51
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De Vita S, Meninno S, Capasso L, Colarusso E, Chini MG, Lauro G, Rinaldi R, De Cicco A, Sian V, Terracciano S, Nebbioso A, Lattanzi A, Bifulco G. 2-Substituted 1,5-benzothiazepine-based HDAC inhibitors exert anticancer activities on human solid and acute myeloid leukemia cell lines. Bioorg Med Chem 2023; 93:117444. [PMID: 37611334 DOI: 10.1016/j.bmc.2023.117444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Herein, we report the development of a new series of histone deacetylase inhibitors (HDACi) containing a 2-substituted 1,5-benzothiazepine scaffold. First, a virtual combinatorial library (∼1.6 × 103 items) was built according to a convenient synthetic route, and then it was submitted to molecular docking experiments on seven HDACs isoforms belonging to classes I and II. Integrated computational filters were used to select the most promising ones that were synthesized through an optimized approach, also amenable to generating both racemic and enantioenriched benzothiazepine-based derivatives. The obtained compounds showed potent HDAC inhibitory activity, especially those containing the sulphone moiety, endowed with IC50 in the nanomolar range. In addition, in vitro outcomes of our synthesized compounds demonstrated a cytotoxic effect on U937 and HCT116 cell lines and an arrest in the G2/M phase (13 ≤ IC50 ≤ 18 µM). Finally, Western blot analyses outlined the modulation of the histone acetyl markers such as H3K9/14, acetyl-tubulin, and the apoptotic indicator p21 in both cancer cell lines, disclosing a good HDAC inhibitor activity exerted by the designed items. Given the key role of HDACs in many cellular pathways, which makes these enzymes appealing and "hot" drug targets, our findings highlighted the importance of these 2-substituted 1,5-benzothiazepine-based compounds (both in the reduced and oxidized version) for the development of novel epidrugs.
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Sara Meninno
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Lucia Capasso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche, Isernia 86090, Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Romolo Rinaldi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Annalisa De Cicco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Veronica Sian
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy.
| | - Alessandra Lattanzi
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy.
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52
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Poonia P, Sharma M, Jha P, Chopra M. Pharmacophore-based virtual screening of ZINC database, molecular modeling and designing new derivatives as potential HDAC6 inhibitors. Mol Divers 2023; 27:2053-2071. [PMID: 36214962 DOI: 10.1007/s11030-022-10540-3] [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: 09/10/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022]
Abstract
To date, many HDAC6 inhibitors have been identified and developed but none is clinically approved as of now. Through this study, we aim to obtain novel HDAC6 selective inhibitors and provide new insights into the detailed structural design of potential HDAC6 inhibitors. A HypoGen-based 3D QSAR HDAC6 pharmacophore was built and used as a query model to screen approximately 8 million ZINC database compounds. First, the ZINC Database was filtered using ADMET, followed by pharmacophore-based library screening. Using fit value and estimated activity cutoffs, a final set of 54 ZINC hits was obtained that were further investigated using molecular docking with the crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with Trichostatin A (PDB ID: 5EDU). Through detailed in silico screening of the ZINC database, we shortlisted three hits as the lead molecules for designing novel HDAC6 inhibitors with better efficacy. Docking with 5EDU, followed by ADMET and TOPKAT analysis of modified ZINC hits provided 9 novel potential HDAC6 inhibitors that possess better docking scores and 2D interactions as compared to the control ZINC hit molecules. Finally, a 50 ns MD analysis run followed by Protein-Ligand Interaction Energy (PLIE) analysis of the top scored hits provided a novel molecule N1 that showed promisingly similar results to that of Ricolinostat (a known HDAC6 inhibitor). The comparable result of the designed hits to established HDAC6 inhibitors suggests that these compounds might prove to be successful HDAC6 inhibitors in future. Designed novel hits that might act as good HDAC6 inhibitors derived from ZINC database using combined molecular docking and modeling approaches.
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Affiliation(s)
- Priya Poonia
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110036, India
| | - Monika Sharma
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110036, India
| | - Prakash Jha
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110036, India
| | - Madhu Chopra
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110036, India.
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53
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Gupta SK, Ali KH, Lee S, Seo YH. Exploring new histone deacetylase 6 inhibitors and their effects on reversing the α-tubulin deacetylation and cell morphology changes caused by methamphetamine. Arch Pharm Res 2023; 46:795-807. [PMID: 37777709 DOI: 10.1007/s12272-023-01467-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Indazole-based HDAC6 inhibitors with novel zinc-binding modifications were synthesized and evaluated to determine their potential to inhibit HDAC6. The analogs were subjected to a histone deacetylase (HDAC) enzyme assay, which led to identification of compounds 3a and 3b. Both compounds demonstrated higher potency and selectivity as HDAC6 inhibitors with IC50 values of 9.1 nM and 9.0 nM, respectively, and highlighted the importance of the hydroxamic acid moiety for binding to Zn2+ inside the catalytic pocket of HDAC enzymes. In the neuroblastoma SH-SY5Y cell line, both compounds efficiently acetylated α-tubulin but not histone H3 at a low concentration of 0.5 µM. Moreover, compounds 3a and 3b effectively reversed the deacetylation of α-tubulin caused by methamphetamine in the SH-SY5Y cell line, suggesting the potential usefulness of HDAC6 selective inhibition in restoring blood brain barrier integrity by reversing methamphetamine-induced deacetylation.
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Affiliation(s)
- Sunil K Gupta
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Khan Hashim Ali
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Sooyeun Lee
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Young Ho Seo
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea.
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54
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Watson PR, Christianson DW. Structure and Function of Kdac1, a Class II Deacetylase from the Multidrug-Resistant Pathogen Acinetobacter baumannii. Biochemistry 2023; 62:2689-2699. [PMID: 37624144 PMCID: PMC10528293 DOI: 10.1021/acs.biochem.3c00288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Proteomics studies indicate that 10% of proteins in the opportunistic pathogen Acinetobacter baumannii are acetylated, suggesting that lysine acetyltransferases and deacetylases function to maintain and regulate a robust bacterial acetylome. As the first step in exploring these fascinating prokaryotic enzymes, we now report the preparation and characterization of the lysine deacetylase Kdac1. We show that Kdac1 catalyzes the deacetylation of free acetyllysine and acetyllysine tetrapeptide assay substrates, and we also report the X-ray crystal structures of unliganded Kdac1 as well as its complex with the hydroxamate inhibitor Citarinostat. Kdac1 is a tetramer in solution and in the crystal; the crystal structure reveals that the L1 loop functions to stabilize quaternary structure, forming inter-subunit hydrogen bonds and salt bridges around a central arginine residue (R30). Surprisingly, the L1 loop partially blocks entry to the active site, but it is sufficiently flexible to allow for the binding of two Citarinostat molecules in the active site. The L12 loop is also important for maintaining quaternary structure; here, a conserved arginine (R278) accepts hydrogen bonds from the backbone carbonyl groups of residues in an adjacent monomer. Structural comparisons with two other prokaryotic lysine deacetylases reveal conserved residues in the L1 and L12 loops that similarly support tetramer assembly. These studies provide a structural foundation for understanding enzymes that regulate protein function in bacteria through reversible lysine acetylation, serving as a first step in the exploration of these enzymes as possible targets for the development of new antibiotics.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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55
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Toro TB, Skripnikova EV, Bornes KE, Zhang K, Watt TJ. Endogenous expression of inactive lysine deacetylases reveals deacetylation-dependent cellular mechanisms. PLoS One 2023; 18:e0291779. [PMID: 37721967 PMCID: PMC10506724 DOI: 10.1371/journal.pone.0291779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
Acetylation of lysine residues is an important and common post-translational regulatory mechanism occurring on thousands of non-histone proteins. Lysine deacetylases (KDACs or HDACs) are a family of enzymes responsible for removing acetylation. To identify the biological mechanisms regulated by individual KDACs, we created HT1080 cell lines containing chromosomal point mutations, which endogenously express either KDAC6 or KDAC8 having single inactivated catalytic domain. Engineered HT1080 cells expressing inactive KDA6 or KDAC8 domains remained viable and exhibited enhanced acetylation on known substrate proteins. RNA-seq analysis revealed that many changes in gene expression were observed when KDACs were inactivated, and that these gene sets differed significantly from knockdown and knockout cell lines. Using GO ontology, we identified several critical biological processes associated specifically with catalytic activity and others attributable to non-catalytic interactions. Treatment of wild-type cells with KDAC-specific inhibitors Tubastatin A and PCI-34051 resulted in gene expression changes distinct from those of the engineered cell lines, validating this approach as a tool for evaluating in-cell inhibitor specificity and identifying off-target effects of KDAC inhibitors. Probing the functions of specific KDAC domains using these cell lines is not equivalent to doing so using previously existing methods and provides novel insight into the catalytic functions of individual KDACs by investigating the molecular and cellular changes upon genetic inactivation.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Elena V. Skripnikova
- Division of Basic and Pharmaceutical Sciences, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kiara E. Bornes
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kun Zhang
- Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, United States of America
- Bioinformatics Core, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
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56
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Qu M, Zhang H, Cheng P, Wubshet AK, Yin X, Wang X, Sun Y. Histone deacetylase 6's function in viral infection, innate immunity, and disease: latest advances. Front Immunol 2023; 14:1216548. [PMID: 37638049 PMCID: PMC10450946 DOI: 10.3389/fimmu.2023.1216548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
In the family of histone-deacetylases, histone deacetylase 6 (HDAC6) stands out. The cytoplasmic class IIb histone deacetylase (HDAC) family is essential for many cellular functions. It plays a crucial and debatable regulatory role in innate antiviral immunity. This review summarises the current state of our understanding of HDAC6's structure and function in light of the three mechanisms by which it controls DNA and RNA virus infection: cytoskeleton regulation, host innate immune response, and autophagy degradation of host or viral proteins. In addition, we summed up how HDAC6 inhibitors are used to treat a wide range of diseases, and how its upstream signaling plays a role in the antiviral mechanism. Together, the findings of this review highlight HDAC6's importance as a new therapeutic target in antiviral immunity, innate immune response, and some diseases, all of which offer promising new avenues for the development of drugs targeting the immune response.
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Affiliation(s)
- Min Qu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huijun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengyuan Cheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ashenafi Kiros Wubshet
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Basic and Diagnostic Sciences, College of Veterinary Science, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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57
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Harding R, Franzoni I, Mann MK, Szewczyk MM, Mirabi B, Ferreira de Freitas R, Owens DDG, Ackloo S, Scheremetjew A, Juarez-Ornelas KA, Sanichar R, Baker RJ, Dank C, Brown PJ, Barsyte-Lovejoy D, Santhakumar V, Schapira M, Lautens M, Arrowsmith CH. Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J Med Chem 2023; 66:10273-10288. [PMID: 37499118 PMCID: PMC10424181 DOI: 10.1021/acs.jmedchem.3c00314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 07/29/2023]
Abstract
Histone deacetylase 6 (HDAC6) inhibition is an attractive strategy for treating numerous cancers, and HDAC6 catalytic inhibitors are currently in clinical trials. The HDAC6 zinc-finger ubiquitin-binding domain (UBD) binds free C-terminal diglycine motifs of unanchored ubiquitin polymer chains and protein aggregates, playing an important role in autophagy and aggresome assembly. However, targeting this domain with small molecule antagonists remains an underdeveloped avenue of HDAC6-focused drug discovery. We report SGC-UBD253 (25), a chemical probe potently targeting HDAC6-UBD in vitro with selectivity over nine other UBDs, except for weak USP16 binding. In cells, 25 is an effective antagonist of HDAC6-UBD at 1 μM, with marked proteome-wide selectivity. We identified SGC-UBD253N (32), a methylated derivative of 25 that is 300-fold less active, serving as a negative control. Together, 25 and 32 could enable further exploration of the biological function of the HDAC6-UBD and investigation of the therapeutic potential of targeting this domain.
