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Wahi A, Jain P, Sinhari A, Jadhav HR. Progress in discovery and development of natural inhibitors of histone deacetylases (HDACs) as anti-cancer agents. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:675-702. [PMID: 37615708 DOI: 10.1007/s00210-023-02674-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
The study of epigenetic translational modifications had drawn great interest for the last few decades. These processes play a vital role in many diseases and cancer is one of them. Histone acetyltransferase (HAT) and histone deacetylases (HDACs) are key enzymes involved in the acetylation and deacetylation of histones and ultimately in post-translational modifications. Cancer frequently exhibits epigenetic changes, particularly disruption in the expression and activity of HDACs. It includes the capacity to regulate proliferative signalling, circumvent growth inhibitors, escape cell death, enable replicative immortality, promote angiogenesis, stimulate invasion and metastasis, prevent immunological destruction, and genomic instability. The majority of tumours develop and spread as a result of HDAC dysregulation. As a result, HDAC inhibitors (HDACis) were developed, and they today stand as a very promising therapeutic approach. One of the most well-known and efficient therapies for practically all cancer types is chemotherapy. However, the efficiency and safety of treatment are constrained by higher toxicity. The same has been observed with the synthetic HDACi. Natural products, owing to many advantages over synthetic compounds for cancer treatment have always been a choice for therapy. Hence, naturally available molecules are of particular interest for HDAC inhibition and HDAC has drawn the attention of the research fraternity due to their potential to offer a diverse array of chemical structures and bioactive compounds. This diversity opens up new avenues for exploring less toxic HDAC inhibitors to reduce side effects associated with conventional synthetic inhibitors. The review presents comprehensive details on natural product HDACi, their mechanism of action and their biological effects. Moreover, this review provides a brief discussion on the structure activity relationship of selected natural HDAC inhibitors and their analogues which can guide future research to discover selective, more potent HDACi with minimal toxicity.
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Affiliation(s)
- Abhishek Wahi
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, DPSRU, New Delhi, 110017, India.
| | - Apurba Sinhari
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
| | - Hemant R Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Vidya Vihar, Pilani, Rajasthan, 333031, India
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2
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Micheletti G, Boga C, Drius G, Bordoni S, Calonghi N. Suberoylanilide Hydroxamic Acid Analogs with Heteroaryl Amide Group and Different Chain Length: Synthesis and Effect on Histone Deacetylase. Molecules 2024; 29:238. [PMID: 38202821 PMCID: PMC10781187 DOI: 10.3390/molecules29010238] [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: 11/17/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
This review covers the last 25 years of the literature on analogs of suberoylanilide hydroxamic acid (SAHA, known also as vorinostat) acting as an HDAC inhibitor. In particular, the topic has been focused on the synthesis and biological activity of compounds where the phenyl group (the surface recognition moiety, CAP) of SAHA has been replaced by an azaheterocycle through a direct bond with amide nitrogen atom, and the methylene chain in the linker region is of variable length. Most of the compounds displayed good to excellent inhibitory activity against HDACs and in many cases showed antiproliferative activity against human cancer cell lines.
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Affiliation(s)
- Gabriele Micheletti
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Carla Boga
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Giacomo Drius
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Silvia Bordoni
- Department of Industrial Chemistry ‘Toso Montanari’, Alma Mater Studiorum, Università di Bologna, Viale Del Risorgimento 4, 40136 Bologna, Italy; (G.D.); (S.B.)
| | - Natalia Calonghi
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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3
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Tan Y, Xiang H, Jin J, He X, Li S, Ye Y. Oxidation/Alkylation of Amino Acids with α-Bromo Carbonyls Catalyzed by Copper and Quick Access to HDAC Inhibitor. J Org Chem 2023; 88:17398-17408. [PMID: 38037667 DOI: 10.1021/acs.joc.3c02218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
A facile and efficient method was reported for Cu-catalyzed selective α-alkylation processes of amino acids/peptides and α-bromo esters/ketones through a radical-radical coupling pathway. The reaction displays an excellent functional group tolerance and broad substrate scope, allowing access to desired products in moderate to excellent yields. Notably, this method is distinguished by site-specificity and exhibits total selectivity for aryl glycine motifs over other amino acid units. Furthermore, the practicality of this strategy is certified by the efficient synthesis of the novel SAHA phenylalanine-containing analogue (SPACA).
