1
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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2
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Liu Y, Wei Y, Wang X, Ma L, Li X, Sun Y, Wu Y, Zhang L, Wang J, Li M, Zhang K, Wei M, Yang G, Yang C. Discovery of novel and bioavailable histone deacetylases and cyclin-dependent kinases dual inhibitor to impair the stemness of leukemia cells. Eur J Med Chem 2023; 249:115140. [PMID: 36736154 DOI: 10.1016/j.ejmech.2023.115140] [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: 10/19/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Acute myeloid leukemia (AML) has been confirmed as one of the most lethal heterogeneous clonal diseases. In addition to being essential for the development and progression of leukemia, leukemic stem cells (LSCs), a subpopulation of leukemia cells with stem cell characteristics, are also primarily responsible for the development of leukemia relapse and drug resistance. Elimination of stemness and induction of AML cell differentiation would become a promising and effective therapeutic strategy. In the present study, a novel class of HDACs/CDKs dual inhibitors was prepared and optimized. An active compound 33a has been identified, which exhibited potent and selective inhibition of CDK9, CDK12, CDK13, HDAC1, HDAC2 and HDAC3 at low nanomolar concentrations and significantly induced differentiation of leukemic stem-like cells and inhibited AML proliferation. Furthermore, the lead compound has relatively adequate oral bioavailability, suggesting that it might be used as a novel strategy to reduce the burden of LSCs and improve the prognosis for AML.
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Affiliation(s)
- Yulin Liu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yujiao Wei
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Xuan Wang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Lan Ma
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Xuechun Li
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yue Sun
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Yanjie Wu
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China
| | - Li Zhang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen, Guangdong, 518000, PR China
| | - Jiefu Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, PR China.
| | - Ming Li
- Cangzhou Institutes for Food and Drug Control, Cangzhou, 061000, PR China.
| | - Kun Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Mingming Wei
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Guang Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
| | - Cheng Yang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300071, PR China.
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3
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Phaosiri C, Yenjai C, Senawong T, Senawong G, Saenglee S, Somsakeesit LO, Kumboonma P. Histone Deacetylase Inhibitory Activity and Antiproliferative Potential of New [6]-Shogaol Derivatives. Molecules 2022; 27:molecules27103332. [PMID: 35630809 PMCID: PMC9144829 DOI: 10.3390/molecules27103332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
Twenty newly synthesized derivatives of [6]-shogaol (4) were tested for inhibitory activity against histone deacetylases. All derivatives showed moderate to good histone deacetylase inhibition at 100 µM with a slightly lower potency than the lead compound. Most potent inhibitors among the derivatives were the pyrazole products, 5j and 5k, and the Michael adduct with pyridine 4c and benzothiazole 4d, with IC50 values of 51, 65, 61 and 60 µM, respectively. They were further evaluated for isoform selectivity via a molecular docking study. Compound 4d showed the best selectivity towards HDAC3, whereas compound 5k showed the best selectivity towards HDAC2. The potential derivatives were tested on five cancer cell lines, including human cervical cancer (HeLa), human colon cancer (HCT116), human breast adenocarcinoma cancer (MCF-7), and cholangiocarcinoma (KKU100 and KKU-M213B) cells with MTT-based assay. The most active histone deacetylase inhibitor 5j exhibited the best antiproliferative activity against HeLa, HCT116, and MCF-7, with IC50 values of 8.09, 9.65 and 11.57 µM, respectively, and a selective binding to HDAC1 based on molecular docking experiments. The results suggest that these compounds can be putative candidates for the development of anticancer drugs via inhibiting HDACs.
