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Cheshmazar N, Hamzeh-Mivehroud M, Hemmati S, Abolhasani H, Heidari F, Charoudeh HN, Zessin M, Schutkowski M, Sippl W, Dastmalchi S. Key structural requirements of benzamide derivatives for histone deacetylase inhibition: design, synthesis and biological evaluation. Future Med Chem 2024; 16:859-872. [PMID: 38623995 PMCID: PMC11188831 DOI: 10.4155/fmc-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
Background: Histone deacetylase inhibitors (HDACIs) are important as anticancer agents. Objective: This study aimed to investigate some key structural features of HDACIs via the design, synthesis and biological evaluation of novel benzamide-based derivatives. Methods: Novel structures, designed using a molecular modification approach, were synthesized and biologically evaluated. Results: The results indicated that a subset of molecules with CH3/NH2 at R2 position possess selective antiproliferative activity. However, only those with an NH2 group showed HDACI activity. Importantly, the shorter the molecule length, the stronger HDACI. Among all, 7j was the most potent HDAC1-3 inhibitor and antiproliferative compound. Conclusion: The results of the present investigation could provide valuable structural knowledge applicable for the development of the HDACIs and benzamide-based antiproliferative agents in the future.
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Affiliation(s)
- Narges Cheshmazar
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
| | - Salar Hemmati
- Drug applied research Center, Tabriz University of Medical Sciences, Tabriz, 5165665811, Iran
| | - Hoda Abolhasani
- Cellular & Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Pharmacology, School of Medicine, Qom University of Medical Sciences, Qom, Iran
| | - Fatemeh Heidari
- Cellular & Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Matthes Zessin
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
- Faculty of Pharmacy, Near East University, PO Box 99138, Nicosia, North Cyprus, Mersin, 10, Turkey
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Esther Rubavathy SM, Rajapandian V, Prakash M. Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics. J Biomol Struct Dyn 2024:1-12. [PMID: 38456827 DOI: 10.1080/07391102.2024.2325104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024]
Abstract
Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic. However, most HDAC inhibitors lack subclass or isoform selectivity, which can be dangerous. Featuring both enhanced selectivity and toxicity profiles, slow-binding HDAC inhibitors offer promising treatment options for a variety of disorders. Diseases like cardiac, neurodegenerative disorders and diabetes are mainly associated with the HDAC1, HDAC2 and HDAC3 enzymes. The AI-based virtual screening tool PyRMD is implemented to identify the potential inhibitors from ∼2 million compounds. Based on the IC50 values, the top 10 compounds were selected for molecular docking. From the docking and ADMET study, the top-ranked three compounds were selected for molecular dynamics (MD) simulations. Further, to get more insights into the binding/unbinding mechanism of the ligand, we have employed the steered molecular dynamics (SMD) simulations. This study assists in developing Amber force field parameters for the HDAC1, HDAC2 and HDAC3 proteins and sheds light on the discovery of a potent drug. Our study suggests that hydroxamic acid derivative (i.e. referred to as Comp-1, CHEMBL600072) is the potential inhibitor for the series of HDAC-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S M Esther Rubavathy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - V Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - M Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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Zhang M, Cai H, Ling D, Pang C, Chang J, Jin Z, Chi YR. Herbicidal Activity of Beflubutamid Analogues as PDS Inhibitors and SAR Analysis and Degradation Dynamics in Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37906815 DOI: 10.1021/acs.jafc.3c04733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In this work, a series of beflubutamid (BF) analogues' postemergent herbicidal activity was evaluated, and the structure-activity relationship (SAR) was discussed. At a dosage of 300 g ai/ha, compounds (Rac)-6h and (Rac)-6q showed excellent herbicidal activity against Amaranthus retroflexus, Abutilon theophrasti, and Medicago sativa, with inhibition rates of 90, 100, and 80% and 100, 100, and 100%, respectively, comparable to that of commercial herbicide BF, which showed inhibition rates of 90, 100, and 100%, respectively. Notably, at dosages of 150 and 300 g ai/ha, the chiral compounds (S)-6h and (S)-6q exhibited higher herbicidal activities than their racemates. Molecular docking results indicated that compounds (S)-BF and (S)-6h have stronger binding affinities with Oryza sativa phytoene desaturase (OsPDS), resulting in a higher herbicidal activity. Additionally, the degradation dynamics half-life of (S)-BF in wheat was determined to be 77.02 h. Consequently, compounds (S)-6h and (S)-6q are promising lead candidates for the development of highly effective herbicides.