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Affiliation(s)
- Yuqiong Tan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Huan Xiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Jiayan Jin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Xingrui He
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Shijun Li
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
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Bülbül EF, Robaa D, Sun P, Mahmoudi F, Melesina J, Zessin M, Schutkowski M, Sippl W. Application of Ligand- and Structure-Based Prediction Models for the Design of Alkylhydrazide-Based HDAC3 Inhibitors as Novel Anti-Cancer Compounds. Pharmaceuticals (Basel) 2023; 16:968. [PMID: 37513880 PMCID: PMC10386743 DOI: 10.3390/ph16070968] [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: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Histone deacetylases (HDAC) represent promising epigenetic targets for several diseases including different cancer types. The HDAC inhibitors approved to date are pan-HDAC inhibitors and most show a poor selectivity profile, side effects, and in particular hydroxamic-acid-based inhibitors lack good pharmacokinetic profiles. Therefore, the development of isoform-selective non-hydroxamic acid HDAC inhibitors is a highly regarded field in medicinal chemistry. In this study, we analyzed different ligand-based and structure-based drug design techniques to predict the binding mode and inhibitory activity of recently developed alkylhydrazide HDAC inhibitors. Alkylhydrazides have recently attracted more attention as they have shown promising effects in various cancer cell lines. In this work, pharmacophore models and atom-based quantitative structure-activity relationship (QSAR) models were generated and evaluated. The binding mode of the studied compounds was determined using molecular docking as well as molecular dynamics simulations and compared with known crystal structures. Calculated free energies of binding were also considered to generate QSAR models. The created models show a good explanation of in vitro data and were used to develop novel HDAC3 inhibitors.
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Affiliation(s)
- Emre F Bülbül
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ping Sun
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Fereshteh Mahmoudi
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jelena Melesina
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Matthes Zessin
- Department of Enzymology, Institute of Biotechnology, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biotechnology, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
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Knoche SM, Brumfield GL, Goetz BT, Sliker BH, Larson AC, Olson MT, Poelaert BJ, Bavari A, Yan Y, Black JD, Solheim JC. The histone deacetylase inhibitor M344 as a multifaceted therapy for pancreatic cancer. PLoS One 2022; 17:e0273518. [PMID: 36126055 PMCID: PMC9488834 DOI: 10.1371/journal.pone.0273518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
The histone deacetylase (HDAC) inhibitor vorinostat, used with gemcitabine and other therapies, has been effective in treatment of experimental models of pancreatic cancer. In this study, we demonstrated that M344, an HDAC inhibitor, is efficacious against pancreatic cancer in vitro and in vivo, alone or with gemcitabine. By 24 hours post-treatment, M344 augments the population of pancreatic cancer cells in G1, and at a later time point (48 hours) it increases apoptosis. M344 inhibits histone H3 deacetylation and slows pancreatic cancer cell proliferation better than vorinostat, and it does not decrease the viability of a non-malignant cell line more than vorinostat. M344 also elevates pancreatic cancer cell major histocompatibility complex (MHC) class I molecule expression, potentially increasing the susceptibility of pancreatic cancer cells to T cell lysis. Taken together, our findings support further investigation of M344 as a pancreatic cancer treatment.