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Affiliation(s)
- Chanokbhorn Phaosiri
- Natural Products Research Unit, Center of Excellence for Innovation in Chemistry, Ministry of Higher Education, Science, Research and Innovation (Implementation Unit-IU, Khon Kaen University), Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (C.P.); (C.Y.)
| | - Chavi Yenjai
- Natural Products Research Unit, Center of Excellence for Innovation in Chemistry, Ministry of Higher Education, Science, Research and Innovation (Implementation Unit-IU, Khon Kaen University), Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (C.P.); (C.Y.)
| | - Thanaset Senawong
- Natural Products Research Unit, Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (T.S.); (G.S.)
| | - Gulsiri Senawong
- Natural Products Research Unit, Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; (T.S.); (G.S.)
| | - Somprasong Saenglee
- Ban Dong Sub-District Administration Organization, Ubolratana District, Khon Kaen 40250, Thailand;
| | - La-or Somsakeesit
- Department of Chemistry, Faculty of Engineering, Rajamangala University of Technology Isan, Khon Kaen 40000, Thailand;
| | - Pakit Kumboonma
- Department of Applied Chemistry, Faculty of Science and Liberal Arts, Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand
- Correspondence:
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4
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Nawar N, Bukhari S, Adile AA, Suk Y, Manaswiyoungkul P, Toutah K, Olaoye OO, Raouf YS, Sedighi A, Garcha HK, Hassan MM, Gwynne W, Israelian J, Radu TB, Geletu M, Abdeldayem A, Gawel JM, Cabral AD, Venugopal C, de Araujo ED, Singh SK, Gunning PT. Discovery of HDAC6-Selective Inhibitor NN-390 with in Vitro Efficacy in Group 3 Medulloblastoma. J Med Chem 2022; 65:3193-3217. [PMID: 35119267 DOI: 10.1021/acs.jmedchem.1c01585] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Histone deacetylase 6 (HDAC6) has been targeted in clinical studies for anticancer effects due to its role in oncogenic transformation and metastasis. Through a second-generation structure-activity relationship (SAR) study, the design, and biological evaluation of the selective HDAC6 inhibitor NN-390 is reported. With nanomolar HDAC6 potency, >200-550-fold selectivity for HDAC6 in analogous HDAC isoform functional assays, potent intracellular target engagement, and robust cellular efficacy in cancer cell lines, NN-390 is the first HDAC6-selective inhibitor to show therapeutic potential in metastatic Group 3 medulloblastoma (MB), an aggressive pediatric brain tumor often associated with leptomeningeal metastases and therapy resistance. MB stem cells contribute to these patients' poor clinical outcomes. NN-390 selectively targets this cell population with a 44.3-fold therapeutic margin between patient-derived Group 3 MB cells in comparison to healthy neural stem cells. NN-390 demonstrated a 45-fold increased potency over HDAC6-selective clinical candidate citarinostat. In summary, HDAC6-selective molecules demonstrated in vitro therapeutic potential against Group 3 MB.
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Affiliation(s)
- Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Shazreh Bukhari
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Ashley A Adile
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Yujin Suk
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Krimo Toutah
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Yasir S Raouf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Harsimran Kaur Garcha
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - William Gwynne
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mulu Geletu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Ayah Abdeldayem
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Justyna M Gawel
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Chitra Venugopal
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Department of Surgery, Faculty of Health Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Sheila K Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Department of Surgery, Faculty of Health Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada.,Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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5
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Toutah K, Nawar N, Timonen S, Sorger H, Raouf YS, Bukhari S, von Jan J, Ianevski A, Gawel JM, Olaoye OO, Geletu M, Abdeldayem A, Israelian J, Radu TB, Sedighi A, Bhatti MN, Hassan MM, Manaswiyoungkul P, Shouksmith AE, Neubauer HA, de Araujo ED, Aittokallio T, Krämer OH, Moriggl R, Mustjoki S, Herling M, Gunning PT. Development of HDAC Inhibitors Exhibiting Therapeutic Potential in T-Cell Prolymphocytic Leukemia. J Med Chem 2021; 64:8486-8509. [PMID: 34101461 PMCID: PMC8237267 DOI: 10.1021/acs.jmedchem.1c00420] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Epigenetic targeting has emerged as an efficacious therapy for hematological cancers. The rare and incurable T-cell prolymphocytic leukemia (T-PLL) is known for its aggressive clinical course. Current epigenetic agents such as histone deacetylase (HDAC) inhibitors are increasingly used for targeted therapy. Through a structure-activity relationship (SAR) study, we developed an HDAC6 inhibitor KT-531, which exhibited higher potency in T-PLL compared to other hematological cancers. KT-531 displayed strong HDAC6 inhibitory potency and selectivity, on-target biological activity, and a safe therapeutic window in nontransformed cell lines. In primary T-PLL patient cells, where HDAC6 was found to be overexpressed, KT-531 exhibited strong biological responses, and safety in healthy donor samples. Notably, combination studies in T-PLL patient samples demonstrated KT-531 synergizes with approved cancer drugs, bendamustine, idasanutlin, and venetoclax. Our work suggests HDAC inhibition in T-PLL could afford sufficient therapeutic windows to achieve durable remission either as stand-alone or in combination with targeted drugs.