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Affiliation(s)
- Meng Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Hui Cai
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Dan Ling
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Chen Pang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Jinming Chang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Zhichao Jin
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Yonggui Robin Chi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
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Flores R, Iqbal S, Sikazwe D. Phenylacetyl-/Trolox- Amides: Synthesis, Sigma-1, HDAC-6, and Antioxidant Activities. Int J Mol Sci 2023; 24:15295. [PMID: 37894975 PMCID: PMC10607876 DOI: 10.3390/ijms242015295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
In search of novel multi-mechanistic approaches for treating Alzheimer's disease (AD), we have embarked on synthesizing single small molecules for probing contributory roles of the following combined disease targets: sigma-1 (σ-1), class IIb histone deacetylase-6 (HDAC-6), and oxidative stress (OS). Herein, we report the synthesis and partial evaluation of 20 amides (i.e., phenylacetic and Trolox or 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid derivatives). Target compounds were conveniently synthesized via amidation by either directly reacting acyl chlorides with amines or condensing acids with amines in the presence of coupling agents 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo [4,5-b] pyridinium 3-oxide hexafluorophosphate (HATU) or 1,1'-carbonyldiimidazole (CDI). Overall, this project afforded compound 8 as a promising lead with σ-1 affinity (Ki = 2.1 μM), HDAC-6 (IC50 = 17 nM), and antioxidant (1.92 Trolox antioxidant equivalents or TEs) activities for optimization in ensuing structure-activity relationship (SAR) studies.
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Affiliation(s)
| | | | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA; (R.F.); (S.I.)
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Cai JH, Zhu XZ, Guo PY, Rose P, Liu XT, Liu X, Zhu YZ. Recent updates in click and computational chemistry for drug discovery and development. Front Chem 2023; 11:1114970. [PMID: 36825226 PMCID: PMC9941707 DOI: 10.3389/fchem.2023.1114970] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/27/2023] [Indexed: 02/09/2023] Open
Abstract
Drug discovery is a costly and time-consuming process with a very high failure rate. Recently, click chemistry and computer-aided drug design (CADD) represent popular areas for new drug development. Herein, we summarized the recent updates in click and computational chemistry for drug discovery and development including clicking to effectively synthesize druggable candidates, synthesis and modification of natural products, targeted delivery systems, and computer-aided drug discovery for target identification, seeking out and optimizing lead compounds, ADMET prediction as well as compounds synthesis, hopefully, inspires new ideas for novel drug development in the future.
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Affiliation(s)
- Jiang Hong Cai
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
| | - Xuan Zhe Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
| | - Peng Yue Guo
- Department of Clinical Pharmacy, School of Pharmacy, Second Military University, Shanghai, China
| | - Peter Rose
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Xiao Tong Liu
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
| | - Xia Liu
- Department of Clinical Pharmacy, School of Pharmacy, Second Military University, Shanghai, China
| | - Yi Zhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China,Shanghai Key Laboratory of Bioactive Small Molecules, Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China,*Correspondence: Yi Zhun Zhu,
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Current trends in development of HDAC-based chemotherapeutics. Life Sci 2022; 308:120946. [PMID: 36096240 DOI: 10.1016/j.lfs.2022.120946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Histone deacetylases (HDACs) are one of the essential epigenetic targets in cancer treatment. These enzymes play key roles in post-translation modification (PTM) and gene expression, and consequently, their inhibitors are about to find their place in pharmacotherapy. Most of the currently approved HDAC inhibitors (HDACIs) are wide-spectrum with poor clinical outcomes and numerous side effects. Therefore, new generations of HDAC-based chemotherapeutics with better clinical outcomes are emerging, e.g., isoform-selective inhibitors, multitargeted HDACIs, as well as HDAC degraders. AIM The review intended to introduce drug design approaches which were used for designing novel agents which can be beneficial in the process of finding new and more effective HDACI-based therapeutics. METHODS PubMed and other databases were searched for literature regarding the structure-function of HDAC isoforms, and strategies used to design HDAC inhibitors. Also, all clinical trials available from the ClinicalTrials site for years 2021-2022 were investigated. KEY FINDINGS It is expected that the future of drug discovery projects in HDAC field will concentrate mostly on issues such as isoform-selectivity, multitargeted HDAC inhibitors and HDAC degraders. Deeper knowledge of the 3D structure of HDACs complexed with inhibitors and extensive delineation of biological roles of HDACs are needed for efficient investigations leading to the discovery of novel potent inhibitors. SIGNIFICANCE Histone deacetylases (HDACs) are one of the important epigenetic targets in cancer treatment drug discovery. Comprehending the structure of HDAC isoforms along with applied drug design strategies can inspire new ideas.
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