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Affiliation(s)
- Shelby M. Knoche
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gabrielle L. Brumfield
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Benjamin T. Goetz
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Bailee H. Sliker
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Alaina C. Larson
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Madeline T. Olson
- Department of Pharmaceutical Sciences, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Brittany J. Poelaert
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Audrey Bavari
- University of Nebraska at Omaha, Omaha, NE, United States of America
| | - Ying Yan
- Department of Radiation Oncology, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jennifer D. Black
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Joyce C. Solheim
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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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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Mayer M, Berger A, Leischner C, Renner O, Burkard M, Böcker A, Noor S, Weiland T, Weiss TS, Busch C, Lauer UM, Bischoff SC, Venturelli S. Preclinical Efficacy and Toxicity Analysis of the Pan-Histone Deacetylase Inhibitor Gossypol for the Therapy of Colorectal Cancer or Hepatocellular Carcinoma. Pharmaceuticals (Basel) 2022; 15:ph15040438. [PMID: 35455435 PMCID: PMC9028974 DOI: 10.3390/ph15040438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Gossypol, a sesquiterpenoid found in cotton seeds, exerts anticancer effects on several tumor entities due to inhibition of DNA synthesis and other mechanisms. In clinical oncology, histone deacetylase inhibitors (HDACi) are applied as anticancer compounds. In this study, we examined whether gossypol harbors HDAC inhibiting activity. In vitro analyses showed that gossypol inhibited class I, II, and IV HDAC, displaying the capability to laterally interact with the respective catalytic center and is, therefore, classified as a pan-HDAC inhibitor. Next, we studied the effects of gossypol on human-derived hepatoma (HepG2) and colon carcinoma (HCT-116) cell lines and found that gossypol induced hyperacetylation of histone protein H3 and/or tubulin within 6 h. Furthermore, incubation with different concentrations of gossypol (5–50 µM) over a time period of 96 h led to a prominent reduction in cellular viability and proliferation of hepatoma (HepG2, Hep3B) and colon carcinoma (HCT-116, HT-29) cells. In-depth analysis of underlying mechanisms showed that gossypol induced apoptosis via caspase activation. For pre-clinical evaluation, toxicity analyses showed toxic effects of gossypol in vitro toward non-malignant primary hepatocytes (PHH), the colon-derived fibroblast cell line CCD-18Co, and the intestinal epithelial cell line CCD 841 CoN at concentrations of ≥5 µM, and embryotoxicity in chicken embryos at ≥2.5 µM. In conclusion, the pronounced inhibitory capacity of gossypol on cancer cells was characterized, and pan-HDACi activity was detected in silico, in vitro, by inhibiting individual HDAC isoenzymes, and on protein level by determining histone acetylation. However, for clinical application, further chemical optimization is required to decrease cellular toxicity.
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Affiliation(s)
- Mascha Mayer
- Institute of Nutritional Medicine and Prevention, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Alexander Berger
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany; (A.B.); (T.W.); (U.M.L.)
| | - Christian Leischner
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (C.L.); (O.R.); (M.B.)
| | - Olga Renner
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (C.L.); (O.R.); (M.B.)
| | - Markus Burkard
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (C.L.); (O.R.); (M.B.)
| | | | - Seema Noor
- Department of Dermatology, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany;
| | - Timo Weiland
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany; (A.B.); (T.W.); (U.M.L.)
| | - Thomas S. Weiss
- Center for Liver Cell Research, Children’s University Hospital (KUNO), University Hospital Regensburg, 93042 Regensburg, Germany;
| | | | - Ulrich M. Lauer
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany; (A.B.); (T.W.); (U.M.L.)
- German Cancer Consortium (DKTK), DKFZ Partner Site, 72076 Tuebingen, Germany
| | - Stephan C. Bischoff
- Institute of Nutritional Medicine and Prevention, University of Hohenheim, 70599 Stuttgart, Germany;
- Correspondence: (S.C.B.); (S.V.); Tel.: +49-711-459-24100 (S.C.B.); +49-711-459-24195 (S.V.)
| | - Sascha Venturelli
- Department of Nutritional Biochemistry, Institute of Nutritional Sciences, University of Hohenheim, 70599 Stuttgart, Germany; (C.L.); (O.R.); (M.B.)