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Affiliation(s)
- Rachel
J. Harding
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ivan Franzoni
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Valence
Discovery Inc., 6666
Rue St-Urbain, Suite 200, Montreal, Quebec H2S 3H1, Canada
| | - Mandeep K. Mann
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Magdalena M. Szewczyk
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bijan Mirabi
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Dominic D. G. Owens
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Suzanne Ackloo
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alexej Scheremetjew
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kevin A. Juarez-Ornelas
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Randy Sanichar
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rachel J. Baker
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Christian Dank
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology & Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mark Lautens
- Davenport
Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Cheryl H. Arrowsmith
- Structural
Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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58
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Yu WC, Yeh TY, Ye CH, Chong PCT, Ho YH, So DK, Yap KY, Peng GR, Shao CH, Jagtap AD, Chern JW, Lin CS, Lin SP, Lin SL, Yu SH, Yu CW. Discovery of HDAC6, HDAC8, and 6/8 Inhibitors and Development of Cell-Based Drug Screening Models for the Treatment of TGF-β-Induced Idiopathic Pulmonary Fibrosis. J Med Chem 2023; 66:10528-10557. [PMID: 37463500 DOI: 10.1021/acs.jmedchem.3c00644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Idiopathic pulmonary fibrosis is incurable, and its progression is difficult to control and thus can lead to pulmonary deterioration. Pan-histone deacetylase inhibitors such as SAHA have shown potential for modulating pulmonary fibrosis yet with off-target effects. Therefore, selective HDAC inhibitors would be beneficial for reducing side effects. Toward this goal, we designed and synthesized 24 novel HDAC6, HDAC8, or dual HDAC6/8 inhibitors and established a two-stage screening platform to rapidly screen for HDAC inhibitors that effectively mitigate TGF-β-induced pulmonary fibrosis. The first stage consisted of a mouse NIH-3T3 fibroblast prescreen and yielded five hits. In the second stage, human pulmonary fibroblasts (HPFs) were used, and four out of the five hits were tested for caco-2 permeability and liver microsome stability to give two potential leads: J27644 (15) and 20. This novel two-stage screen platform will accelerate the discovery and reduce the cost of developing HDAC inhibitors to mitigate TGF-β-induced pulmonary fibrosis.
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Affiliation(s)
- Wei-Chieh Yu
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Tsung-Yu Yeh
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
| | - Chih-Hung Ye
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | | | - Yi-Hsun Ho
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
| | - Dorothy Kazuno So
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Kah Yi Yap
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Guan-Ru Peng
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Chi-Hsuan Shao
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
| | - Ajit Dhananjay Jagtap
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
| | - Ji-Wang Chern
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 106, Taiwan
| | - Shau-Ping Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Center of Systems Biology, National Taiwan University, Taipei 106, Taiwan
- The Research Center of Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 106, Taiwan
| | - Shuei-Liong Lin
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Integrated Diagnostics & Therapeutics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Shu-Han Yu
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Chao-Wu Yu
- National Taiwan University, School of Pharmacy, College of Medicine, Taipei 100, Taiwan
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59
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Watson PR, Stollmaier JG, Christianson DW. Crystal Structure of Histone Deacetylase 6 Complexed with ( R )-Lipoic Acid, an Essential Cofactor in Central Carbon Metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552419. [PMID: 37609266 PMCID: PMC10441330 DOI: 10.1101/2023.08.08.552419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The enzyme cofactor ( R )-lipoic acid plays a critical role in central carbon metabolism due to its catalytic function in the generation of acetyl-CoA, which links glycolysis with the tricarboxylic acid cycle. This cofactor is also essential for the generation of succinyl CoA within the tricarboxylic acid cycle. However, the biological functions of ( R )-lipoic acid extend beyond metabolism owing to its facile redox chemistry. Most recently, the reduced form of ( R )-lipoic acid, ( R )-dihydrolipoic acid, has been shown to inhibit histone deacetylases (HDACs) with selectivity for the inhibition of HDAC6. Here, we report the 2.4 Å-resolution X-ray crystal structure of the HDAC6-( R )-dihydrolipoic acid complex, and we report a dissociation constant (K D ) of 350 nM for this complex as determined by isothermal titration calorimetry. The crystal structure illuminates key affinity determinants in the enzyme active site, including thiolate-Zn 2+ coordination and S-π interactions in the F583-F643 aromatic crevice. This study provides the first visualization of the connection between HDAC function and the biological response to oxidative stress: the dithiol moiety of ( R )-dihydrolipoic acid can serve as a redox-regulated pharmacophore capable of simultaneously targeting the catalytic Zn 2+ ion and the aromatic crevice in the active site of HDAC6.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Juana Goulart Stollmaier
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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60
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Liu F, Liu C, Chai Q, Zhao C, Meng H, Xue X, Yao TP, Zhang Y. Discovery of the First Irreversible HDAC6 Isoform Selective Inhibitor with Potent Anti-Multiple Myeloma Activity. J Med Chem 2023; 66:10080-10091. [PMID: 37463038 DOI: 10.1021/acs.jmedchem.3c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
In our previous research, a series of phenylsulfonylfuroxan-based hydroxamates were developed, among which compound 1 exhibited remarkable in vitro and in vivo antitumor potency due to its histone deacetylase (HDAC) inhibitory and nitric oxide (NO)-donating activities. Herein, the in-depth study of compound 1 revealed that this HDAC inhibitor-NO donor hybrid could enduringly increase the intracellular levels of acetyl histones and acetyl α-tubulin, which could be ascribed to its irreversible inhibition toward class I HDACs and HDAC6. Structural modification of compound 1 led to a novel phenylsulfonylfuroxan-based hydroxamate 4, which exhibited considerable HDAC6 inhibitory activity and selectivity. Furthermore, compound 4 could inhibit intracellular HDAC6 both selectively and irreversibly. To the best of our knowledge, this is the first research reporting the irreversible inhibition of HDAC6. It was also demonstrated that compared with ACY-241 (a reversible HDAC6 inhibitor in clinical trials), the irreversible HDAC6 selective inhibitor 4 exhibited not only superior anti-multiple myeloma activity but also improved therapeutic index.
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Affiliation(s)
- Fengling Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chunxi Liu
- Department of Pharmacy, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Qipeng Chai
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chunlong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Hongwei Meng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Xia Xue
- Department of Pharmacy, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Tso-Pang Yao
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
| | - Yingjie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P.R. China
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Cellupica E, Caprini G, Fossati G, Mirdita D, Cordella P, Marchini M, Rocchio I, Sandrone G, Stevenazzi A, Vergani B, Steinkühler C, Vanoni MA. The Importance of the "Time Factor" for the Evaluation of Inhibition Mechanisms: The Case of Selected HDAC6 Inhibitors. BIOLOGY 2023; 12:1049. [PMID: 37626935 PMCID: PMC10452033 DOI: 10.3390/biology12081049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Histone deacetylases (HDACs) participate with histone acetyltransferases in the modulation of the biological activity of a broad array of proteins, besides histones. Histone deacetylase 6 is unique among HDAC as it contains two catalytic domains, an N-terminal microtubule binding region and a C-terminal ubiquitin binding domain. Most of its known biological roles are related to its protein lysine deacetylase activity in the cytoplasm. The design of specific inhibitors is the focus of a large number of medicinal chemistry programs in the academy and industry because lowering HDAC6 activity has been demonstrated to be beneficial for the treatment of several diseases, including cancer, and neurological and immunological disorders. Here, we show how re-evaluation of the mechanism of action of selected HDAC6 inhibitors, by monitoring the time-dependence of the onset and relief of the inhibition, revealed instances of slow-binding/slow-release inhibition. The same approach, in conjunction with X-ray crystallography, in silico modeling and mass spectrometry, helped to propose a model of inhibition of HDAC6 by a novel difluoromethyloxadiazole-based compound that was found to be a slow-binding substrate analog of HDAC6, giving rise to a tightly bound, long-lived inhibitory derivative.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Doris Mirdita
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy;
| | - Paola Cordella
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Barbara Vergani
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
| | - Christian Steinkühler
- Research and Development, Italfarmaco Group, Via dei Lavoratori 54, 20092 Cinisello Balsamo, Italy; (E.C.); (G.C.); (G.F.); (P.C.); (M.M.); (I.R.); (G.S.); (A.S.); (B.V.)
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Motlová L, Šnajdr I, Kutil Z, Andris E, Ptáček J, Novotná A, Nováková Z, Havlínová B, Tueckmantel W, Dráberová H, Majer P, Schutkowski M, Kozikowski A, Rulíšek L, Bařinka C. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6). ACS Chem Biol 2023. [PMID: 37392419 PMCID: PMC10367051 DOI: 10.1021/acschembio.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG‡ ≈ 21 kcal·mol-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF3 or -CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.
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Affiliation(s)
- Lucia Motlová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Ivan Šnajdr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Jakub Ptáček
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Adéla Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Zora Nováková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Barbora Havlínová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Werner Tueckmantel
- StarWise Therapeutics LLC, University Research Park, Inc., Madison, Wisconsin 53719, United States
| | - Helena Dráberová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Alan Kozikowski
- StarWise Therapeutics LLC, University Research Park, Inc., Madison, Wisconsin 53719, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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Geurs S, Clarisse D, De Bosscher K, D'hooghe M. The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs. J Med Chem 2023. [PMID: 37276138 DOI: 10.1021/acs.jmedchem.3c00226] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Histone deacetylases (HDACs) are enzymes pursued as drug targets in various cancers and several non-oncological conditions, such as inflammation and neurodegenerative disorders. In the past decade, HDAC inhibitors (HDACi) have emerged as relevant pharmaceuticals, with many efforts devoted to the development of new representatives. However, the growing safety concerns regarding the established hydroxamic acid-based HDAC inhibitors tend to drive current research more toward the design of inhibitors bearing alternative zinc-binding groups (ZBGs). This Perspective presents an overview of all non-hydroxamic acid ZBGs that have been incorporated into the clinically approved prototypical HDACi, suberoylanilide hydroxamic acid (vorinostat). This provides the unique opportunity to compare the inhibition potential and biological effects of different ZBGs in a direct way, as the compounds selected for this Perspective differ only in their ZBG. To that end, different strategies used to select a ZBG, its properties, activity, and liabilities are discussed.
