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Vaidya GN, Rana P, Venkatesh A, Chatterjee DR, Contractor D, Satpute DP, Nagpure M, Jain A, Kumar D. Paradigm shift of "classical" HDAC inhibitors to "hybrid" HDAC inhibitors in therapeutic interventions. Eur J Med Chem 2020; 209:112844. [PMID: 33143937 DOI: 10.1016/j.ejmech.2020.112844] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
'Epigenetic' regulation of genes via post-translational modulation of proteins is the current mainstay approach for the disease therapies, particularly explored in the Histone Deacetylase (HDAC) class of enzymes. Mainly sight saw in cancer chemotherapeutics, HDAC inhibitors have also found a promising role in other diseases (neurodegenerative disorders, cardiovascular diseases, and viral infections) and successfully entered in various combination therapies (pre-clinical/clinical stages). The prevalent flexibility in the structural design of HDAC inhibitors makes them easily tuneable to merge with other pharmacophore modules for generating multi-targeted single hybrids as a novel tactic to overcome drawbacks of polypharmacy. Herein, we reviewed the putative role of prevalent HDAC hybrids inhibitors in the current and prospective stage as a translational approach to overcome the limitations of the existing conventional drug candidates (parent molecule) when used either alone (drug resistance, solubility issues, adverse side effects, selectivity profile) or in combination (pharmacokinetic interactions, patient compliance) for treating various diseases.
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Affiliation(s)
- Gargi Nikhil Vaidya
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Pooja Rana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Ashwini Venkatesh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Darshan Contractor
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Dinesh Parshuram Satpute
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Mithilesh Nagpure
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India
| | - Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India; Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India.
| | - Dinesh Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj, Gandhinagar, 382355, Gujarat, India.
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Amin SA, Adhikari N, Jha T. Design of Aminopeptidase N Inhibitors as Anti-cancer Agents. J Med Chem 2018; 61:6468-6490. [DOI: 10.1021/acs.jmedchem.7b00782] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
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3
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Structural exploration for the refinement of anticancer matrix metalloproteinase-2 inhibitor designing approaches through robust validated multi-QSARs. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Affiliation(s)
- Xun Li
- Department of Medicinal Chemistry, Key laboratory of Chemistry and Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, PR China
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Design, synthesis, biological evaluation and molecular docking study on peptidomimetic analogues of XK469. Eur J Med Chem 2016; 124:311-325. [DOI: 10.1016/j.ejmech.2016.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 11/19/2022]
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Paetz C, Hammerbacher A, Menezes RC, Feistel F, Weigel C, Voigt K, Schneider B. Chemical Composition and Antimicrobial Activity of Populus nigra Shoot Resin. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The chemical composition of Populus nigra shoot resin has been investigated by chromatographic and spectroscopic methods. The analyses resulted in identification of 19 known compounds. The resin exhibited low activity against selected microorganisms.
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Affiliation(s)
- Christian Paetz
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
| | - Almuth Hammerbacher
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
| | - Riya C. Menezes
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
| | - Felix Feistel
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology, Jena Microbial Resource Collection, Adolf-Reichwein-Straβe 23, 07745 Jena, Germany
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research and Infection Biology, Jena Microbial Resource Collection, Adolf-Reichwein-Straβe 23, 07745 Jena, Germany
| | - Bernd Schneider
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
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Total synthesis of tubastrine and 3-dehydroxy tubastrine by microwave-assisted cross-coupling reactions. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Halder AK, Mallick S, Shikha D, Saha A, Saha KD, Jha T. Design of dual MMP-2/HDAC-8 inhibitors by pharmacophore mapping, molecular docking, synthesis and biological activity. RSC Adv 2015. [DOI: 10.1039/c5ra12606a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent analyses have highlighted the promotion of cancer migration and invasion, mediated through HDAC via MMP-2 and MMP-9.
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Affiliation(s)
- Amit K. Halder
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
| | - Sumana Mallick
- Cancer Biology & Inflammatory Disorder Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Deep Shikha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
| | - Achintya Saha
- Department of Chemical Technology
- University of Calcutta
- Kolkata 700009
- India
| | - Krishna D. Saha
- Cancer Biology & Inflammatory Disorder Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Tarun Jha
- Natural Science Laboratory
- Division of Medicinal and Pharmaceutical Chemistry
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
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Halder AK, Saha A, Jha T. Exploring QSAR and pharmacophore mapping of structurally diverse selective matrix metalloproteinase-2 inhibitors. J Pharm Pharmacol 2013; 65:1541-54. [DOI: 10.1111/jphp.12133] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/23/2013] [Indexed: 12/27/2022]
Abstract
Abstract
Objectives and Methods
Matrix metalloproteinase-2 (MMP-2) is a potential target in metastases. Regression (conventional 2D QSAR) and classification (recursive partitioning (RP), Bayesian modelling) QSAR, pharmacophore mapping and 3D QSAR (comparative molecular field analysis and comparative molecular similarity analysis) were performed on 202 MMP-2 inhibitors.