- Department of Vegetative and Clinical Physiology, Institute of Physiology, University of Tuebingen, 72074 Tuebingen, Germany
- Correspondence: (S.C.B.); (S.V.); Tel.: +49-711-459-24100 (S.C.B.); +49-711-459-24195 (S.V.)
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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9
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Li Y, Sang S, Ren W, Pei Y, Bian Y, Chen Y, Sun H. Inhibition of Histone Deacetylase 6 (HDAC6) as a therapeutic strategy for Alzheimer's disease: A review (2010-2020). Eur J Med Chem 2021; 226:113874. [PMID: 34619465 DOI: 10.1016/j.ejmech.2021.113874] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 01/27/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative disorders, which is characterized by the primary risk factor, age. Several attempts have been made to treat AD, while most of them end in failure. However, with the deepening study of pathogenesis of AD, the expression of HDAC6 in the hippocampus, which plays a major role of the memory formation, is becoming worth of notice. Neurofibrillary tangles (NFTs), a remarkable lesion in AD, has been characterized in association with the abnormal accumulation of hyperphosphorylated Tau, which is mainly caused by the high expression of HDAC6. On the other hand, the hypoacetylated tubulin induced by HDAC6 is also fatal for the neuronal transport, which is the key impact of the formation of axons and dendrites. Overall, the significantly increased expression of HDAC6 in brain regions is deleterious to neuron survival in AD patients. Based on the above research, the inhibition of HDAC6 seems to be a potential therapeutic method for the treatment of AD. Up to now, various types of HDAC6 inhibitors have been discovered. This review mainly analyzes the HDAC6 inhibitors reported amid 2010-2020 in terms of their structure, selectivity and pharmacological impact towards AD. And we aim at facilitating the design and development of better HDAC6 inhibitors in the future.
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Affiliation(s)
- Yunheng Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shenghu Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Weijie Ren
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yaoyao Bian
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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10
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Pflieger M, Sönnichsen M, Horstick‐Muche N, Yang J, Schliehe‐Diecks J, Schöler A, Borkhardt A, Hamacher A, Kassack MU, Hansen FK, Bhatia S, Kurz T. Oxa Analogues of Nexturastat A Demonstrate Improved HDAC6 Selectivity and Superior Antileukaemia Activity. ChemMedChem 2021; 16:1798-1803. [PMID: 33629513 PMCID: PMC8251746 DOI: 10.1002/cmdc.202001011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/19/2021] [Indexed: 01/03/2023]
Abstract
The acetylome is important for maintaining the homeostasis of cells. Abnormal changes can result in the pathogenesis of immunological or neurological diseases, and degeneration can promote the manifestation of cancer. In particular, pharmacological intervention in the acetylome with pan-histone deacetylase (HDAC) inhibitors is clinically validated. However, these drugs exhibit an undesirable risk-benefit profile due to severe side effects. Selective HDAC inhibitors might promote patient compliance and represent a valuable opportunity in personalised medicine. Therefore, we envisioned the development of HDAC6-selective inhibitors. During our lead structure identification, we demonstrated that an alkoxyurea-based connecting unit proves to be beneficial for HDAC6 selectivity and established the synthesis of alkoxyurea-based hydroxamic acids. Herein, we report highly potent N-alkoxyurea-based hydroxamic acids with improved HDAC6 preference compared to nexturastat A. We further validated the biological activity of these oxa analogues of nexturastat A in a broad subset of leukaemia cell lines and demonstrated their superior anti-proliferative properties compared to nexturastat A.