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Affiliation(s)
- Krimo Toutah
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Nabanita Nawar
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Sanna Timonen
- Hematology
Research Unit Helsinki, Helsinki University
Hospital Comprehensive Cancer Center, Helsinki, 00029 HUS, Finland
- Translational
Immunology Research Program and Department of Clinical Chemistry and
Hematology, University of Helsinki, Helsinki, 00014 Helsinki, Finland
- Institute
for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014 Helsinki, Finland
| | - Helena Sorger
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Yasir S. Raouf
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Shazreh Bukhari
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jana von Jan
- Department
of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
(CIO ABCD), University of Cologne (UoC), 50923 Cologne, Germany
- Excellence
Cluster for Cellular Stress Response and Aging-Associated Diseases
(CECAD), UoC, 50923 Cologne, Germany
- Center
for Molecular Medicine Cologne (CMMC), UoC, 50923 Cologne, Germany
| | - Aleksandr Ianevski
- Institute
for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014 Helsinki, Finland
| | - Justyna M. Gawel
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Olasunkanmi O. Olaoye
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mulu Geletu
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Ayah Abdeldayem
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Johan Israelian
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Tudor B. Radu
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Abootaleb Sedighi
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Muzaffar N. Bhatti
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Muhammad Murtaza Hassan
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Pimyupa Manaswiyoungkul
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Andrew E. Shouksmith
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Heidi A. Neubauer
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Elvin D. de Araujo
- Centre
for Medicinal Chemistry, University of Toronto
Mississauga, 3359 Mississauga
Road, Mississauga, Ontario L5L 1C6, Canada
| | - Tero Aittokallio
- Institute
for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014 Helsinki, Finland
- Department
of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
- Oslo Centre
for Biostatistics and Epidemiology, University
of Oslo, 0316 Oslo, Norway
| | - Oliver H. Krämer
- Department
of Toxicology, University Medical Center, 55131 Mainz, Germany
| | - Richard Moriggl
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Satu Mustjoki
- Hematology
Research Unit Helsinki, Helsinki University
Hospital Comprehensive Cancer Center, Helsinki, 00029 HUS, Finland
- Translational
Immunology Research Program and Department of Clinical Chemistry and
Hematology, University of Helsinki, Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine
Flagship, 00014 Helsinki, Finland
| | - Marco Herling
- Department
of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
(CIO ABCD), University of Cologne (UoC), 50923 Cologne, Germany
- Excellence
Cluster for Cellular Stress Response and Aging-Associated Diseases
(CECAD), UoC, 50923 Cologne, Germany
- Center
for Molecular Medicine Cologne (CMMC), UoC, 50923 Cologne, Germany
| | - Patrick T. Gunning
- Department
of Chemical and Physical Sciences, University
of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Centre
for Medicinal Chemistry, University of Toronto
Mississauga, 3359 Mississauga
Road, Mississauga, Ontario L5L 1C6, Canada
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6
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Nong Y, Hou Y, Pu Y, Li S, Lan Y. Development and Validation of High-Content Analysis for Screening HDAC6-Selective Inhibitors. SLAS DISCOVERY 2021; 26:628-641. [PMID: 33783263 DOI: 10.1177/24725552211002463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Throughout recent decades, histone deacetylase (HDAC) inhibitors have shown encouraging potential in cancer treatment, and several pan-HDAC inhibitors have been approved for treating malignant cancers. Numerous adverse effects of pan-HDAC inhibitors have been reported, however, during preclinical and clinical evaluations. To avoid undesirable responses, an increasing number of investigations are focusing on the development of isotype-selective HDAC inhibitors. In this study, we present an effective and quantitative cellular assay using high-content analysis (HCA) to determine compounds' inhibition of the activity of HDAC6 and Class I HDAC isoforms, by detecting the acetylation of their corresponding substrates (i.e., α-tubulin and histone H3). Several conditions that are critical for HCA assays, such as cell seeding number, fixation and permeabilization reagent, and antibody dilution, have been fully validated in this study. We used selective HDAC6 inhibitors and inhibitors targeting different HDAC isoforms to optimize and validate the capability of the HCA assay. The results indicated that the HCA assay is a robust assay for quantifying compounds' selectivity of HDAC6 and Class I HDAC isoforms in cells. Moreover, we screened a panel of compounds for HDAC6 selectivity using this HCA assay, which provided valuable information for the structure-activity relationship (SAR). In summary, our results suggest that the HCA assay is a powerful tool for screening selective HDAC6 inhibitors.