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Affiliation(s)
- Silke Geurs
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Dorien Clarisse
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Karolien De Bosscher
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B-9052 Ghent, Belgium
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Aleksandrova Y, Munkuev A, Mozhaitsev E, Suslov E, Tsypyshev D, Chaprov K, Begunov R, Volcho K, Salakhutdinov N, Neganova M. Elaboration of the Effective Multi-Target Therapeutic Platform for the Treatment of Alzheimer's Disease Based on Novel Monoterpene-Derived Hydroxamic Acids. Int J Mol Sci 2023; 24:ijms24119743. [PMID: 37298694 DOI: 10.3390/ijms24119743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Novel monoterpene-based hydroxamic acids of two structural types were synthesized for the first time. The first type consisted of compounds with a hydroxamate group directly bound to acyclic, monocyclic and bicyclic monoterpene scaffolds. The second type included hydroxamic acids connected with the monoterpene moiety through aliphatic (hexa/heptamethylene) or aromatic linkers. An in vitro analysis of biological activity demonstrated that some of these molecules had powerful HDAC6 inhibitory activity, with the presence of a linker area in the structure of compounds playing a key role. In particular, it was found that hydroxamic acids containing a hexa- and heptamethylene linker and (-)-perill fragment in the Cap group exhibit excellent inhibitory activity against HDAC6 with IC50 in the submicromolar range from 0.56 ± 0.01 µM to 0.74 ± 0.02 µM. The results of the study of antiradical activity demonstrated the presence of moderate ability for some hydroxamic acids to scavenge 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2ROO• radicals. The correlation coefficient between the DPPH radical scavenging activity and oxygen radical absorbance capacity (ORAC) value was R2 = 0.8400. In addition, compounds with an aromatic linker based on para-substituted cinnamic acids, having a monocyclic para-menthene skeleton as a Cap group, 35a, 38a, 35b and 38b, demonstrated a significant ability to suppress the aggregation of the pathological β-amyloid peptide 1-42. The 35a lead compound with a promising profile of biological activity, discovered in the in vitro experiments, demonstrated neuroprotective effects on in vivo models of Alzheimer's disease using 5xFAD transgenic mice. Together, the results obtained demonstrate a potential strategy for the use of monoterpene-derived hydroxamic acids for treatment of various aspects of Alzheimer's disease.
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Affiliation(s)
- Yulia Aleksandrova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severnij Pr. 1, Chernogolovka 142432, Russia
| | - Aldar Munkuev
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Evgenii Mozhaitsev
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Evgenii Suslov
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Dmitry Tsypyshev
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Kirill Chaprov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severnij Pr. 1, Chernogolovka 142432, Russia
| | - Roman Begunov
- Biology and Ecology Faculty of P. G. Demidov Yaroslavl State University, Matrosova Ave., 9, Yaroslavl 150003, Russia
| | - Konstantin Volcho
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Nariman Salakhutdinov
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Margarita Neganova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severnij Pr. 1, Chernogolovka 142432, Russia
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Li Z, Duan P, Qiu R, Fang L, Fang P, Xiao S. HDAC6 Degrades nsp8 of Porcine Deltacoronavirus through Deacetylation and Ubiquitination to Inhibit Viral Replication. J Virol 2023; 97:e0037523. [PMID: 37133375 PMCID: PMC10231189 DOI: 10.1128/jvi.00375-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that has the potential to infect humans. Histone deacetylase 6 (HDAC6) is a unique type IIb cytoplasmic deacetylase with both deacetylase activity and ubiquitin E3 ligase activity, which mediates a variety of cellular processes by deacetylating histone and nonhistone substrates. In this study, we found that ectopic expression of HDAC6 significantly inhibited PDCoV replication, while the reverse effects could be observed after treatment with an HDAC6-specific inhibitor (tubacin) or knockdown of HDAC6 expression by specific small interfering RNA. Furthermore, we demonstrated that HDAC6 interacted with viral nonstructural protein 8 (nsp8) in the context of PDCoV infection, resulting in its proteasomal degradation, which was dependent on the deacetylation activity of HDAC6. We further identified the key amino acid residues lysine 46 (K46) and K58 of nsp8 as acetylation and ubiquitination sites, respectively, which were required for HDAC6-mediated degradation. Through a PDCoV reverse genetics system, we confirmed that recombinant PDCoV with a mutation at either K46 or K58 exhibited resistance to the antiviral activity of HDAC6, thereby exhibiting higher replication compared with wild-type PDCoV. Collectively, these findings contribute to a better understanding of the function of HDAC6 in regulating PDCoV infection and provide new strategies for the development of anti-PDCoV drugs. IMPORTANCE As an emerging enteropathogenic coronavirus with zoonotic potential, porcine deltacoronavirus (PDCoV) has sparked tremendous attention. Histone deacetylase 6 (HDAC6) is a critical deacetylase with both deacetylase activity and ubiquitin E3 ligase activity and is extensively involved in many important physiological processes. However, little is known about the role of HDAC6 in the infection and pathogenesis of coronaviruses. Our present study demonstrates that HDAC6 targets PDCoV-encoded nonstructural protein 8 (nsp8) for proteasomal degradation through the deacetylation at the lysine 46 (K46) and the ubiquitination at K58, suppressing viral replication. Recombinant PDCoV with a mutation at K46 and/or K58 of nsp8 displayed resistance to the antiviral activity of HDAC6. Our work provides significant insights into the role of HDAC6 in regulating PDCoV infection, opening avenues for the development of novel anti-PDCoV drugs.
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Affiliation(s)
- Zhuang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Panpan Duan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Runhui Qiu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Puxian Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Liu X, Yan W, Wang S, Lu M, Yang H, Chai X, Shi H, Zhang Y, Jia Q. Discovery of selective HDAC6 inhibitors based on a multi-layer virtual screening strategy. Comput Biol Med 2023; 160:107036. [PMID: 37196455 DOI: 10.1016/j.compbiomed.2023.107036] [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: 02/02/2023] [Revised: 04/30/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
The abnormal enhancement of histone deacetylase 6 (HDAC6) has been demonstrated to be closely related to the occurrence and development of various malignant tumors, attracting extensive attention as a promising target for cancer therapy. Currently, only limited selective HDAC6 inhibitors have entered clinical trials, making the rapid discovery of selective HDAC6 inhibitors with safety profiles particularly urgent. In this study, a multi-layer virtual screening workflow was established, and the representative compounds screened were biologically evaluated in combination with enzyme inhibitory and anti-tumor cell proliferation experiments. The experimental results showed that the screened compounds L-25, L-32, L-45 and L-81 exhibited nanomolar inhibitory activity against HDAC6, and exerted a certain degree of anti-proliferative activities against tumor cells, especially the cytotoxicity of L-45 to A375 (IC50 = 11.23 ± 1.27 μM) and the cytotoxicity of L-81 against HCT-116 (IC50 = 12.25 ± 1.13 μM). Additionally, the molecular mechanisms underlying the subtype selective inhibitory activities of the selected compounds were further elucidated using computational approaches, and the hotspot residues on HDAC6 contributing to the ligands' binding were identified. In summary, this study established a multi-layer screening scheme to quickly and effectively screen out hit compounds with enzyme inhibitory activity and anti-tumor cell proliferation, providing novel scaffolds for the subsequent anti-tumor drug design based on HDAC6 target.
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Affiliation(s)
- Xingang Liu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China; Key Laboratory of Innovative Drug Research and Evaluation of Hebei Province, Shijiazhuang, 050017, China
| | - Wenying Yan
- Department of Clinical Pharmacy, The Third Hospital of Hebei Medical University, Shijiazhuang, 050051, China
| | - Songsong Wang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China; Key Laboratory of Innovative Drug Research and Evaluation of Hebei Province, Shijiazhuang, 050017, China
| | - Ming Lu
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Hao Yang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xu Chai
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China
| | - He Shi
- The Fourth Hospital of Shijiazhuang, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, 050000, China.
| | - Yang Zhang
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China; Key Laboratory of Innovative Drug Research and Evaluation of Hebei Province, Shijiazhuang, 050017, China.
| | - Qingzhong Jia
- School of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, China; The Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China; Key Laboratory of Innovative Drug Research and Evaluation of Hebei Province, Shijiazhuang, 050017, China.
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Zhu Y, Feng M, Wang B, Zheng Y, Jiang D, Zhao L, Mamun MAA, Kang H, Nie H, Zhang X, Guo N, Qin S, Wang N, Liu H, Gao Y. New insights into the non-enzymatic function of HDAC6. Biomed Pharmacother 2023; 161:114438. [PMID: 37002569 DOI: 10.1016/j.biopha.2023.114438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Histone deacetylase 6 (HDAC6) is a class IIb histone deacetylase that contains two catalytic domains and a zinc-finger ubiquitin binding domain (ZnF-UBP) domain. The deacetylation function of HDAC6 has been extensively studied with common substrates such as α-tubulin, cortactin, and Hsp90. Apart from its deacetylase activity, HDAC6 ZnF-UBP binds to unanchored ubiquitin of specific sequences and serves as a carrier for transporting aggregated proteins. As a result, aggresomes are formed and protein degradation is facilitated by the autophagy-lysosome pathway. This HDAC6-dependent microtubule transport can be used by cells to assemble and activate inflammasomes, which play a critical role in immune regulation. Even viruses can benefit from the carrier of HDAC6 to assist in uncoating their surfaces during their infection cycle. However, HDAC6 is also capable of blocking virus invasion and replication in a non-enzymatic manner. Given these non-enzymatic functions, HDAC6 is closely associated with various diseases, including neurodegeneration, inflammasome-associated diseases, cancer, and viral infections. Small molecule inhibitors targeting the ubiquitin binding pocket of HDAC6 have been investigated. In this review, we focus on mechanisms in non-enzymatic functions of HDAC6 and discuss the rationality and prospects of therapeutic strategies by intervening the activation of HDAC6 ZnF-UBP in concrete diseases.
