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Lin X, Kong D, Chen ZS. Editorial: Chemo-Radiation-Resistance in Cancer Therapy. Front Pharmacol 2022; 13:904063. [PMID: 35662703 PMCID: PMC9159921 DOI: 10.3389/fphar.2022.904063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Xiaoping Lin
- State Key Laboratory of Oncology in South China, Department of Nuclear Medicine, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dexin Kong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Institute for Biotechnology, St. John's University, Queens, New York, NY, United States
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Cybularczyk-Cecotka M, Predygier J, Crespi S, Szczepanik J, Giedyk M. Photocatalysis in Aqueous Micellar Media Enables Divergent C–H Arylation and N-Dealkylation of Benzamides. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Jędrzej Predygier
- Institute of Organic Chemistry, Polish Academy of Sciences; Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Stefano Crespi
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Joanna Szczepanik
- Institute of Organic Chemistry, Polish Academy of Sciences; Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Maciej Giedyk
- Institute of Organic Chemistry, Polish Academy of Sciences; Kasprzaka 44/52, 01-224 Warsaw, Poland
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Kumbhar N, Nimal S, Barale S, Kamble S, Bavi R, Sonawane K, Gacche R. Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Sci Rep 2022; 12:1712. [PMID: 35110603 PMCID: PMC8810932 DOI: 10.1038/s41598-022-05698-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 02/08/2023] Open
Abstract
In the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model 'Hypo 1' showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
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Affiliation(s)
- Navanath Kumbhar
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India
| | - Snehal Nimal
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India
| | - Sagar Barale
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Subodh Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Rohit Bavi
- School of Chemical Science, Punyashlok Ahilyadevi Holkar Solapur University, Solapur, Maharashtra (MS), 413255, India
| | - Kailas Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, Maharashtra (MS), 416004, India
| | - Rajesh Gacche
- Department of Biotechnology, Savitribai Phule Pune University Pune, Pune, Maharashtra (MS), 411007, India.
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