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Dewaker V, Srivastava PN, Verma S, Srivastava AK, Prabhakar YS. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:13432-13455. [PMID: 34662251 DOI: 10.1080/07391102.2021.1989037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Designing an inhibitor having strong affinity in the active site pocket is the cherished goal of structure based drug designing. To achieve this, it is considerably important to predict which structural scaffold is better suited for change to increase affinity. We have explored five HDAC2 co-crystals having PDB ligand code-SHH (vorinostat), LLX, 20Y, IWX (BRD4884) and 6EZ (BRD7232). For analyzing protein-ligand interaction at an atomistic level, we have employed the NAMD molecular dynamics (MD) package. The obtained 100 ns long MD trajectories were subjected to quantitative estimations of non-bonding energies (NBEs) for inferring their interactions with the whole protein or its composite active site (CAS). In addition, relative ΔGbind was calculated to rank the inhibitors. These inhibitors' NBEs reveal that the phenyl moieties are the major structural scaffold where modifications should be attempted. We designed new compounds (NCs) via introducing hydroxyl groups at 4,5 position of the phenyl moiety of 6EZ, called NC1. Improvement in NC1 further encouraged us for CAP modification by isochromane and isoindoline moieties in place of oxabicyclooctane in NC1, resulting in NC2 and NC3. We also explored trifluoromethyl oxadiazole in 6EZ (NC4 and NC5) and SHH (NC6 and NC7). This moiety acts as a ZBG in NC4 while acting as a part of the foot-pocket in the rest. NC2 and NC6 have highest favorable NBEs among all studied ligands due increased favorable electrostatic contribution. We expect these NBEs data will provide atomistic level insights and benefit in designing new and improved HDAC2 inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Pratik Narain Srivastava
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saroj Verma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India.,College of Pharmacy, Shree Guru Gobind Singh Tricentenary University, Gurugram, Haryana, India
| | - Ajay K Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
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Chen Y, Du F, Tang L, Xu J, Zhao Y, Wu X, Li M, Shen J, Wen Q, Cho CH, Xiao Z. Carboranes as unique pharmacophores in antitumor medicinal chemistry. Mol Ther Oncolytics 2022; 24:400-416. [PMID: 35141397 PMCID: PMC8807988 DOI: 10.1016/j.omto.2022.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Carborane is a carbon-boron molecular cluster that can be viewed as a 3D analog of benzene. It features special physical and chemical properties, and thus has the potential to serve as a new type of pharmacophore for drug design and discovery. Based on the relative positions of two cage carbons, icosahedral closo-carboranes can be classified into three isomers, ortho-carborane (o-carborane, 1,2-C2B10H12), meta-carborane (m-carborane, 1,7-C2B10H12), and para-carborane (p-carborane, 1,12-C2B10H12), and all of them can be deboronated to generate their nido- forms. Cage compound carborane and its derivatives have been demonstrated as useful chemical entities in antitumor medicinal chemistry. The applications of carboranes and their derivatives in the field of antitumor research mainly include boron neutron capture therapy (BNCT), as BNCT/photodynamic therapy dual sensitizers, and as anticancer ligands. This review summarizes the research progress on carboranes achieved up to October 2021, with particular emphasis on signaling transduction pathways, chemical structures, and mechanistic considerations of using carboranes.
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Affiliation(s)
- Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Liyao Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jinrun Xu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Zhangang Xiao
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Luzhou Key Laboratory of Cell Therapy & Cell Drugs, Southwest Medical University, Luzhou 646000, China
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Messner K, Vuong B, Tranmer GK. The Boron Advantage: The Evolution and Diversification of Boron’s Applications in Medicinal Chemistry. Pharmaceuticals (Basel) 2022; 15:ph15030264. [PMID: 35337063 PMCID: PMC8948683 DOI: 10.3390/ph15030264] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In this review, the history of boron’s early use in drugs, and the history of the use of boron functional groups in medicinal chemistry applications are discussed. This includes diazaborines, boronic acids, benzoxaboroles, boron clusters, and carboranes. Furthermore, critical developments from these functional groups are highlighted along with recent developments, which exemplify potential prospects. Lastly, the application of boron in the form of a prodrug, softdrug, and as a nanocarrier are discussed to showcase boron’s emergence into new and exciting fields. Overall, we emphasize the evolution of organoboron therapeutic agents as privileged structures in medicinal chemistry and outline the impact that boron has had on drug discovery and development.