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Affiliation(s)
- Marc Pflieger
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Nadine Horstick‐Muche
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Jing Yang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
- Department of MedicineYangzhou Polytechnic CollegeWest Wenchang Road 458Yangzhou225009P.R. China
| | - Julian Schliehe‐Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical FacultyLeipzig UniversityBrüderstraße 3404103LeipzigGermany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Matthias U. Kassack
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Finn K. Hansen
- Pharmaceutical and Cell Biological Chemistry, Pharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
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11
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Elmezayen AD, Al-Obaidi A, Yelekçi K. Discovery of novel isoform-selective histone deacetylases 5 and 9 inhibitors through combined ligand-based pharmacophore modeling, molecular mocking, and molecular dynamics simulations for cancer treatment. J Mol Graph Model 2021; 106:107937. [PMID: 34049193 DOI: 10.1016/j.jmgm.2021.107937] [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: 01/30/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022]
Abstract
Class IIa histone deacetylases (HDACs) 5 and 9 play crucial roles in several human disorders such as cancer, making them important targets for drug design. Continuous research is pursed to overcome the cytotoxicity side effect that comes with the currently available broad-spectrum HDACs inhibitors. Herein, common features of active HDACs inhibitors in clinical trials and use have been calculated to generate the best pharmacophore hypothesis. Guner-Henry scoring system was used to validate the generated hypotheses. Hypo1 of HDAC5 and Hypo2 of HDAC9 exhibited the most statistically significance hypotheses. Compounds with fit value of 3 and more were examined by QuickVina 2 docking tool to calculate their binding affinity toward all class IIa HDACs. A total of 6 potential selective compounds were subjected to 100 molecular dynamics (MD) simulation to examine their binding modes. The free binding energy calculations were computed according to the MM-PBSA method. Proposed selective compounds displayed good stability with their targets and thus they may offer potent leads for the designing of HDAC5 and HDAC9 isoform selective inhibitors.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
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12
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Binding Free Energy (BFE) Calculations and Quantitative Structure-Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 ( smHDAC8) Inhibitors. Molecules 2021; 26:molecules26092584. [PMID: 33925246 PMCID: PMC8125515 DOI: 10.3390/molecules26092584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 01/02/2023] Open
Abstract
Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC50 values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.
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13
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Melesina J, Simoben CV, Praetorius L, Bülbül EF, Robaa D, Sippl W. Strategies To Design Selective Histone Deacetylase Inhibitors. ChemMedChem 2021; 16:1336-1359. [PMID: 33428327 DOI: 10.1002/cmdc.202000934] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/15/2022]
Abstract
This review classifies drug-design strategies successfully implemented in the development of histone deacetylase (HDAC) inhibitors, which have many applications including cancer treatment. Our focus is on especially demanded selective HDAC inhibitors and their structure-activity relationships in relation to corresponding protein structures. The main part of the paper is divided into six subsections each narrating how optimization of one of six structural features can influence inhibitor selectivity. It starts with the impact of the zinc binding group on selectivity, continues with the optimization of the linker placed in the substrate binding tunnel as well as the adjustment of the cap group interacting with the surface of the protein, and ends with the addition of groups targeting class-specific sub-pockets: the side-pocket-, lower-pocket- and foot-pocket-targeting groups. The review is rounded off with a conclusion and an outlook on the future of HDAC inhibitor design.
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Affiliation(s)
- Jelena Melesina
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Conrad V Simoben
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Lucas Praetorius
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Emre F Bülbül
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
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14
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Simoben CV, Qaseem A, Moumbock AFA, Telukunta KK, Günther S, Sippl W, Ntie‐Kang F. Pharmacoinformatic Investigation of Medicinal Plants from East Africa. Mol Inform 2020; 39:e2000163. [PMID: 32964659 PMCID: PMC7685152 DOI: 10.1002/minf.202000163] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/22/2020] [Indexed: 12/18/2022]
Abstract
Medicinal plants have widely been used in the traditional treatment of ailments and have been proven effective. Their contribution still holds an important place in modern drug discovery due to their chemical, and biological diversities. However, the poor documentation of traditional medicine, in developing African countries for instance, can lead to the loss of knowledge related to such practices. In this study, we present the Eastern Africa Natural Products Database (EANPDB) containing the structural and bioactivity information of 1870 unique molecules isolated from about 300 source species from the Eastern African region. This represents the largest collection of natural products (NPs) from this geographical region, covering literature data of the period from 1962 to 2019. The computed physicochemical properties and toxicity profiles of each compound have been included. A comparative analysis of some physico-chemical properties like molecular weight, H-bond donor/acceptor, logPo/w , etc. as well scaffold diversity analysis has been carried out with other published NP databases. EANPDB was combined with the previously published Northern African Natural Products Database (NANPDB), to form a merger African Natural Products Database (ANPDB), containing ∼6500 unique molecules isolated from about 1000 source species (freely available at http://african-compounds.org). As a case study, latrunculins A and B isolated from the sponge Negombata magnifica (Podospongiidae) with previously reported antitumour activities, were identified via substructure searching as molecules to be explored as putative binders of histone deacetylases (HDACs).