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Affiliation(s)
- Yunhong Nong
- Discovery Project Unit, HitGen, Chengdu, Sichuan, China
| | - Yanyan Hou
- Discovery Project Unit, HitGen, Chengdu, Sichuan, China
| | - Yuting Pu
- Discovery Project Unit, HitGen, Chengdu, Sichuan, China
| | - Si Li
- Discovery Project Unit, HitGen, Chengdu, Sichuan, China
| | - Yan Lan
- Discovery Project Unit, HitGen, Chengdu, Sichuan, China
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7
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020; 59:17525-17532. [DOI: 10.1002/anie.202001205] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/14/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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8
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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9
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Gawel JM, Shouksmith AE, Raouf YS, Nawar N, Toutah K, Bukhari S, Manaswiyoungkul P, Olaoye OO, Israelian J, Radu TB, Cabral AD, Sina D, Sedighi A, de Araujo ED, Gunning PT. PTG-0861: A novel HDAC6-selective inhibitor as a therapeutic strategy in acute myeloid leukaemia. Eur J Med Chem 2020; 201:112411. [PMID: 32615502 DOI: 10.1016/j.ejmech.2020.112411] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 12/25/2022]
Abstract
Dysregulated Histone Deacetylase (HDAC) activity across multiple human pathologies have highlighted this family of epigenetic enzymes as critical druggable targets, amenable to small molecule intervention. While efficacious, current approaches using non-selective HDAC inhibitors (HDACi) have been shown to cause a range of undesirable clinical toxicities. To circumvent this, recent efforts have focused on the design of highly selective HDACi as a novel therapeutic strategy. Beyond roles in regulating transcription, the unique HDAC6 (with two catalytic domains) regulates the deacetylation of α-tubulin; promoting growth factor-controlled cell motility, cell division, and metastatic hallmarks. Recent studies have linked aberrant HDAC6 function in various hematological cancers including acute myeloid leukaemia and multiple myeloma. Herein, we report the discovery, in vitro characterization, and biological evaluation of PTG-0861 (JG-265), a novel HDAC6-selective inhibitor with strong isozyme-selectivity (∼36× ) and low nanomolar potency (IC50 = 5.92 nM) against HDAC6. This selectivity profile was rationalized via in silico docking studies and also observed in cellulo through cellular target engagement. Moreover, PTG-0861 achieved relevant potency against several blood cancer cell lines (e.g. MV4-11, MM1S), whilst showing limited cytotoxicity against non-malignant cells (e.g. NHF, HUVEC) and CD-1 mice. In examining compound stability and cellular permeability, PTG-0861 revealed a promising in vitro pharmacokinetic (PK) profile. Altogether, in this study we identified a novel and potent HDAC6-selective inhibitor (∼4× more selective than current clinical standards - citarinostat, ricolinostat), which achieves cellular target engagement, efficacy in hematological cancer cells with a promising safety profile and in vitro PK.
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Affiliation(s)
- Justyna M Gawel
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
| | - Andrew E Shouksmith
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
| | - Yasir S Raouf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Nabanita Nawar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Krimo Toutah
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
| | - Shazreh Bukhari
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Diana Sina
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Abootaleb Sedighi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359, Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada; Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada.