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Affiliation(s)
- Katia Messner
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Billy Vuong
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
| | - Geoffrey K. Tranmer
- Rady Faculty of Health Science, College of Pharmacy, University of Manitoba, Winnipeg, MB R3E 0T5, Canada; (K.M.); (B.V.)
- Department of Chemistry, Faculty of Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
- Correspondence:
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Selg C, Schöler A, Schliehe-Diecks J, Hanl M, Sinatra L, Borkhardt A, Sárosi MB, Bhatia S, Hey-Hawkins E, Hansen FK. Borinostats: solid-phase synthesis of carborane-capped histone deacetylase inhibitors with a tailor-made selectivity profile. Chem Sci 2021; 12:11873-11881. [PMID: 34659728 PMCID: PMC8442681 DOI: 10.1039/d1sc02268g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
The elevated expression of histone deacetylases (HDACs) in various tumor types renders their inhibition an attractive strategy for epigenetic therapeutics. One key issue in the development of improved HDAC inhibitors (HDACis) is the selectivity for single HDAC isoforms over unspecific pan inhibition to minimize off-target toxicity. Utilizing the carborane moiety as a fine-tuning pharmacophore, we herein present a robust solid phase synthetic approach towards tailor-made HDACis meeting both ends of the selectivity spectrum, namely pan inhibition and highly selective HDAC6 inhibition.
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Affiliation(s)
- Christoph Selg
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Maria Hanl
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Laura Sinatra
- Institute for Drug Discovery, Medical Faculty, Leipzig University Brüderstraße 34 04103 Leipzig Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Menyhárt B Sárosi
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University Johannisallee 29 04103 Leipzig Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University Düsseldorf Düsseldorf Germany
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University Johannisallee 29 04103 Leipzig Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
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Couto M, Alamón C, Nievas S, Perona M, Dagrosa MA, Teixidor F, Cabral P, Viñas C, Cerecetto H. Bimodal Therapeutic Agents Against Glioblastoma, One of the Most Lethal Forms of Cancer. Chemistry 2020; 26:14335-14340. [PMID: 32738078 DOI: 10.1002/chem.202002963] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/26/2020] [Indexed: 12/17/2022]
Abstract
About 95 % of people diagnosed with glioblastoma die within five years. Glioblastoma is the most aggressive central nervous system tumour. It is necessary to make progress in the glioblastoma treatment so that advanced chemotherapy drugs or radiation therapy or, ideally, two-in-one hybrid systems should be implemented. Tyrosine kinase receptors-inhibitors and boron neutron capture therapy (BNCT), together, could provide a therapeutic strategy. In this work, sunitinib decorated-carborane hybrids were prepared and biologically evaluated identifying excellent antitumoral- and BNCT-agents. One of the selected hybrids was studied against glioma-cells and found to be 4 times more cytotoxic than sunitinib and 1.7 times more effective than 10 B-boronophenylalanine fructose complex when the cells were irradiated with neutrons.
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Affiliation(s)
- Marcos Couto
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica (IQB), Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.,Institut de Ciències dels Materials de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAB, 08193, Bellaterra, Spain
| | - Catalina Alamón
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica (IQB), Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Susana Nievas
- Department of Boron Neutron Capture Therapy, National Atomic Energy Commission (CNEA), Buenos Aires, Argentina
| | - Marina Perona
- Department of Radiobiology, CNEA, Buenos Aires, Argentina
| | | | - Francesc Teixidor
- Institut de Ciències dels Materials de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAB, 08193, Bellaterra, Spain
| | - Pablo Cabral
- Área de Radiofarmacia, Centro de Investigaciones Nucleares (CIN), Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400, Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciències dels Materials de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAB, 08193, Bellaterra, Spain
| | - Hugo Cerecetto
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica (IQB), Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.,Área de Radiofarmacia, Centro de Investigaciones Nucleares (CIN), Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400, Montevideo, Uruguay
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