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Affiliation(s)
- Conrad V. Simoben
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Ammar Qaseem
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Aurélien F. A. Moumbock
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Kiran K. Telukunta
- ELIXIR@PSB, VIB-UGent Center for Plant Systems BiologyTechnologiepark 719052GhentBelgium
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Wolfgang Sippl
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Fidele Ntie‐Kang
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
- Department of Chemistry, Faculty of ScienceUniversity of BueaP.O. Box 63Buea CM00237Cameroon
- Institut für BotanikTechnische Universität DresdenZellescherWeg 20b01217DresdenGermany
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15
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Cheng Y, He C, Wang M, Ma X, Mo F, Yang S, Han J, Wei X. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct Target Ther 2019; 4:62. [PMID: 31871779 PMCID: PMC6915746 DOI: 10.1038/s41392-019-0095-0] [Citation(s) in RCA: 590] [Impact Index Per Article: 118.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 02/05/2023] Open
Abstract
Epigenetic alternations concern heritable yet reversible changes in histone or DNA modifications that regulate gene activity beyond the underlying sequence. Epigenetic dysregulation is often linked to human disease, notably cancer. With the development of various drugs targeting epigenetic regulators, epigenetic-targeted therapy has been applied in the treatment of hematological malignancies and has exhibited viable therapeutic potential for solid tumors in preclinical and clinical trials. In this review, we summarize the aberrant functions of enzymes in DNA methylation, histone acetylation and histone methylation during tumor progression and highlight the development of inhibitors of or drugs targeted at epigenetic enzymes.
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Affiliation(s)
- Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Manni Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelei Ma
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Fei Mo
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyong Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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16
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Peng X, Liao G, Sun P, Yu Z, Chen J. An Overview of HDAC Inhibitors and their Synthetic Routes. Curr Top Med Chem 2019; 19:1005-1040. [DOI: 10.2174/1568026619666190227221507] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 01/19/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
Epigenetics play a key role in the origin, development and metastasis of cancer. Epigenetic processes include DNA methylation, histone acetylation, histone methylation, and histone phosphorylation, among which, histone acetylation is the most common one that plays important roles in the regulation of normal cellular processes, and is controlled by histone deacetylases (HDACs) and histone acetyltransferases (HATs). HDACs are involved in the regulation of many key cellular processes, such as DNA damage repair, cell cycle control, autophagy, metabolism, senescence and chaperone function, and can lead to oncogene activation. As a result, HDACs are considered to be an excellent target for anti-cancer therapeutics like histone deacetylase inhibitors (HDACi) which have attracted much attention in the last decade. A wide-ranging knowledge of the role of HDACs in tumorigenesis, and of the action of HDACi, has been achieved. The primary purpose of this paper is to summarize recent HDAC inhibitors and the synthetic routes as well as to discuss the direction for the future development of new HDAC inhibitors.