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Affiliation(s)
- Yuanzai Zhu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Mengkai Feng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Yichao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Dandan Jiang
- Department of Pharmacy, People's Hospital of Henan Province, Zhengzhou University, Henan 450001, China
| | - Lijuan Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - M A A Mamun
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Huiqin Kang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Haiqian Nie
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiya Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ningjie Guo
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Shangshang Qin
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Hongmin Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
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68
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Watson PR, Gupta S, Hosseinzadeh P, Brown BP, Baker D, Christianson DW. Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. ACS Chem Biol 2023; 18:959-968. [PMID: 37027789 PMCID: PMC10130746 DOI: 10.1021/acschembio.3c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Histone deacetylases (HDACs) are essential for the regulation of myriad biological processes, and their aberrant function is implicated in cancer, neurodegeneration, and other diseases. The cytosolic isozyme HDAC6 is unique among the greater family of deacetylases in that it contains two catalytic domains, CD1 and CD2. HDAC6 CD2 is responsible for tubulin deacetylase and tau deacetylase activities, inhibition of which is a key goal as new therapeutic approaches are explored. Of particular interest as HDAC inhibitors are naturally occurring cyclic tetrapeptides such as Trapoxin A or HC Toxin, or the cyclic depsipeptides Largazole and Romidepsin. Even more intriguing are larger, computationally designed macrocyclic peptide inhibitors. Here, we report the 2.0 Å resolution crystal structure of HDAC6 CD2 complexed with macrocyclic octapeptide 1. Comparison with the previously reported structure of the complex with macrocyclic octapeptide 2 reveals that a potent thiolate-zinc interaction made by the unnatural amino acid (S)-2-amino-7-sulfanylheptanoic acid contributes to nanomolar inhibitory potency for each inhibitor. Apart from this zinc-binding residue, octapeptides adopt strikingly different overall conformations and make few direct hydrogen bonds with the protein. Intermolecular interactions are dominated by water-mediated hydrogen bonds; in essence, water molecules appear to cushion the enzyme-octapeptide interface. In view of the broad specificity observed for protein substrates of HDAC6 CD2, we suggest that the binding of macrocyclic octapeptides may mimic certain features of the binding of macromolecular protein substrates.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Suchetana Gupta
- Department of Bioengineering, Knight Campus, University of Oregon, Eugene, OR 97403 United States
| | - Parisa Hosseinzadeh
- Department of Bioengineering, Knight Campus, University of Oregon, Eugene, OR 97403 United States
| | - Benjamin P. Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235 United States
| | - David Baker
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA 98195 United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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69
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Toro TB, Bornes KE, Watt TJ. Lysine Deacetylase Substrate Selectivity: Distinct Interaction Surfaces Drive Positive and Negative Selection for Residues Following Acetyllysine. Biochemistry 2023; 62:1464-1483. [PMID: 37043688 PMCID: PMC10157890 DOI: 10.1021/acs.biochem.3c00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Lysine acetylation is a post-translational modification that is reversed by lysine deacetylases (KDACs). The goal of this work was to identify determinants of substrate specificity for KDACs, focusing on short-range interactions occurring with residues immediately following the acetyllysine. Using a fluorescence-based in vitro assay, we determined the activity for each enzyme with a limited panel of derivative substrate peptides, revealing a distinct reactivity profile for each enzyme. We mapped the interaction surface for KDAC6, KDAC8, and KDAC1 with the +1 and +2 substrate residues (with respect to acetyllysine) based on enzyme-substrate interaction pairs observed in molecular dynamics simulations. Characteristic residues in each KDAC interact preferentially with particular substrate residues and correlate with either enhanced or inhibited activity. Although nonpolar aromatic residues generally enhanced activity with all KDACs, the manner in which each enzyme interacted with these residues is distinct. Furthermore, each KDAC has distinctive interactions that correlate with lower activity, primarily ionic in nature. KDAC8 exhibited the most diverse and widest range of effects, while KDAC6 was sensitive only to the +1 position and KDAC1 selectivity was primarily driven by negative selection. The substrate preferences were validated for KDAC6 and KDAC8 using a set of peptides derived from known acetylated proteins. Overall, we determined how KDAC6, KDAC8, and KDAC1 achieve substrate specificity with residues following the acetyllysine. These new insights into KDAC specificity will be critical for identifying novel substrates of particular KDACs, designing KDAC-specific inhibitors, and demonstrate a general framework for understanding substrate specificity for other enzyme classes.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Kiara E Bornes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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70
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Mansour RES, Abdulwahab HG, El-Sehrawi HM. Novel benzimidazole-linked (thio)barbiturates as non-hydroxamate HDAC6 inhibitors targeting leukemia: Design, synthesis, and structure-activity relationship. Arch Pharm (Weinheim) 2023:e2200433. [PMID: 36942938 DOI: 10.1002/ardp.202200433] [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: 08/15/2022] [Revised: 02/10/2023] [Accepted: 02/25/2023] [Indexed: 03/23/2023]
Abstract
Based on the well-established pharmacophoric features required for histone deacetylase (HDAC) inhibition, novel easy-to-prepare benzimidazole-linked (thio)barbiturate derivatives were designed and synthesized as HDAC6 inhibitors. The proposed structures of the title compounds were confirmed based on their spectral data and elemental analyses. The newly synthesized compounds were screened in vitro against HDAC6. All tested compounds showed potent HDAC6 inhibition at the nanomolar level. Several compounds displayed a remarkable HDAC6 inhibitory activity (IC50 = 48.85-75.62 nM), superior to that of the reference drug suberoylanilide hydroxamic acid (SAHA; IC50 = 91.73 nM). The most potent derivatives were further assessed for their in vitro anticancer activity against two human leukemia cell lines. Thiobarbiturate 3e was two times more potent than SAHA against the tested cells. The detailed structure-activity relationship was also described. Furthermore, molecular docking simulation revealed the ability of the title compounds to chelate the catalytic Zn+2 ion located within the binding pocket of HDAC6. In silico evaluation of physicochemical properties indicated that the target compounds are promising candidates in terms of pharmacokinetic aspects.
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Affiliation(s)
- Reda El-Sayed Mansour
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Hanan Gaber Abdulwahab
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Hend M El-Sehrawi
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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71
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Zheng YC, Kang HQ, Wang B, Zhu YZ, Mamun MAA, Zhao LF, Nie HQ, Liu Y, Zhao LJ, Zhang XN, Gao MM, Jiang DD, Liu HM, Gao Y. Curriculum vitae of HDAC6 in solid tumors. Int J Biol Macromol 2023; 230:123219. [PMID: 36642357 DOI: 10.1016/j.ijbiomac.2023.123219] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Histone deacetylase 6 (HDAC6) is the only member of the HDAC family that resides primarily in the cytoplasm with two catalytic domains and a ubiquitin-binding domain. HDAC6 is highly expressed in various solid tumors and participates in a wide range of biological activities, including hormone receptors, the p53 signaling pathway, and the kinase cascade signaling pathway due to its unique structural foundation and abundant substrate types. Additionally, HDAC6 can function as an oncogenic factor in solid tumors, boosting tumor cell proliferation, invasion and metastasis, drug resistance, stemness, and lowering tumor cell immunogenicity, so assisting in carcinogenesis. Pan-HDAC inhibitors for cancer prevention are associated with potential cardiotoxicity in clinical investigations. It's interesting that HDAC6 silencing didn't cause any significant harm to normal cells. Currently, the use of HDAC6 specific inhibitors, individually or in combination, is among the most promising therapies in solid tumors. This review's objective is to give a general overview of the structure, biological functions, and mechanism of HDAC6 in solid tumor cells and in the immunological milieu and discuss the preclinical and clinical trials of selective HDAC6 inhibitors. These endeavors highlight that targeting HDAC6 could effectively kill tumor cells and enhance patients' immunity during solid tumor therapy.
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Affiliation(s)
- Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hui-Qin Kang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China; Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China
| | - Yuan-Zai Zhu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - M A A Mamun
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Long-Fei Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hai-Qian Nie
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Liu
- Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Henan 450001, China
| | - Li-Juan Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiao-Nan Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Mei-Mei Gao
- Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Henan 450001, China
| | - Dan-Dan Jiang
- Department of Pharmacy, People's Hospital of Henan Province, Zhengzhou University, Henan 450001, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
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72
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Phenolic compounds as histone deacetylase inhibitors: binding propensity and interaction insights from molecular docking and dynamics simulations. Amino Acids 2023:10.1007/s00726-023-03249-6. [PMID: 36781452 DOI: 10.1007/s00726-023-03249-6] [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: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023]
Abstract
Histone deacetylases are well-established target enzymes involved in the pathology of different diseases including cancer and neurodegenerative disorders. The approved HDAC inhibitor drugs are associated with cellular toxicities. Different phenolic compounds have been shown to possess inhibitory activities against HDACs and are, therefore, considered safer alternatives to synthetic compounds. Here, we elucidated the binding mode and calculated the binding propensity of some of the top phenolic compounds against different isoforms representing different classes of Zn2+ ion-containing HDACs using the molecular docking approach. Our data reaffirmed the activity of the studied phenolic compounds against HDACs. Binding interaction analysis suggested that these compounds can block the activity of HDACs with or without binding to the active site zinc metal ion. Furthermore, molecular dynamics (MD) simulations were carried out on the selected crystal and docking complexes of each selected HDAC isoform. Analysis of root-mean-square displacement (RMSD) showed that the phenolic compounds demonstrated a stable binding mode over 50 ns in a way that is comparable to the cocrystal ligands. Together, these findings can aid future efforts in the search for natural inhibitors of HDACs.
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73
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Shukla S, Komarek J, Novakova Z, Nedvedova J, Ustinova K, Vankova P, Kadek A, Uetrecht C, Mertens H, Barinka C. In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach. FEBS J 2023; 290:821-836. [PMID: 36062318 DOI: 10.1111/febs.16616] [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: 11/05/2021] [Revised: 07/08/2022] [Accepted: 09/02/2022] [Indexed: 02/04/2023]
Abstract
Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains, and a holistic picture of the full-length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modelling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in-solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration-dependent manner, and its oligomerization is mediated via the positively charged N-terminal microtubule-binding domain. Our findings provide the first insights into the structure of full-length human HDAC6 and can be used as a basis for further research into structure function and physiological studies of this unique deacetylase.
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Affiliation(s)
- Shivam Shukla
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Department of Physical Chemistry, Faculty of Natural Science, Charles University, Prague, Czech Republic
| | - Jan Komarek
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Nedvedova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Kseniya Ustinova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Pavla Vankova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Alan Kadek
- Leibniz Institute of Virology (LIV), Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany
| | - Charlotte Uetrecht
- Leibniz Institute of Virology (LIV), Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany.,Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Department of Health Sciences and Biomedicine, School of Life Sciences, University of Siegen, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory (EMBL)-Hamburg Outstation, c/o DESY, Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
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74
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Kong SJ, Nam G, Boggu PR, Park GM, Kang JE, Park HJ, Jung YH. Synthesis and biological evaluation of novel N-benzyltriazolyl-hydroxamate derivatives as selective histone deacetylase 6 inhibitors. Bioorg Med Chem 2023; 79:117154. [PMID: 36645952 DOI: 10.1016/j.bmc.2023.117154] [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: 10/06/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Histone deacetylases (HDAC) regulate post-translational acetylation and the inhibition of these enzymes has emerged as an intriguing disease therapeutic. Among them, class IIb HDAC6 has the unique characteristic of mainly deacetylating cytoplasmic proteins, suggesting clinical applications for neurodegenerative diseases, inflammation, and cancer. In this study, we designed a novel N-benzyltriazolyl-hydroxamate scaffold based on the known HDAC6 inhibitors nexturastat A and tubastatin A. Among the 27 derivatives, 3-fluoro-4-((3-(2-fluorophenyl)-1H-1,2,4-triazol-1-yl)methyl)-N-hydroxybenzamide 4u (HDAC6 IC50 = 7.08 nM) showed nanomolar HDAC6 inhibitory activity with 42-fold selectivity over HDAC1. Structure-activity relationship (SAR) and computational docking studies were conducted to optimize the triazole capping group. Docking analysis revealed that the capping group aligned with the conserved L1 pocket of HDAC6 and was associated with subtype selectivity. Overall, our study explored the triazole-based biaryl capping group and its substitution and orientation, suggesting a rationale for the design of HDAC6-selective inhibitors.