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10
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Wang S, Zeng P, Zhu X, Lei C, Huang Y, Nie Z. Chimeric Peptides Self-Assembling on Titanium Carbide MXenes as Biosensing Interfaces for Activity Assay of Post-translational Modification Enzymes. Anal Chem 2020; 92:8819-8826. [DOI: 10.1021/acs.analchem.0c00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shigong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Pan Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Xiaohua Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
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11
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Daniel L, Gotsbacher MP, Richardson-Sanchez T, Tieu W, Codd R. Exploring hydroxamic acid inhibitors of HDAC1 and HDAC2 using small molecule tools and molecular or homology modelling. Bioorg Med Chem Lett 2019; 29:2581-2586. [PMID: 31400937 DOI: 10.1016/j.bmcl.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Hydroxamic acid compounds 1-10 containing a N-hydroxycinnamamide scaffold and a 4-(benzylamino)methyl cap group that was either unsubstituted (1) or substituted with one (2-4) or two (5-10) methoxy groups in variable positions were prepared as inhibitors of Zn(II)-containing histone deacetylases (HDACs). The 3,4- (9) and 3,5- (10) bis-methoxy-substituted compounds were the least potent against HeLa nuclear extract, HDAC1 and HDAC2. Molecular modelling showed methoxy groups in the 3-, 4- and 5-position, but not the 2-position, had unfavourable steric interactions with the G32-H33-P34 triad on a loop at the surface of the HDAC2 active site cavity. An HDAC1 homology model showed potential ionic (E243..K288) and cation-pi (K247..F292) interactions between helix 10 and helix 11 that were absent in HDAC2 ((G243..K288) and (K247..V292)). This surface-located interhelical constraint could inform the design of bitopic HDAC1 and HDAC2 selective ligands using an allosteric approach, and/or protein-protein interaction (PPI) inhibitors.
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Affiliation(s)
- Lydia Daniel
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Michael P Gotsbacher
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Tomas Richardson-Sanchez
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology), The University of Sydney, New South Wales 2006, Australia.
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12
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Aboukhatwa SM, Hanigan TW, Taha TY, Neerasa J, Ranjan R, El-Bastawissy EE, Elkersh MA, El-Moselhy TF, Frasor J, Mahmud N, McLachlan A, Petukhov PA. Structurally Diverse Histone Deacetylase Photoreactive Probes: Design, Synthesis, and Photolabeling Studies in Live Cells and Tissue. ChemMedChem 2019; 14:1096-1107. [PMID: 30921497 PMCID: PMC6548601 DOI: 10.1002/cmdc.201900114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/28/2019] [Indexed: 01/27/2023]
Abstract
Histone deacetylase (HDAC) activity is modulated in vivo by post-translational modifications and formation of multiprotein complexes. Novel chemical tools to study how these factors affect engagement of HDAC isoforms by HDAC inhibitors (HDACi) in cells and tissues are needed. In this study, a synthetic strategy to access chemically diverse photoreactive probes (PRPs) was developed and used to prepare seven novel HDAC PRPs 9-15. The class I HDAC isoform engagement by PRPs was determined in biochemical assays and photolabeling experiments in live SET-2, HepG2, HuH7, and HEK293T cell lines and in mouse liver tissue. Unlike the HDAC protein abundance and biochemical activity against recombinant HDACs, the chemotype of the PRPs and the type of cells were key in defining the engagement of HDAC isoforms in live cells. Our findings suggest that engagement of HDAC isoforms by HDACi in vivo may be substantially modulated in a cell- and tissue-type-dependent manner.
