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Cellupica E, Gaiassi A, Rocchio I, Rovelli G, Pomarico R, Sandrone G, Caprini G, Cordella P, Cukier C, Fossati G, Marchini M, Bebel A, Airoldi C, Palmioli A, Stevenazzi A, Steinkühler C, Vergani B. Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6. Int J Mol Sci 2024; 25:5885. [PMID: 38892072 PMCID: PMC11172862 DOI: 10.3390/ijms25115885] [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: 04/24/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aureliano Gaiassi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Grazia Rovelli
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Roberta Pomarico
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Paola Cordella
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Cyprian Cukier
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aleksandra Bebel
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Christian Steinkühler
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Barbara Vergani
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
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2
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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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Nath B, Phaneuf D, Julien JP. Axonal Transport Defect in Gigaxonin Deficiency Rescued by Tubastatin A. Neurotherapeutics 2023; 20:1215-1228. [PMID: 37268847 PMCID: PMC10457258 DOI: 10.1007/s13311-023-01393-1] [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] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Giant axonal neuropathy (GAN) is a disease caused by a deficiency of gigaxonin, a mediator of the degradation of intermediate filament (IF) proteins. A lack of gigaxonin alters the turnover of IF proteins, provoking accumulation and disorganization of neurofilaments (NFs) in neurons, a hallmark of the disease. However, the effects of IF disorganization on neuronal function remain unknown. Here, we report that cultured embryonic dorsal root ganglia (DRG) neurons derived from Gan-/- mice exhibit accumulations of IF proteins and defects in fast axonal transport of organelles. Kymographs generated by time-lapse microscopy revealed substantial reduction of anterograde movements of mitochondria and lysosomes in axons of Gan-/- DRG neurons. Treatment of Gan-/- DRG neurons with Tubastatin A (TubA) increased the levels of acetylated tubulin and it restored the normal axonal transport of these organelles. Furthermore, we tested the effects of TubA in a new mouse model of GAN consisting of Gan-/- mice with overexpression of peripherin (Prph) transgene. Treatment of 12-month-old Gan-/-;TgPer mice with TubA led to a slight amelioration of motor function, especially a significant improvement of gait performance as measured by footprint analyses. Moreover, TubA treatment reduced the abnormal accumulations of Prph and NF proteins in spinal neurons and it boosted the levels of Prph transported into peripheral nerve axons. These results suggest that drug inhibitors of histone deacetylase aiming to enhance axonal transport should be considered as a potential treatment for GAN disease.
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Affiliation(s)
- Banshi Nath
- CERVO Brain Research Centre, 2601, de La Canardière, Québec City, Québec, G1J2G3, Canada
| | - Daniel Phaneuf
- CERVO Brain Research Centre, 2601, de La Canardière, Québec City, Québec, G1J2G3, Canada
| | - Jean-Pierre Julien
- CERVO Brain Research Centre, 2601, de La Canardière, Québec City, Québec, G1J2G3, Canada.
- Department of Psychiatry and Neuroscience, Université Laval, Québec City, Québec, Canada.
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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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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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Banerjee S, Sharma S, Thakur A, Sachdeva R, Sharma R, Nepali K, Liou JP. N-Heterocycle based Degraders (PROTACs) Manifesting Anticancer Efficacy: Recent Advances. Curr Drug Targets 2023; 24:1184-1208. [PMID: 37946353 DOI: 10.2174/0113894501273969231102095615] [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: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Proteolysis Targeting Chimeras (PROTACs) technology has emerged as a promising strategy for the treatment of undruggable therapeutic targets. Researchers have invested a great effort in developing druggable PROTACs; however, the problems associated with PROTACs, including poor solubility, metabolic stability, cell permeability, and pharmacokinetic profile, restrict their clinical utility. Thus, there is a pressing need to expand the size of the armory of PROTACs which will escalate the chances of pinpointing new PROTACs with optimum pharmacokinetic and pharmacodynamics properties. N- heterocycle is a class of organic frameworks that have been widely explored to construct new and novel PROTACs. This review provides an overview of recent efforts of medicinal chemists to develop N-heterocycle-based PROTACs as effective cancer therapeutics. Specifically, the recent endeavors centred on the discovery of PROTACs have been delved into various classes based on the E3 ligase they target (MDM2, IAP, CRBN, and other E3 ligases). Mechanistic insights revealed during the biological assessment of recently furnished Nheterocyclic- based PROTACs constructed via the utilization of ligands for various E3 ligases have been discussed.
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Affiliation(s)
- Suddhasatwa Banerjee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Ritika Sachdeva
- College of Medicine, Taipei Medical University, Taipei, 110031, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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Jo H, Shim K, Jeoung D. The Crosstalk between FcεRI and Sphingosine Signaling in Allergic Inflammation. Int J Mol Sci 2022; 23:ijms232213892. [PMID: 36430378 PMCID: PMC9695510 DOI: 10.3390/ijms232213892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Sphingolipid molecules have recently attracted attention as signaling molecules in allergic inflammation diseases. Sphingosine-1-phosphate (S1P) is synthesized by two isoforms of sphingosine kinases (SPHK 1 and SPHK2) and is known to be involved in various cellular processes. S1P levels reportedly increase in allergic inflammatory diseases, such as asthma and anaphylaxis. FcεRI signaling is necessary for allergic inflammation as it can activate the SPHKs and increase the S1P level; once S1P is secreted, it can bind to the S1P receptors (S1PRs). The role of S1P signaling in various allergic diseases is discussed. Increased levels of S1P are positively associated with asthma and anaphylaxis. S1P can either induce or suppress allergic skin diseases in a context-dependent manner. The crosstalk between FcεRI and S1P/SPHK/S1PRs is discussed. The roles of the microRNAs that regulate the expression of the components of S1P signaling in allergic inflammatory diseases are also discussed. Various reports suggest the role of S1P in FcεRI-mediated mast cell (MC) activation. Thus, S1P/SPHK/S1PRs signaling can be the target for developing anti-allergy drugs.
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Jo H, Shim K, Jeoung D. Targeting HDAC6 to Overcome Autophagy-Promoted Anti-Cancer Drug Resistance. Int J Mol Sci 2022; 23:ijms23179592. [PMID: 36076996 PMCID: PMC9455701 DOI: 10.3390/ijms23179592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Histone deacetylases (HDACs) regulate gene expression through the epigenetic modification of chromatin structure. HDAC6, unlike many other HDACs, is present in the cytoplasm. Its deacetylates non-histone proteins and plays diverse roles in cancer cell initiation, proliferation, autophagy, and anti-cancer drug resistance. The development of HDAC6-specific inhibitors has been relatively successful. Mechanisms of HDAC6-promoted anti-cancer drug resistance, cancer cell proliferation, and autophagy are discussed. The relationship between autophagy and anti-cancer drug resistance is discussed. The effects of combination therapy, which includes HDAC6 inhibitors, on the sensitivity of cancer cells to chemotherapeutics and immune checkpoint blockade are presented. A summary of clinical trials involving HDAC6-specific inhibitors is also presented. This review presents HDAC6 as a valuable target for developing anti-cancer drugs.
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