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Affiliation(s)
- Sun Ju Kong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gibeom Nam
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pulla Reddy Boggu
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gi Min Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ji Eun Kang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyun-Ju Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Young Hoon Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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75
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Zeleke TZ, Pan Q, Chiuzan C, Onishi M, Li Y, Tan H, Alvarez MJ, Honan E, Yang M, Chia PL, Mukhopadhyay P, Kelly S, Wu R, Fenn K, Trivedi MS, Accordino M, Crew KD, Hershman DL, Maurer M, Jones S, High A, Peng J, Califano A, Kalinsky K, Yu J, Silva J. Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer. NATURE CANCER 2023; 4:257-275. [PMID: 36585452 PMCID: PMC9992270 DOI: 10.1038/s43018-022-00489-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 11/10/2022] [Indexed: 12/31/2022]
Abstract
Inhibiting individual histone deacetylase (HDAC) is emerging as well-tolerated anticancer strategy compared with pan-HDAC inhibitors. Through preclinical studies, we demonstrated that the sensitivity to the leading HDAC6 inhibitor (HDAC6i) ricolinstat can be predicted by a computational network-based algorithm (HDAC6 score). Analysis of ~3,000 human breast cancers (BCs) showed that ~30% of them could benefice from HDAC6i therapy. Thus, we designed a phase 1b dose-escalation clinical trial to evaluate the activity of ricolinostat plus nab-paclitaxel in patients with metastatic BC (MBC) (NCT02632071). Study results showed that the two agents can be safely combined, that clinical activity is identified in patients with HR+/HER2- disease and that the HDAC6 score has potential as predictive biomarker. Analysis of other tumor types also identified multiple cohorts with predicted sensitivity to HDAC6i's. Mechanistically, we have linked the anticancer activity of HDAC6i's to their ability to induce c-Myc hyperacetylation (ac-K148) promoting its proteasome-mediated degradation in sensitive cancer cells.
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Affiliation(s)
- Tizita Z Zeleke
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Codruta Chiuzan
- Feinstein Institutes for Medical Research, Northwell Health, New York, USA
| | | | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.,DarwinHealth, Inc., New York, NY, USA
| | - Erin Honan
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Min Yang
- Acetylon Pharmaceuticals, Boston, MA, USA
| | - Pei Ling Chia
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Partha Mukhopadhyay
- Graduate School, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Sean Kelly
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ruby Wu
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Kathleen Fenn
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Meghna S Trivedi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Melissa Accordino
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Katherine D Crew
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Dawn L Hershman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | - Simon Jones
- Regenacy Pharmaceuticals, Inc., Waltham, MA, USA
| | - Anthony High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kevin Kalinsky
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA.
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jose Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA.
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76
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Noce B, Di Bello E, Zwergel C, Fioravanti R, Valente S, Rotili D, Masotti A, Salik Zeya Ansari M, Trisciuoglio D, Chakrabarti A, Romier C, Robaa D, Sippl W, Jung M, Häberli C, Keiser J, Mai A. Chemically Diverse S. mansoni HDAC8 Inhibitors Reduce Viability in Worm Larval and Adult Stages. ChemMedChem 2023; 18:e202200510. [PMID: 36250286 DOI: 10.1002/cmdc.202200510] [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: 09/21/2022] [Revised: 10/16/2022] [Indexed: 02/05/2023]
Abstract
Schistosoma mansoni HDAC8 is a reliable target to fight schistosomiasis, and several inhibitors have been reported in the literature up to now. Nevertheless, only a few displayed selectivity over the human deacetylases and some exhibited very low or no activity against parasite larvae and/or adult worms. We report here the in vitro enzyme and biological activity of a small library of HDAC inhibitors from our lab, in many cases exhibiting submicromolar/nanomolar potency against smHDAC8 and diverse degrees of selectivity over hHDAC1 and/or hHDAC6. Such compounds were tested against schistosomula, and a selection of them against the adult forms of S. mansoni, to detect their effect on viability. Some of them showed the highest viability reduction for the larval stage with IC50 values around 1 μM and/or displayed ∼40-50 % activity in adult worms at 10 μM, joined to moderate to no toxicity in human fibroblast MRC-5 cells.
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Affiliation(s)
- Beatrice Noce
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Elisabetta Di Bello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, 00146, Rome, Italy
| | | | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology, National Research Council (CNR), 00185, Rome, Italy
| | - Alokta Chakrabarti
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 67404, Illkirch Cedex, France
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Cécile Häberli
- Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland.,University of Basel, Basel, 4001, Switzerland
| | - Jennifer Keiser
- Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland.,University of Basel, Basel, 4001, Switzerland
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy.,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185, Rome, Italy
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77
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Hey J, Llamazares Prada M, Plass C. HDAC6 score: to treat or not to treat? NATURE CANCER 2023; 4:156-158. [PMID: 36585451 DOI: 10.1038/s43018-022-00494-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Maria Llamazares Prada
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Cancer-Transitional Research and Exchange Program, German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany. .,Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg, Germany.
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78
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Yan J, Yue K, Fan X, Xu X, Wang J, Qin M, Zhang Q, Hou X, Li X, Wang Y. Synthesis and bioactivity evaluation of ferrocene-based hydroxamic acids as selective histone deacetylase 6 inhibitors. Eur J Med Chem 2023; 246:115004. [PMID: 36516583 DOI: 10.1016/j.ejmech.2022.115004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Histone deacetylase 6 (HDAC6) is involved in multiple regulatory processes and emerges as a promising target for treating cancer and neurodegenerative diseases. Benefited from the unique sandwich conformation of ferrocene, a series of ferrocene-based hydroxamic acids have been developed as novel HDAC6 inhibitors in this paper, especially the two ansa-ferrocenyl complexes with IC50s at the nanomolar level. [3]-Ferrocenophane hydroxamic acid analog II-5 displays the most potent inhibitory activity on HDAC6 and establishes remarkable selectivity towards other HDAC isoforms. Compound II-5 dose-dependently induces accumulation of acetylated α-tubulin while having a negligible effect on the level of acetylated Histone H3, confirming its isoform selectivity. Further biological evaluation of II-5 on cancer cells corroborates its antiproliferative effect, which mainly contributed to the induction of cellular apoptosis. It is worth noting that compound II-5 demonstrates an optimal profile on human plasma stability. These results strengthen ferrocene's unique role in developing selective protein inhibitors and indicate that compound II-5 may be a suitable lead for further evaluation and development for treating HDAC6-associated disorders and diseases.
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Affiliation(s)
- Jiangkun Yan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Kairui Yue
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Xuejing Fan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Ximing Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Marine Biomedical Research Institute of Qingdao, Qingdao, Shandong, 266071, PR China
| | - Jing Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Mengting Qin
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China
| | - Qianer Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Xiaohan Hou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China
| | - Xiaoyang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China.
| | - Yong Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 26003, Shandong, PR China; Laboratory for Marine Drugs and Bioproducts, Center for Innovation Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266200, PR China.
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79
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Tolomeu HV, Fraga CAM. Imidazole: Synthesis, Functionalization and Physicochemical Properties of a Privileged Structure in Medicinal Chemistry. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020838. [PMID: 36677894 PMCID: PMC9865940 DOI: 10.3390/molecules28020838] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/19/2023]
Abstract
Imidazole was first synthesized by Heinrich Debus in 1858 and was obtained by the reaction of glyoxal and formaldehyde in ammonia, initially called glyoxaline. The current literature provides much information about the synthesis, functionalization, physicochemical characteristics and biological role of imidazole. Imidazole is a structure that, despite being small, has a unique chemical complexity. It is a nucleus that is very practical and versatile in its construction/functionalization and can be considered a rich source of chemical diversity. Imidazole acts in extremely important processes for the maintenance of living organisms, such as catalysis in enzymatic processes. Imidazole-based compounds with antibacterial, anti-inflammatory, antidiabetic, antiparasitic, antituberculosis, antifungal, antioxidant, antitumor, antimalarial, anticancer, antidepressant and many others make up the therapeutic arsenal and new bioactive compounds proposed in the most diverse works. The interest and importance of imidazole-containing analogs in the field of medicinal chemistry is remarkable, and the understanding from the development of the first blockbuster drug cimetidine explores all the chemical and biological concepts of imidazole in the context of research and development of new drugs.
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Affiliation(s)
- Heber Victor Tolomeu
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Correspondence: ; Tel.: +55-21-39386447
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80
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Ashraf QF, Quilates EJ, Olaoye OO, de Araujo ED, Gunning PT. Fluorescence Polarization-Based Competition Assays to Evaluate Histone Deacetylase 6 Inhibitors. Methods Mol Biol 2023; 2589:481-492. [PMID: 36255644 DOI: 10.1007/978-1-0716-2788-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an emerging clinical target for the treatment of several hematological cancers and central nervous system disorders. HDAC6 catalyzes the deacetylation of lysine residues on substrates such as tubulin, with profound implications in key cellular processes, including cellular motility and migration. This critical deacetylation activity occurs at the catalytic domain 2 (CD2) of HDAC6, and small molecule inhibitors of HDAC6 are designed to target CD2. We briefly highlight previously reported strategies for recombinant bacterial expression and purification of the HDAC6 CD2. We aim to discuss competition assays that have been used to evaluate the potency of potential HDAC6 inhibitors against CD2 via displacement of pre-bound fluorescent HDAC-probes. Moreover, we elaborate on previous protocols that have been employed in inhibitor screening and present an HDAC6-selective probe that also enables rapid and reliable high-throughput screening of new chemical entities designed to target the HDAC6 CD2.
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Affiliation(s)
- Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Erica J Quilates
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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81
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Cellupica E, Caprini G, Cordella P, Cukier C, Fossati G, Marchini M, Rocchio I, Sandrone G, Vanoni MA, Vergani B, Źrubek K, Stevenazzi A, Steinkühler C. Difluoromethyl-1,3,4-oxadiazoles are slow-binding substrate analog inhibitors of histone deacetylase 6 with unprecedented isotype selectivity. J Biol Chem 2023; 299:102800. [PMID: 36528061 PMCID: PMC9860109 DOI: 10.1016/j.jbc.2022.102800] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) is an attractive drug development target because of its role in the immune response, neuropathy, and cancer. Knockout mice develop normally and have no apparent phenotype, suggesting that selective inhibitors should have an excellent therapeutic window. Unfortunately, current HDAC6 inhibitors have only moderate selectivity and may inhibit other HDAC subtypes at high concentrations, potentially leading to side effects. Recently, substituted oxadiazoles have attracted attention as a promising novel HDAC inhibitor chemotype, but their mechanism of action is unknown. Here, we show that compounds containing a difluoromethyl-1,3,4-oxadiazole (DFMO) moiety are potent and single-digit nanomolar inhibitors with an unprecedented greater than 104-fold selectivity for HDAC6 over all other HDAC subtypes. By combining kinetics, X-ray crystallography, and mass spectrometry, we found that DFMO derivatives are slow-binding substrate analogs of HDAC6 that undergo an enzyme-catalyzed ring opening reaction, forming a tight and long-lived enzyme-inhibitor complex. The elucidation of the mechanism of action of DFMO derivatives paves the way for the rational design of highly selective inhibitors of HDAC6 and possibly of other HDAC subtypes as well with potentially important therapeutic implications.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Paola Cordella
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Cyprian Cukier
- Department of Biochemistry, Selvita S.A., Kraków, Poland
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | | | - Barbara Vergani
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
| | - Karol Źrubek
- Department of Biochemistry, Selvita S.A., Kraków, Poland
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, Cinisello Balsamo, Italy
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82
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Wang L, Sanchez J, Hess D, Matthias P. Immunoprecipitation of HDAC6 and Interacting Proteins. Methods Mol Biol 2023; 2589:493-508. [PMID: 36255645 DOI: 10.1007/978-1-0716-2788-4_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The lysine deacetylase HDAC6 has unique structural and functional properties: It contains tandem catalytic domains that can deacetylate a variety of proteins and a zinc finger domain that binds ubiquitin. HDAC6 has been implicated in a variety of biological processes, normal or pathological, such as cellular motility, stress response, cancer, neurodegeneration, or viral infection. Due to this, HDAC6 is considered an attractive therapeutic target, and there is a major interest to identify small molecule inhibitors. To gain a mechanistic understanding of how HDAC6 impacts these different biological processes, there is a continued need to discover additional substrates as well as interacting proteins in different paradigms. One approach to achieve this is to perform HDAC6 immunoprecipitations to identify partner proteins. We describe here our optimized protocols to immunoprecipitate HDAC6 with the goal to identify or validate interacting proteins.