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Affiliation(s)
- Xiaopeng Peng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Guochao Liao
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
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17
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M344 promotes nonamyloidogenic amyloid precursor protein processing while normalizing Alzheimer's disease genes and improving memory. Proc Natl Acad Sci U S A 2017; 114:E9135-E9144. [PMID: 29073110 PMCID: PMC5664514 DOI: 10.1073/pnas.1707544114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hundreds of failed clinical trials with Alzheimer’s disease (AD) patients over the last fifteen years demonstrate that the one-target–one-disease approach is not effective in AD. In silico, structure-based, multitarget drug design approaches to treat multifactorial diseases have not been successful in the context of AD either. Here, we show that M344, an inhibitor of class I and IIB histone deacetylases, affects multiple AD-related genes, including those related to both early- and late-onset AD. We also show that M344 improves memory in the 3xTg AD mouse model. This work endorses a shift to a multitargeted approach to the treatment of AD, supporting the therapeutic potential of a single small molecule with an epigenetic mechanism of action. Alzheimer’s disease (AD) comprises multifactorial ailments for which current therapeutic strategies remain insufficient to broadly address the underlying pathophysiology. Epigenetic gene regulation relies upon multifactorial processes that regulate multiple gene and protein pathways, including those involved in AD. We therefore took an epigenetic approach where a single drug would simultaneously affect the expression of a number of defined AD-related targets. We show that the small-molecule histone deacetylase inhibitor M344 reduces beta-amyloid (Aβ), reduces tau Ser396 phosphorylation, and decreases both β-secretase (BACE) and APOEε4 gene expression. M344 increases the expression of AD-relevant genes: BDNF, α-secretase (ADAM10), MINT2, FE65, REST, SIRT1, BIN1, and ABCA7, among others. M344 increases sAPPα and CTFα APP metabolite production, both cleavage products of ADAM10, concordant with increased ADAM10 gene expression. M344 also increases levels of immature APP, supporting an effect on APP trafficking, concurrent with the observed increase in MINT2 and FE65, both shown to increase immature APP in the early secretory pathway. Chronic i.p. treatment of the triple transgenic (APPsw/PS1M146V/TauP301L) mice with M344, at doses as low as 3 mg/kg, significantly prevented cognitive decline evaluated by Y-maze spontaneous alternation, novel object recognition, and Barnes maze spatial memory tests. M344 displays short brain exposure, indicating that brief pulses of daily drug treatment may be sufficient for long-term efficacy. Together, these data show that M344 normalizes several disparate pathogenic pathways related to AD. M344 therefore serves as an example of how a multitargeting compound could be used to address the polygenic nature of multifactorial diseases.
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18
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Lu W, Yao X, Ouyang P, Dong N, Wu D, Jiang X, Wu Z, Zhang C, Xu Z, Tang Y, Zou S, Liu M, Li J, Zeng M, Lin P, Cheng F, Huang J. Drug Repurposing of Histone Deacetylase Inhibitors That Alleviate Neutrophilic Inflammation in Acute Lung Injury and Idiopathic Pulmonary Fibrosis via Inhibiting Leukotriene A4 Hydrolase and Blocking LTB4 Biosynthesis. J Med Chem 2017; 60:1817-1828. [PMID: 28218840 DOI: 10.1021/acs.jmedchem.6b01507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Acute lung injury (ALI) and idiopathic pulmonary fibrosis (IPF) are both serious public health problems with high incidence and mortality rate in adults, and with few drugs available for the efficient treatment in clinic. In this study, we identified that two known histone deacetylase (HDAC) inhibitors, suberanilohydroxamic acid (SAHA, 1) and its analogue 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide (2), are effective inhibitors of Leukotriene A4 hydrolase (LTA4H), a key enzyme in the biosynthesis of leukotriene B4 (LTB4), across a panel of 18 HDAC inhibitors, using enzymatic assay, thermofluor assay, and X-ray crystallographic investigation. Importantly, both 1 and 2 markedly diminish early neutrophilic inflammation in mouse models of ALI and IPF under a clinical safety dose. Detailed mechanisms of down-regulation of proinflammatory cytokines by 1 or 2 were determined in vivo. Collectively, 1 and 2 would provide promising agents with well-known clinical safety for potential treatment in patients with ALI and IPF via pharmacologically inhibiting LAT4H and blocking LTB4 biosynthesis.