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Affiliation(s)
- Shaimaa M Aboukhatwa
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Thomas W Hanigan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Taha Y Taha
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Jayaprakash Neerasa
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
| | - Rajeev Ranjan
- Section of Hematology/Oncology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Eman E El-Bastawissy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Mohamed A Elkersh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University, Alexandria, 21311, Egypt
| | - Tarek F El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Jonna Frasor
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Nadim Mahmud
- Section of Hematology/Oncology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Alan McLachlan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Pavel A Petukhov
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, 60612, USA
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13
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Kumboonma P, Senawong T, Saenglee S, Yenjai C, Phaosiri C. New histone deacetylase inhibitors from the twigs of Melanorrhoea usitata. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2209-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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14
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The structural requirements of histone deacetylase inhibitors: C4-modified SAHA analogs display dual HDAC6/HDAC8 selectivity. Eur J Med Chem 2017; 143:1790-1806. [PMID: 29150330 DOI: 10.1016/j.ejmech.2017.10.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/28/2017] [Accepted: 10/28/2017] [Indexed: 01/29/2023]
Abstract
Histone deacetylase (HDAC) enzymes govern the post-translational acetylation state of lysine residues on protein substrates, leading to regulatory changes in cell function. Due to their role in cancers, HDAC proteins have emerged as promising targets for cancer treatment. Four HDAC inhibitors have been approved as anti-cancer therapeutics, including SAHA (Suberoylanilide hydroxamic acid, Vorinostat, Zolinza). SAHA is a nonselective HDAC inhibitor that targets most of the eleven HDAC isoforms. The nonselectivity of SAHA might account for its clinical side effects, but certainly limits its use as a chemical tool to study cancer-related HDAC cell biology. Herein, the nonselective HDAC inhibitor SAHA was modified at the C4 position of the linker to explore activity and selectivity. Several C4-modified SAHA analogs exhibited dual HDAC6/8 selectivity. Interestingly, (R)-C4-benzyl SAHA displayed 520- to 1300-fold selectivity for HDAC6 and HDAC8 over HDAC1, 2, and 3, with IC50 values of 48 and 27 nM with HDAC6 and 8, respectively. In cellulo testing of the inhibitors was consistent with the observed in vitro selectivity. Docking studies provided a structural rationale for selectivity. The C4-SAHA analogs represent useful chemical tools to understand the role of HDAC6 and HDAC8 in cancer biology and exciting lead compounds for targeting of both HDAC6 and HDAC8 in various cancers.
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15
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Negmeldin AT, Pflum MKH. The structural requirements of histone deacetylase inhibitors: SAHA analogs modified at the C5 position display dual HDAC6/8 selectivity. Bioorg Med Chem Lett 2017. [PMID: 28648461 DOI: 10.1016/j.bmcl.2017.06.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histone deacetylase (HDAC) proteins have emerged as important targets for anti-cancer drugs, with four small molecules approved for use in the clinic. Suberoylanilide hydroxamic acid (Vorinostat, SAHA) was the first FDA-approved HDAC inhibitor for cancer treatment. However, SAHA inhibits most of the eleven HDAC isoforms. To understand the structural requirements of HDAC inhibitor selectivity and develop isoform selective HDAC inhibitors, SAHA analogs modified in the linker at the C5 position were synthesized and tested for potency and selectivity. C5-modified SAHA analogs displayed dual selectivity to HDAC6 and HDAC8 over HDAC 1, 2, and 3, with only a modest reduction in potency. These findings are consistent with prior work showing that modification of the linker region of SAHA can alter isoform selectivity. The observed HDAC6/8 selectivity of C5-modified SAHA analogs provide guidance toward development of isoform selective HDAC inhibitors and more effective anti-cancer drugs.
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Affiliation(s)
- Ahmed T Negmeldin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, United States.
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16
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Negmeldin AT, Padige G, Bieliauskas AV, Pflum MKH. Structural Requirements of HDAC Inhibitors: SAHA Analogues Modified at the C2 Position Display HDAC6/8 Selectivity. ACS Med Chem Lett 2017; 8:281-286. [PMID: 28337317 DOI: 10.1021/acsmedchemlett.6b00124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 02/07/2017] [Indexed: 11/28/2022] Open
Abstract
Histone deacetylase (HDAC) proteins are epigenetic regulators that deacetylate protein substrates, leading to subsequent changes in cell function. HDAC proteins are implicated in cancers, and several HDAC inhibitors have been approved by the FDA as anticancer drugs, including SAHA (suberoylanilide hydroxamic acid; Vorinostat and Zolinza). Unfortunately, SAHA inhibits most HDAC isoforms, which limits its use as a pharmacological tool and may lead to side effects in the clinic. In this work SAHA analogues substituted at the C2 position were synthesized and screened for HDAC isoform selectivity in vitro and in cells. The most potent and selective compound, C2-n-hexyl SAHA, displayed submicromolar potency with 49- to 300-fold selectivity for HDAC6 and HDAC8 compared to HDAC1, -2, and -3. Docking studies provided a structural rationale for selectivity. Modification of the nonselective inhibitor SAHA generated HDAC6/HDAC8 dual selective inhibitors, which can be useful lead compounds toward developing pharmacological tools and more effective anticancer drugs.