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jacint Sanchez
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
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83
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Langousis G, Sanchez J, Kempf G, Matthias P. Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol Biol 2023; 2589:467-480. [PMID: 36255643 DOI: 10.1007/978-1-0716-2788-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain. HDAC6 is involved in various biological processes, such as cell motility or stress responses, and has been implicated in pathologies ranging from cancer to neurodegeneration. Due to this broad range of functions, there has been considerable interest in developing HDAC6-specific small molecule inhibitors, several of which are already available. The crystal structure of the tandem catalytic domains of zebrafish HDAC6 has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains. Further dissection of the biochemical properties of HDAC6 and the development of novel inhibitors will benefit from being able to routinely express high-quality protein. We present here our optimized protocol for expression and crystallization of the zebrafish tandem catalytic domains.
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Affiliation(s)
| | - Jacint Sanchez
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
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84
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Sixto-López Y, Gómez-Vidal JA, de Pedro N, Bello M, Rosales-Hernández MC, Correa-Basurto J. In silico design of HDAC6 inhibitors with neuroprotective effects. J Biomol Struct Dyn 2022; 40:14204-14222. [PMID: 34784487 DOI: 10.1080/07391102.2021.2001378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
HDAC6 has emerged as a molecular target to treat neurodegenerative disorders, due to its participation in protein aggregate degradation, oxidative stress process, mitochondrial transport, and axonal transport. Thus, in this work we have designed a set of 485 compounds with hydroxamic and bulky-hydrophobic moieties that may function as HDAC6 inhibitors with a neuroprotective effect. These compounds were filtered by their predicted ADMET properties and their affinity to HDAC6 demonstrated by molecular docking and molecular dynamics simulations. The combination of in silico with in vitro neuroprotective results allowed the identification of a lead compound (FH-27) which shows neuroprotective effect that could be due to HDAC6 inhibition. Further, FH-27 chemical moiety was used to design a second series of compounds improving the neuroprotective effect from 2- to 10-fold higher (YSL-99, YSL-109, YSL-112, YSL-116 and YSL-121; 1.25 ± 0.67, 1.82 ± 1.06, 7.52 ± 1.78, 5.59 and 5.62 ± 0.31 µM, respectively). In addition, the R enantiomer of FH-27 (YSL-106) was synthesized, showing a better neuroprotective effect (1.27 ± 0.60 µM). In conclusion, we accomplish the in silico design, synthesis, and biological evaluation of hydroxamic acid derivatives with neuroprotective effect as suggested by an in vitro model. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yudibeth Sixto-López
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico.,Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - José Antonio Gómez-Vidal
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - Nuria de Pedro
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
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85
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Shi L, Song Z, Li C, Deng F, Xia Y, Huang J, Wu X, Zhu J. HDAC6 Inhibition Alleviates Ischemia- and Cisplatin-Induced Acute Kidney Injury by Promoting Autophagy. Cells 2022; 11:cells11243951. [PMID: 36552715 PMCID: PMC9776591 DOI: 10.3390/cells11243951] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone deacetylase (HDAC) 6 exists exclusively in cytoplasm and deacetylates cytoplasmic proteins such as α-tubulin. HDAC6 dysfunction is associated with several pathological conditions in renal disorders, including UUO-induced fibrotic kidneys and rhabdomyolysis-induced nephropathy. However, the role of HDAC6 in ischemic acute kidney injury (AKI) and the mechanism by which HDAC6 inhibition protects tubular cells after AKI remain unclear. In the present study, we observed that HDAC6 was markedly activated in kidneys subjected to ischemia- and cisplatin (cis)-induced AKI treatment. Pharmacological inhibition of HDAC6 alleviated renal impairment and renal tubular damage after ischemia and cisplatin treatment. HDAC6 dysfunction was associated with decreased acetylation of α-tubulin at the residue of lysine 40 and autophagy. HDAC6 inhibition preserved acetyl-α-tubulin-enhanced autophagy flux in AKI and cultured tubular cells. Genetic ablation of the renal tubular (RT) Atg7 gene or pharmacological inhibition of autophagy suppressed the protective effects of HDAC6. Taken together, our study indicates that HDAC6 contributes to ischemia- and cisplatin-induced AKI by inhibiting autophagy and the acetylation of α-tubulin. These results suggest that HDAC6 could be a potential target for ischemic and nephrotoxic AKI.
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Affiliation(s)
- Lang Shi
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430064, China
| | - Zhixia Song
- Department of Nephrology, The First Clinical Medical College of Three Gorges University, Center People’s Hospital of Yichang, Yichang 443000, China
| | - Chenglong Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430064, China
| | - Fangjing Deng
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430064, China
| | - Yao Xia
- Department of Nephrology, The First Clinical Medical College of Three Gorges University, Center People’s Hospital of Yichang, Yichang 443000, China
| | - Jing Huang
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430064, China
| | - Xiongfei Wu
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430064, China
- Correspondence: (X.W.); (J.Z.)
| | - Jiefu Zhu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430064, China
- Correspondence: (X.W.); (J.Z.)
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86
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Liu X, Wang S, Shi X, Lu M, Wang C, Li X, Zhang Y, Jia Q, Liu H. Do biological activities of selective histone deacetylase 6 (HDAC6) inhibitors rely on the modification of cap group? J Mol Recognit 2022; 35:e2988. [PMID: 36054561 DOI: 10.1002/jmr.2988] [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: 01/04/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 01/05/2023]
Abstract
Nowadays, significant progress has been made in the development of selective histone deacetylase 6 (HDAC6) inhibitors, exerting great potential in the treatment of various malignant tumors and neurodegenerative diseases. Previously, selective inhibitory activities of HDAC inhibitors were generally considered sensitive to the interactions between the Cap group and the binding site of HDAC6, and a large number of selective HDAC6 inhibitors have been designed and synthesized based on the strategy. However, some inhibitors without Cap group could also exhibit excellent potency and selective inhibition towards HDAC6, and in this study, BRD9757 and compound 8, as capless selective HDAC6 inhibitors, were selected as molecular probes to explore the difference of their binding interactions in HDAC1&6. Through the analysis of binding-free energies and conformational rearrangements after 1 μs molecular dynamics simulation, it could be learned that although the residues in the binding site remained highly consistent, the binding mechanisms of BRD9757 and compound 8 in HDAC1&6 were different, which will provide valuable hints for the discovery of novel selective HDAC6 inhibitors.
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Affiliation(s)
- Xingang Liu
- Department of Hematology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Songsong Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China.,Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoxing Shi
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Ming Lu
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chengzhao Wang
- Department of Hematology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xuedong Li
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Yang Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Qingzhong Jia
- Department of Pharmacology, Hebei Medical University, Shijiazhuang, China
| | - Haisheng Liu
- Department of Hematology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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87
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Anestopoulos I, Kyriakou S, Tragkola V, Paraskevaidis I, Tzika E, Mitsiogianni M, Deligiorgi MV, Petrakis G, Trafalis DT, Botaitis S, Giatromanolaki A, Koukourakis MI, Franco R, Pappa A, Panayiotidis MI. Targeting the epigenome in malignant melanoma: Facts, challenges and therapeutic promises. Pharmacol Ther 2022; 240:108301. [PMID: 36283453 DOI: 10.1016/j.pharmthera.2022.108301] [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: 06/06/2022] [Revised: 10/03/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022]
Abstract
Malignant melanoma is the most lethal type of skin cancer with high rates of mortality. Although current treatment options provide a short-clinical benefit, acquired-drug resistance highlights the low 5-year survival rate among patients with advanced stage of the disease. In parallel, the involvement of an aberrant epigenetic landscape, (e.g., alterations in DNA methylation patterns, histone modifications marks and expression of non-coding RNAs), in addition to the genetic background, has been also associated with the onset and progression of melanoma. In this review article, we report on current therapeutic options in melanoma treatment with a focus on distinct epigenetic alterations and how their reversal, by specific drug compounds, can restore a normal phenotype. In particular, we concentrate on how single and/or combinatorial therapeutic approaches have utilized epigenetic drug compounds in being effective against malignant melanoma. Finally, the role of deregulated epigenetic mechanisms in promoting drug resistance to targeted therapies and immune checkpoint inhibitors is presented leading to the development of newly synthesized and/or improved drug compounds capable of targeting the epigenome of malignant melanoma.
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Affiliation(s)
- I Anestopoulos
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - S Kyriakou
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - V Tragkola
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - I Paraskevaidis
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - E Tzika
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | | | - M V Deligiorgi
- Laboratory of Pharmacology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - G Petrakis
- Saint George Hospital, Chania, Crete, Greece
| | - D T Trafalis
- Laboratory of Pharmacology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - S Botaitis
- Department of Surgery, Alexandroupolis University Hospital, Democritus University of Thrace School of Medicine, Alexandroupolis, Greece
| | - A Giatromanolaki
- Department of Pathology, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - M I Koukourakis
- Radiotherapy / Oncology, Radiobiology & Radiopathology Unit, Department of Medicine, School of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - R Franco
- Redox Biology Centre, University of Nebraska-Lincoln, Lincoln, NE, USA; School of Veterinary Medicine & Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - A Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - M I Panayiotidis
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus.
