methods) into account for virtually selecting or developing a series of probable selective MMP2 inhibitors. Though existing matrix metalloproteinase inhibitors have shown plausible pan-matrix metalloproteinase (MMP) activity, they have resulted in various adverse effects leading to their being rescinded in later phases of clinical trials. Therefore a review of the ligand-based designing methods of MMP2 inhibitors would result in an explicit route map toward successfully designing and synthesizing novel and selective MMP2 inhibitors.
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Das S, Amin SA, Jha T. Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Naïve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:655-687. [PMID: 34355614 DOI: 10.1080/1062936x.2021.1955414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Gelatinases [gelatinase A - matrix metalloproteinase-2 (MMP-2), gelatinase B - matrix metalloproteinase-9 (MMP-9)] play key roles in many disease conditions including cancer. Despite some research work on gelatinases inhibitors both jointly and individually had been reported, challenges still exist in achieving potency as well as selectivity. Here in part I of a series of work, we have reported the structural requirement of some arylsulfonamides. In particular, regression-based 2D-QSARs, topomer CoMFA (comparative molecular field analysis) and Bayesian classification models were constructed to refine structural features for attaining better gelatinase inhibitory activity. The 2D-QSAR models exhibited good statistical significance. The descriptors nsssN, SHBint6, SHBint7, PubchemFP629 were directly correlated with the MMP-2 binding affinities whereas nsssN, SHBint10 and AATS2i were directly proportional to MMP-9 binding affinities. The topomer CoMFA results indicated that the steric and electrostatic fields play key roles in gelatinase inhibition. The established Naïve Bayes prediction models were evaluated by fivefold cross validation and an external test set. Furthermore, important molecular descriptors related to MMP-2 and MMP-9 binding affinities and some active/inactive fragments were identified. Thus, these observations may be helpful for further work of aryl sulphonamide based gelatinase inhibitors in future.
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Affiliation(s)
- S Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Jha T, Adhikari N, Saha A, Amin SA. Multiple molecular modelling studies on some derivatives and analogues of glutamic acid as matrix metalloproteinase-2 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:43-68. [PMID: 29254380 DOI: 10.1080/1062936x.2017.1406986] [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: 10/23/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
Matrix metalloproteinase-2 (MMP-2) is a potential target in anticancer drug discovery due to its association with angiogenesis, metastasis and tumour progression. In this study, 67 glutamic acid derivatives, synthesized and evaluated as MMP-2 inhibitors, were taken into account for multi-QSAR modelling study (regression-based 2D-QSAR, classification-based LDA-QSAR, Bayesian classification QSAR, HQSAR, 3D-QSAR CoMFA and CoMSIA as well as Open3DQSAR). All these QSAR studies were statistically validated individually. Regarding the 3D-QSAR analysis, the Open3DQSAR results were better than CoMFA and CoMSIA, although all these 3D-QSAR models supported each other. The importance of biphenylsulphonyl moiety over phenylacetyl/naphthylacetyl moieties was established due to its association with favourable steric and hydrophobic characters. HQSAR, LDA-QSAR and Bayesian classification QSAR studies also suggested that the biphenylsulphonamido group was better than the phenylacetylcarboxamido function. Additionally, glutamines were proven to be far better inhibitors than isoglutamines. Observations obtained from the current study were revalidated and supported by the earlier reported molecular modelling studies. Depending on these observations, newer glutamic acid-based compounds may be designed further in future for potent MMP-2 inhibitory activity.
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Affiliation(s)
- T Jha
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry , Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - N Adhikari
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry , Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - A Saha
- b Department of Chemical Technology , University of Calcutta , Kolkata , India
| | - S A Amin
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry , Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
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Adhikari N, Amin SA, Saha A, Jha T. Understanding Chemico-Biological Interactions of Glutamate MMP-2 Inhibitors through Rigorous Alignment-Dependent 3D-QSAR Analyses. ChemistrySelect 2017. [DOI: 10.1002/slct.201701330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory; Division of Medicinal and Pharmaceutical Chemistry; Department of Pharmaceutical Technology; Jadavpur University; Kolkata 700032, West Bengal India
| | - Sk Abdul Amin
- Natural Science Laboratory; Division of Medicinal and Pharmaceutical Chemistry; Department of Pharmaceutical Technology; Jadavpur University; Kolkata 700032, West Bengal India
| | - Achintya Saha
- Department of Chemical Technology; University of Calcutta; 92, APC Ray Road Kolkata 700009 India
| | - Tarun Jha
- Natural Science Laboratory; Division of Medicinal and Pharmaceutical Chemistry; Department of Pharmaceutical Technology; Jadavpur University; Kolkata 700032, West Bengal India
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Rathee D, Lather V, Dureja H. Pharmacophore modeling and 3D QSAR studies for prediction of matrix metalloproteinases inhibitory activity of hydroxamate derivatives. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.biori.2017.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kong D, Li M, Wang R, Zi G, Hou G. Highly efficient asymmetric hydrogenation of cyano-substituted acrylate esters for synthesis of chiral γ-lactams and amino acids. Org Biomol Chem 2016; 14:1216-20. [DOI: 10.1039/c5ob02422f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly efficient Rh-catalyzed asymmetric hydrogenation of 3-cyano acrylate esters is reported for the first time, which provides straightforward access to chiral cyano compounds with excellent enantioselectivities (up to 98% ee) and high turnover numbers (TON up to 10 000).
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Affiliation(s)
- Duanyang Kong
- Key Laboratory of Radiopharmaceuticals
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Meina Li
- Key Laboratory of Radiopharmaceuticals
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Rui Wang
- Key Laboratory of Radiopharmaceuticals
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guofu Zi
- Key Laboratory of Radiopharmaceuticals
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guohua Hou
- Key Laboratory of Radiopharmaceuticals
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
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Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D. In silico study of MMP inhibition. Org Biomol Chem 2009; 7:3817-25. [DOI: 10.1039/b910543c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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