Key findings
Quality of the regression models was justified by internal (Q2) and external (R2Pred) cross-validation parameters. Stepwise regression was used to develop linear model (Q2 = 0.822, R2Pred = 0.667). Genetic algorithm developed linear (Q2 = 0.845, R2Pred = 0.638) and spline model (Q2 = 0.882, R2Pred = 0.644). The RP and Bayesian models showed cross-validated area under receiver operating characteristic curve (AUCROC_CV) of 0.805 and 0.979 respectively. QSAR models depicted importance of descriptors like five-membered rings, fractional positively charged surface area, lipophilocity and so on. Higher molecular volume was found to be detrimental. Pharmacophore mapping was performed with two tools – Hypogen and PHASE. Both models indicated that one hydrophobic and three hydrogen bond acceptor features are essential. The Pharmacophore-aligned structures were used for CoMFA (Q2 of 0.586 and R2Pred of 0.689) and CoMSIA (Q2 of 0.673 and R2Pred of 0.758), results of which complied with the other analyses.
Conclusions
All modelling techniques were compared to each other. The current study may help in designing novel MMP-2 inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Hahnenkamp A, Schäfers M, Bremer C, Höltke C. Design and synthesis of small-molecule fluorescent photoprobes targeted to aminopeptdase N (APN/CD13) for optical imaging of angiogenesis. Bioconjug Chem 2013; 24:1027-38. [PMID: 23642127 DOI: 10.1021/bc400074w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report here the synthesis of a nonpeptide, small-molecule fluorescent imaging agent with high affinity to aminopeptidase N (APN/CD13), a key player in a variety of pathophysiological angiogenic processes. On the basis of a recently described lead structure, we synthesized three putative precursor compounds by introducing polyethylene glycol (PEG) spacers comprising amino groups for dye labeling. Different attachment sites resulted in substantial differences in target affinity, cell toxicity, and target imaging performance. In comparison to bestatin, a natural inhibitor of many aminopeptidases, two of our compounds (22, 23) exhibit comparable inhibition potency, while a third (21) does not show any inhibiting effect. Cell binding assays with APN-positive BT-549 and APN-negative BT-20 cells and the final fluorescent probes Cy 5.5-21 and Cy 5.5-23 confirm these findings. The favorable characteristics of Cy 5.5-23 will now be proven in in vivo experiments with murine models of high APN expression and may serve as a tool to better understand APN pathophysiology.
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Affiliation(s)
- Anke Hahnenkamp
- Department of Clinical Radiology, Albert-Schweitzer-Campus 1/A16, University Hospital Muenster, D-48149 Muenster, Germany
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Halder AK, Saha A, Jha T. Exploration of structural and physicochemical requirements and search of virtual hits for aminopeptidase N inhibitors. Mol Divers 2013; 17:123-37. [PMID: 23341006 PMCID: PMC7089330 DOI: 10.1007/s11030-013-9422-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 01/07/2013] [Indexed: 11/28/2022]
Abstract
Aminopeptidase N (APN) inhibitors have been reported to be effective in treating of life threatening diseases including cancer. Validated ligand- and structure-based pharmacophore mapping approaches were combined with Bayesian modeling and recursive partitioning to identify structural and physicochemical requirements for highly active APN inhibitors. Based on the assumption that ligand- and structure-based pharmacophore models are complementary, the efficacy of 'multiple pharmacophore screening' for filtering true positive virtual hits was investigated. These multiple pharmacophore screening methods were utilized to search novel virtual hits for APN inhibition. The number of hits was refined and reduced by recursive partitioning, drug-likeliness, pharmacokinetic property prediction, and comparative molecular-docking studies. Four compounds were proposed as the potential virtual hits for APN enzyme inhibition.
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Affiliation(s)
- Amit K. Halder
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata, 700032 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, P.O. Box 17020, Kolkata, 700032 India
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Cyclic enediyne–amino acid chimeras as new aminopeptidase N inhibitors. Amino Acids 2012; 43:2087-100. [DOI: 10.1007/s00726-012-1292-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/03/2012] [Indexed: 10/28/2022]
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Design, Synthesis, and Preliminary Activity Evaluation of Novel Peptidomimetics as Aminopeptidase N/CD13 Inhibitors. Arch Pharm (Weinheim) 2011; 344:494-504. [DOI: 10.1002/ardp.201100109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 04/21/2011] [Accepted: 04/29/2011] [Indexed: 11/07/2022]
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