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88
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Ruzic D, Ellinger B, Djokovic N, Santibanez JF, Gul S, Beljkas M, Djuric A, Ganesan A, Pavic A, Srdic-Rajic T, Petkovic M, Nikolic K. Discovery of 1-Benzhydryl-Piperazine-Based HDAC Inhibitors with Anti-Breast Cancer Activity: Synthesis, Molecular Modeling, In Vitro and In Vivo Biological Evaluation. Pharmaceutics 2022; 14:pharmaceutics14122600. [PMID: 36559094 PMCID: PMC9785542 DOI: 10.3390/pharmaceutics14122600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Isoform-selective histone deacetylase (HDAC) inhibition is promoted as a rational strategy to develop safer anti-cancer drugs compared to non-selective HDAC inhibitors. Despite this presumed benefit, considerably more non-selective HDAC inhibitors have undergone clinical trials. In this report, we detail the design and discovery of potent HDAC inhibitors, with 1-benzhydryl piperazine as a surface recognition group, that differ in hydrocarbon linker. In vitro HDAC screening identified two selective HDAC6 inhibitors with nanomolar IC50 values, as well as two non-selective nanomolar HDAC inhibitors. Structure-based molecular modeling was employed to study the influence of linker chemistry of synthesized inhibitors on HDAC6 potency. The breast cancer cell lines (MDA-MB-231 and MCF-7) were used to evaluate compound-mediated in vitro anti-cancer, anti-migratory, and anti-invasive activities. Experiments on the zebrafish MDA-MB-231 xenograft model revealed that a novel non-selective HDAC inhibitor with a seven-carbon-atom linker exhibits potent anti-tumor, anti-metastatic, and anti-angiogenic effects when tested at low micromolar concentrations.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), 22525 Hamburg, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, University of Belgrade, Dr. Subotića 4, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), 22525 Hamburg, Germany
| | - Milan Beljkas
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Ana Djuric
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Arasu Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Aleksandar Pavic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Milos Petkovic
- Department of Organic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
- Correspondence: (M.P.); (K.N.)
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
- Correspondence: (M.P.); (K.N.)
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89
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Reßing N, Schliehe-Diecks J, Watson PR, Sönnichsen M, Cragin AD, Schöler A, Yang J, Schäker-Hübner L, Borkhardt A, Christianson DW, Bhatia S, Hansen FK. Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia. J Med Chem 2022; 65:15457-15472. [PMID: 36351184 PMCID: PMC9691607 DOI: 10.1021/acs.jmedchem.2c01418] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Using a microwave-assisted protocol, we synthesized 16 peptoid-capped HDAC inhibitors (HDACi) with fluorinated linkers and identified two hit compounds. In biochemical and cellular assays, 10h stood out as a potent unselective HDACi with remarkable cytotoxic potential against different therapy-resistant leukemia cell lines. 10h demonstrated prominent antileukemic activity with low cytotoxic activity toward healthy cells. Moreover, 10h exhibited synergistic interactions with the DNA methyltransferase inhibitor decitabine in AML cell lines. The comparison of crystal structures of HDAC6 complexes with 10h and its nonfluorinated counterpart revealed a similar occupation of the L1 loop pocket but slight differences in zinc coordination. The substitution pattern of the acyl residue turned out to be crucial in terms of isoform selectivity. The introduction of an isopropyl group onto the phenyl ring provided the highly HDAC6-selective inhibitor 10p, which demonstrated moderate synergy with decitabine and exceeded the HDAC6 selectivity of tubastatin A.
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Affiliation(s)
- Nina Reßing
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121Bonn, Germany
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103Leipzig, Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225Düsseldorf, Germany
| | - Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225Düsseldorf, Germany
| | - Abigail D Cragin
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103Leipzig, Germany
| | - Jing Yang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225Düsseldorf, Germany
- Department of Medicine, Yangzhou Polytechnic College, West Wenchang Road 458, Yangzhou225009, P. R. China
| | - Linda Schäker-Hübner
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121Bonn, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225Düsseldorf, Germany
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania19104-6323, United States
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225Düsseldorf, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121Bonn, Germany
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90
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Si L, Lai T, Zhao J, Jin Y, Qi M, Li M, Fu H, Shi X, Ma L, Guo R. Identification of a novel pyridine derivative with inhibitory activity against ovarian cancer progression in vivo and in vitro. Front Pharmacol 2022; 13:1064485. [DOI: 10.3389/fphar.2022.1064485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022] Open
Abstract
Ovarian cancer is the second leading cause of death of female gynecological malignant tumor patients worldwide. Although surgery and chemotherapy have achieved dramatic achievement, the mortality remains high, resulting in the demand for new specific drug discovery. Disrupting ovarian cancer growth via histone deacetylase (HDAC) inhibition is a strategy for cancer therapy or prevention. In this work, we synthesized a novel pyridine derivative named compound H42 and investigated its anti-cancer activity in vivo and in vitro. We found that compound H42 inhibited ovarian cancer cell proliferation with IC50 values of 0.87 μM (SKOV3) and 5.4 μM (A2780). Further studies confirmed that compound H42 induced apoptosis, intracellular ROS production, and DNA damage. Moreover, compound H42 downregulated the expression of histone deacetylase 6 (HDAC6) with a distinct increase in the acetylation of α-tubulin and heat shock protein 90 (HSP90), followed by the degradation of cyclin D1, resulting in cell cycle arrest at the G0/G1 phase. Importantly, ectopic expression of HDAC6 induced deacetylation of HSP90 and α-tubulin, while HDAC6 knockdown upregulated the acetylation of HSP90 and α-tubulin. However, in the nude xenograft mouse study, compound H42 treatment can inhibit ovarian cancer growth without obvious toxicity. These findings indicated that compound H42 inhibited ovarian cancer cell proliferation through inducing cell cycle arrest at the G0/G1 phase via regulating HDAC6-mediated acetylation, suggesting compound H42 could serve as a lead compound for further development of ovarian cancer therapeutic agents.
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91
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Royce SG, Licciardi PV, Beh RC, Bourke JE, Donovan C, Hung A, Khurana I, Liang JJ, Maxwell S, Mazarakis N, Pitsillou E, Siow YY, Snibson KJ, Tobin MJ, Ververis K, Vongsvivut J, Ziemann M, Samuel CS, Tang MLK, El-Osta A, Karagiannis TC. Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant, and epigenetic mechanisms. Cell Mol Life Sci 2022; 79:579. [DOI: 10.1007/s00018-022-04609-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022]
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92
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Sreenivasmurthy SG, Iyaswamy A, Krishnamoorthi S, Reddi RN, Kammala AK, Vasudevan K, Senapati S, Zhu Z, Su CF, Liu J, Guan XJ, Chua KK, Cheung KH, Chen H, Zhang HJ, Zhang Y, Song JX, Kumar Durairajan SS, Li M. Bromo-protopine, a novel protopine derivative, alleviates tau pathology by activating chaperone-mediated autophagy for Alzheimer’s disease therapy. Front Mol Biosci 2022; 9:1030534. [PMID: 36387280 PMCID: PMC9643865 DOI: 10.3389/fmolb.2022.1030534] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Emerging evidence from Alzheimer’s disease (AD) patients suggests that reducing tau pathology can restore cognitive and memory loss. To reduce tau pathology, it is critical to find brain-permeable tau-degrading small molecules that are safe and effective. HDAC6 inhibition has long been considered a safe and effective therapy for tau pathology. Recently, we identified protopine as a dibenzazecine alkaloid with anti-HDAC6 and anti-AD activities. In this study, we synthesized and tested novel protopine derivatives for their pharmacological action against AD. Among them, bromo-protopine (PRO-Br) demonstrated a two-fold increase in anti-HDAC6 activity and improved anti-tau activities compared to the parent compound in both in vitro and in vivo AD models. Furthermore, molecular docking results showed that PRO-Br binds to HDAC6, with a ∆G value of −8.4 kcal/mol and an IC50 value of 1.51 µM. In neuronal cell lines, PRO-Br reduced pathological tau by inducing chaperone-mediated autophagy (CMA). In 3xTg-AD and P301S tau mice models, PRO-Br specifically decreased the pathogenic hyperphosphorylated tau clumps and led to the restoration of memory functions. In addition, PRO-Br treatment promoted the clearance of pathogenic tau by enhancing the expression of molecular chaperones (HSC70) and lysosomal markers (LAMP2A) via CMA in AD models. Our data strongly suggest that administration of the brain-permeable protopine derivative PRO-Br, could be a viable anti-tau therapeutic strategy for AD.
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Affiliation(s)
- Sravan Gopalkrishnashetty Sreenivasmurthy
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Ashok Iyaswamy
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Senthilkumar Krishnamoorthi
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Centre for Trans-disciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospitals, Chennai, India
| | - Rambabu N. Reddi
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ananth Kumar Kammala
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Department of Obstetrics and Gynecology, Division of Basic and Translational Research, The University of Texas Medical Branch, Galveston, United States
| | | | - Sanjib Senapati
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Zhou Zhu
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Cheng-Fu Su
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Jia Liu
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Xin-Jie Guan
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ka-Kit Chua
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - King-Ho Cheung
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Hubiao Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Hong-Jie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Yuan Zhang
- Department of Neurosurgery, Shenzhen Key Laboratory of Neurosurgery, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ju-Xian Song
- Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Siva Sundara Kumar Durairajan
- Mycobiology and Neurodegenerative Disease Research Laboratory, Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, India
- *Correspondence: Min Li, ; Siva Sundara Kumar Durairajan,
| | - Min Li
- Mr. and Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
- *Correspondence: Min Li, ; Siva Sundara Kumar Durairajan,
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93
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Lu D, Wang C, Qu L, Yin F, Li S, Luo H, Zhang Y, Liu X, Chen X, Luo Z, Cui N, Kong L, Wang X. Histone Deacetylase and Enhancer of Zeste Homologue 2 Dual Inhibitors Presenting a Synergistic Effect for the Treatment of Hematological Malignancies. J Med Chem 2022; 65:12838-12859. [DOI: 10.1021/acs.jmedchem.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dehua Lu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lailiang Qu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Fucheng Yin
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Shang Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Heng Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yonglei Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xingchen Liu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xinye Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhongwen Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ningjie Cui
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaobing Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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94
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Watson PR, Bai P, Wang C, Cragin AD, Hooker JM, Christianson DW. Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Biochemistry 2022; 61:1945-1954. [PMID: 36073962 PMCID: PMC9489680 DOI: 10.1021/acs.biochem.2c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bavarostat (EKZ-001) is a selective inhibitor of histone deacetylase 6 (HDAC6) that contains a meta-fluorophenylhydroxamate Zn2+-binding group. The recently determined crystal structure of its complex with HDAC6 from Danio rerio (zebrafish) revealed that the meta-fluoro substituent binds exclusively in an aromatic crevice defined by F583 and F643 rather than being oriented out toward solvent. To explore the binding of inhibitor C-F groups in this fluorophilic crevice, we now report a series of 10 simple fluorophenylhydroxamates bearing one or more fluorine atoms with different substitution patterns. Inhibitory potencies against human and zebrafish HDAC6 range widely from 121 to >30,000 nM. The best inhibitory potency is measured for meta-difluorophenylhydroxamate (5) with IC50 = 121 nM against human HDAC6; the worst inhibitory potencies are measured for ortho-fluorophenylhydroxamate (1) as well as fluorophenylhydroxamates 4, 7, 9, and 10, although there are some variations in activity trends against human and zebrafish HDAC6. These studies show that aromatic ring fluorination at the meta position(s) does not improve inhibitory activity against human HDAC6 relative to the nonfluorinated parent compound phenylhydroxamate (IC50 = 120 nM), but meta-fluorination does not seriously compromise inhibitory activity either. Crystal structures of selected zebrafish HDAC6-fluorophenylhydroxamate complexes reveal that the fluoroaromatic ring is uniformly accommodated in the F583-F643 aromatic crevice, so ring fluorination does not perturb the inhibitor binding conformation. However, hydroxamate-Zn2+ coordination is bidentate for some inhibitors and monodentate for others. These studies will inform design strategies underlying the design of 18F-labeled HDAC6 inhibitors intended for positron emission tomography.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - Abigail D. Cragin
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Jacob M. Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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95
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Keuler T, König B, Bückreiß N, Kraft FB, König P, Schäker-Hübner L, Steinebach C, Bendas G, Gütschow M, Hansen FK. Development of the first non-hydroxamate selective HDAC6 degraders. Chem Commun (Camb) 2022; 58:11087-11090. [PMID: 36098075 DOI: 10.1039/d2cc03712b] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The targeted degradation of histone deacetylase 6 (HDAC6) by heterobifunctional degraders constitutes a promising approach to treat HDAC6-driven diseases. Previous HDAC6 selective degraders utilised a hydroxamic acid as a zinc-binding group (ZBG) which features mutagenic and genotoxic potential. Here we report the development of a new class of selective HDAC6 degraders based on a difluoromethyl-1,3,4-oxadiazole warhead as ZBG.