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Affiliation(s)
- Ahmed T. Negmeldin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Geetha Padige
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Anton V. Bieliauskas
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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17
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Almaliti J, Al-Hamashi AA, Negmeldin AT, Hanigan CL, Perera L, Pflum MKH, Casero RA, Tillekeratne LMV. Largazole Analogues Embodying Radical Changes in the Depsipeptide Ring: Development of a More Selective and Highly Potent Analogue. J Med Chem 2016; 59:10642-10660. [PMID: 27809521 DOI: 10.1021/acs.jmedchem.6b01271] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A number of analogues of the marine-derived histone deacetylase inhibitor largazole incorporating major structural changes in the depsipeptide ring were synthesized. Replacing the thiazole-thiazoline fragment of largazole with a bipyridine group gave analogue 7 with potent cell growth inhibitory activity and an activity profile similar to that of largazole, suggesting that conformational change accompanying switching hybridization from sp3 to sp2 at C-7 is well tolerated. Analogue 7 was more class I selective compared to largazole, with at least 464-fold selectivity for class I HDAC proteins over class II HDAC6 compared to a 22-fold selectivity observed with largazole. To our knowledge 7 represents the first example of a potent and highly cytotoxic largazole analogue not containing a thiazoline ring. The elimination of a chiral center derived from the unnatural amino acid R-α-methylcysteine makes the molecule more amenable to chemical synthesis, and coupled with its increased class I selectivity, 7 could serve as a new lead compound for developing selective largazole analogues.
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Affiliation(s)
- Jehad Almaliti
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan , Amman, 11942, Jordan
| | - Ayad A Al-Hamashi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States
| | - Ahmed T Negmeldin
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Christin L Hanigan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine , Bunting/Blaustein Cancer Research Building 1, Room 551, 1650 Orleans Street, Baltimore, Maryland 21231, United States
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Robert A Casero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine , Bunting/Blaustein Cancer Research Building 1, Room 551, 1650 Orleans Street, Baltimore, Maryland 21231, United States
| | - L M Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States
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18
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Hsu CW, Shou D, Huang R, Khuc T, Dai S, Zheng W, Klumpp-Thomas C, Xia M. Identification of HDAC Inhibitors Using a Cell-Based HDAC I/II Assay. ACTA ACUST UNITED AC 2016; 21:643-52. [PMID: 26858181 DOI: 10.1177/1087057116629381] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/07/2016] [Indexed: 12/21/2022]
Abstract
Histone deacetylases (HDACs) are a class of epigenetic enzymes that regulate gene expression by histone deacetylation. Altered HDAC function has been linked to cancer and neurodegenerative diseases, making HDACs popular therapeutic targets. In this study, we describe a screening approach for identification of compounds that inhibit endogenous class I and II HDACs. A homogeneous, luminogenic HDAC I/II assay was optimized in a 1536-well plate format in several human cancer cell lines, including HCT116 and human neural stem cells. The assay confirmed 37 known HDAC inhibitors from two libraries of known epigenetics-active compounds. Using the assay, we identified a group of potential HDAC inhibitors by screening the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection of 2527 small-molecule drugs. The selected compounds showed similar HDAC I/II inhibitory potency and efficacy values in both HCT116 and neural stem cells. Several previously unidentified HDAC inhibitors were further evaluated and profiled for their selectivity against a panel of 10 HDAC I/II isoforms using fluorogenic HDAC biochemical assays. In summary, our results show that several novel HDAC inhibitors, including nafamostat and piceatannol, have been identified using the HDAC I/II cell-based assay, and multiple cell types have been validated for high-throughput screening of large chemical libraries.
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Affiliation(s)
- Chia-Wen Hsu
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - David Shou
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Thai Khuc
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Sheng Dai
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | | | - Menghang Xia
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
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