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Affiliation(s)
- Tim Keuler
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Beate König
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Nico Bückreiß
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Fabian B Kraft
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Philipp König
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Linda Schäker-Hübner
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Christian Steinebach
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Gerd Bendas
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
| | - Finn K Hansen
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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96
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Yue K, Sun S, Jia G, Qin M, Hou X, Chou CJ, Huang C, Li X. First-in-Class Hydrazide-Based HDAC6 Selective Inhibitor with Potent Oral Anti-Inflammatory Activity by Attenuating NLRP3 Inflammasome Activation. J Med Chem 2022; 65:12140-12162. [PMID: 36073117 DOI: 10.1021/acs.jmedchem.2c00853] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report the first highly selective HDAC6 inhibitor with hydrazide as the zinc-binding group (ZBG), which displays superior pharmacokinetic properties to the current hydroxamic acid inhibitors. Structure-activity relationship study reveals that ethyl group substituent hydrazide-based ZBG and cap group with more substantial rigidity and larger volume increase the HDAC6 selectivity of designed compounds. Representative inhibitor 35m exhibits potent HDAC6 inhibitory activity with an IC50 value of 0.019 μM. To our surprise, 35m establishes significant improvement in the pharmacokinetic property with much higher AUC0-inf (10292 ng·h/mL) and oral bioavailability (93.4%) than hydroximic acid-based HDAC6 inhibitors Tubastatin A and ACY-1215. Low-dose 35m remarkably decreases LPS-induced IL-1β release both in vitro and in vivo by blocking the activation of NLRP3, indicating that 35m can be a potential orally active therapeutic agent for the treatment of NLRP3-related diseases.
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Affiliation(s)
- Kairui Yue
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Simin Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Geng Jia
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Mengting Qin
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Xiaohan Hou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - C James Chou
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Chao Huang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China
| | - Xiaoyang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
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97
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Nguyen HP, Tran QD, Nguyen CQ, Hoa TP, Duy Binh T, Nhu Thao H, Hue BTB, Tuan NT, Le Dang Q, Quoc Chau Thanh N, Van Ky N, Pham MQ, Yang SG. Anti-multiple myeloma potential of resynthesized belinostat derivatives: an experimental study on cytotoxic activity, drug combination, and docking studies. RSC Adv 2022; 12:22108-22118. [PMID: 36043105 PMCID: PMC9364358 DOI: 10.1039/d2ra01969h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Multiple myeloma is a deadly cancer that is a complex and multifactorial disease. In the present study, 12 belinostat derivatives (four resynthesized and eight new), HDAC inhibitors, were resynthesized via either Knoevenagel condensation, or Wittig reaction, or Heck reaction. Then an evaluation of the antiproliferative activities against myeloma cells MOPC-315 was carried out. Amongst them, compound 7f was the most bioactive compound with an IC50 of 0.090 ± 0.016 μM, being 3.5-fold more potent than the reference belinostat (IC50 = 0.318 ± 0.049 μM). Furthermore, we also confirmed the inhibitory activity of 7f in a cellular model. Additionally, we found that the inhibitory activity of 7f against histone deacetylase 6 catalytic activity (HDAC6) is more potent than that of belinostat. Finally, we observed the strong synergistic interaction between the derivative 7f and the proteasome bortezomib inhibitor (CI = 0.26), while belinostat and bortezomib showed synergism with a CI value of 0.36. Taken together, the above results suggest that 7f is a promising HDAC inhibitor deserving further investigation.
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Affiliation(s)
- Hong Phuong Nguyen
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Quang De Tran
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Cuong Quoc Nguyen
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Tran Phuong Hoa
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Tran Duy Binh
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Huynh Nhu Thao
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Bui Thi Buu Hue
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Nguyen Trong Tuan
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Quang Le Dang
- Institute for Tropical Technology, Vietnam Academy of Science and Technology Hanoi 10000 Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam
| | - Nguyen Quoc Chau Thanh
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Nguyen Van Ky
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam
| | - Su-Geun Yang
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
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98
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Design, Synthesis, and biological evaluation of HDAC6 inhibitors based on Cap modification strategy. Bioorg Chem 2022; 125:105874. [DOI: 10.1016/j.bioorg.2022.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022]
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99
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Herp D, Ridinger J, Robaa D, Shinsky SA, Schmidtkunz K, Yesiloglu TZ, Bayer T, Steimbach RR, Herbst‐Gervasoni CJ, Merz A, Romier C, Sehr P, Gunkel N, Miller AK, Christianson DW, Oehme I, Sippl W, Jung M. First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement. Chembiochem 2022; 23:e202200180. [PMID: 35608330 PMCID: PMC9308754 DOI: 10.1002/cbic.202200180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2022] [Indexed: 11/06/2022]
Abstract
Histone deacetylases (HDACs) are important epigenetic regulators involved in many diseases, especially cancer. Five HDAC inhibitors have been approved for anticancer therapy and many are in clinical trials. Among the 11 zinc-dependent HDACs, HDAC10 has received relatively little attention by drug discovery campaigns, despite its involvement, e. g., in the pathogenesis of neuroblastoma. This is due in part to a lack of robust enzymatic conversion assays. In contrast to the protein lysine deacetylase and deacylase activity of most other HDAC subtypes, it has recently been shown that HDAC10 has strong preferences for deacetylation of oligoamine substrates like acetyl-putrescine or -spermidine. Hence, it is also termed a polyamine deacetylase (PDAC). Here, we present the first fluorescent enzymatic conversion assay for HDAC10 using an aminocoumarin-labelled acetyl-spermidine derivative to measure its PDAC activity, which is suitable for high-throughput screening. Using this assay, we identified potent inhibitors of HDAC10-mediated spermidine deacetylation in vitro. Based on the oligoamine preference of HDAC10, we also designed inhibitors with a basic moiety in appropriate distance to the zinc binding hydroxamate that showed potent inhibition of HDAC10 with high selectivity, and we solved a HDAC10-inhibitor structure using X-ray crystallography. We could demonstrate selective cellular target engagement for HDAC10 but a lysosomal phenotype in neuroblastoma cells that was previously associated with HDAC10 inhibition was not observed. Thus, we have developed new chemical probes for HDAC10 that allow further clarification of the biological role of this enzyme.
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Affiliation(s)
- Daniel Herp
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104FreiburgGermany
| | - Johannes Ridinger
- Hopp Children's Cancer Center Heidelberg (KiTZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- Clinical Cooperation Unit Pediatric OncologyGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)Im Neuenheimer Feld 28069120HeidelbergGermany
| | - Dina Robaa
- Institute of PharmacyMartin-Luther University of Halle-Wittenberg06120Halle (Saale)Halle/SaaleGermany
| | - Stephen A. Shinsky
- Roy and Diana Vagelos LaboratoriesDepartment of ChemistryUniversity of Pennsylvania231 South 34th StreetPhiladelphiaPennsylvania19104-6323USA
| | - Karin Schmidtkunz
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104FreiburgGermany
| | - Talha Z. Yesiloglu
- Institute of PharmacyMartin-Luther University of Halle-Wittenberg06120Halle (Saale)Halle/SaaleGermany
| | - Theresa Bayer
- Institute of PharmacyMartin-Luther University of Halle-Wittenberg06120Halle (Saale)Halle/SaaleGermany
| | | | - Corey J. Herbst‐Gervasoni
- Roy and Diana Vagelos LaboratoriesDepartment of ChemistryUniversity of Pennsylvania231 South 34th StreetPhiladelphiaPennsylvania19104-6323USA
| | - Annika Merz
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104FreiburgGermany
| | - Christophe Romier
- Université de StrasbourgCNRSINSERMInstitut de Génétique et de Biologie Moléculaire et CellulaireUMR 7104, U 125867404IllkirchFrance
- IGBMCDepartment of Integrated Structural Biology1 rue Laurent Fries, B.P. 1014267404Illkirch CedexFrance
| | - Peter Sehr
- Chemical Biology Core FacilityEuropean Molecular Biology Laboratory69117HeidelbergGermany
| | - Nikolas Gunkel
- German Cancer Consortium (DKTK)Im Neuenheimer Feld 28069120HeidelbergGermany
- Cancer Drug Development GroupIm Neuenheimer Feld 28069120HeidelbergGermany
| | - Aubry K. Miller
- German Cancer Consortium (DKTK)Im Neuenheimer Feld 28069120HeidelbergGermany
- Cancer Drug Development GroupIm Neuenheimer Feld 28069120HeidelbergGermany
| | - David W. Christianson
- Roy and Diana Vagelos LaboratoriesDepartment of ChemistryUniversity of Pennsylvania231 South 34th StreetPhiladelphiaPennsylvania19104-6323USA
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- Clinical Cooperation Unit Pediatric OncologyGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)Im Neuenheimer Feld 28069120HeidelbergGermany
| | - Wolfgang Sippl
- Institute of PharmacyMartin-Luther University of Halle-Wittenberg06120Halle (Saale)Halle/SaaleGermany
| | - Manfred Jung
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104FreiburgGermany
- German Cancer Consortium (DKTK), Partner site FreiburgHugstetter Str. 5579106FreiburgGermany
- CIBSS - Centre for Integrative Biological Signalling StudiesUniversity of Freiburg (Germany)
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100
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Kurapati C, Paidikondala K, Badavath VN, Parveen S, Singh OV, Gundla R. Design, and synthesis of N‐benzyl Spiro‐piperidine hydroxamic acid‐based derivatives: HDAC inhibitory activity and drug‐likeness prediction. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chidvilas Kurapati
- Department of Chemistry, School of Science GITAM Deemed to be University Hyderabad Telangana India
| | - Kalyani Paidikondala
- Department of Chemistry KG Reddy College of Engineering & Technology Hyderabad Telangana India
| | - Vishnu Nayak Badavath
- School of Pharmacy & Technology Management SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Hyderabad India
| | - Sabnam Parveen
- Chitkara School of Pharmacy Chitkara University Rajpura Punjab India
| | - Om V. Singh
- Department of Chemistry, School of Science GITAM Deemed to be University Hyderabad Telangana India
| | - Rambabu Gundla
- Department of Chemistry, School of Science GITAM Deemed to be University Hyderabad Telangana India
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