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Affiliation(s)
- Weiqiang Lu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China.,Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Xue Yao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Ping Ouyang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Ningning Dong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Dang Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Xingwu Jiang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Chen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Zhongyu Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Shien Zou
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University , Shanghai 200011, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University , Shanghai 200241, China
| | - Jian Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
| | - Minghua Zeng
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education), School of Chemistry & Chemical Engineering, Guangxi Normal University , Guilin 541004, China
| | - Ping Lin
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041, Sichuan, China
| | - Feixiong Cheng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041, Sichuan, China.,Center for Complex Networks Research, Northeastern University , Boston, Massachusetts 02115, United States.,Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts 02215, United States
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai 200237, China
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19
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Ferreira RC, Popova EY, James J, Briones MRS, Zhang SS, Barnstable CJ. Histone Deacetylase 1 Is Essential for Rod Photoreceptor Differentiation by Regulating Acetylation at Histone H3 Lysine 9 and Histone H4 Lysine 12 in the Mouse Retina. J Biol Chem 2016; 292:2422-2440. [PMID: 28028172 DOI: 10.1074/jbc.m116.756643] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/22/2016] [Indexed: 01/19/2023] Open
Abstract
Histone acetylation has a regulatory role in gene expression and is necessary for proper tissue development. To investigate the specific roles of histone deacetylases (HDACs) in rod differentiation in neonatal mouse retinas, we used a pharmacological approach that showed that inhibition of class I but not class IIa HDACs caused the same phenotypic changes seen with broad spectrum HDAC inhibitors, most notably a block in the differentiation of rod photoreceptors. Inhibition of HDAC1 resulted in increase of acetylation of lysine 9 of histone 3 (H3K9) and lysine 12 of histone 4 (H4K12) but not lysine 27 of histone 3 (H3K27) and led to maintained expression of progenitor-specific genes such as Vsx2 and Hes1 with concomitant block of expression of rod-specific genes. ChiP experiments confirmed these changes in the promoters of a group of progenitor genes. Based on our results, we suggest that HDAC1-specific inhibition prevents progenitor cells of the retina from exiting the cell cycle and differentiating. HDAC1 may be an essential epigenetic regulator of the transition from progenitor cells to terminally differentiated photoreceptors.
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Affiliation(s)
- Renata C Ferreira
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Evgenya Y Popova
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Jessica James
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033
| | - Marcelo R S Briones
- Laboratory of Evolutionary Genomics and Biocomplexity, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04039-032, Brazil
| | - Samuel S Zhang
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
| | - Colin J Barnstable
- From the Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, Pennsylvania 17033, .,Penn State Hershey Eye Center, Hershey, Pennsylvania 17033, and
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20
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Choubey SK, Jeyaraman J. A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study. J Mol Graph Model 2016; 70:54-69. [DOI: 10.1016/j.jmgm.2016.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 09/10/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022]
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21
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Zhang F, Huang Q, Yan J, Chen Z. Histone Acetylation Induced Transformation of B-DNA to Z-DNA in Cells Probed through FT-IR Spectroscopy. Anal Chem 2016; 88:4179-82. [DOI: 10.1021/acs.analchem.6b00400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fengqiu Zhang
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
- School of Nuclear Science and Technology, University of Science & Technology of China, Hefei, China
- Henan
Key Laboratory of Ion-beam Bioengineering, School of Physical Engineering, Zhengzhou University, Zhengzhou, China
| | - Qing Huang
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
- School of Nuclear Science and Technology, University of Science & Technology of China, Hefei, China
| | - Jingwen Yan
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
| | - Zhu Chen
- Institute
of Technical Biology and Agriculture Engineering, Hefei Institutes
of Physical Science, Key Laboratory
of Ion-beam Bioengineering, Chinese Academy of Sciences, Hefei, China
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Abstract
SIGNIFICANCE Epigenetic inactivation of pivotal genes involved in cell growth is a hallmark of human pathologies, in particular cancer. Histone acetylation balance obtained through opposing actions of histone deacetylases (HDACs) and histone acetyltransferases is one epigenetic mechanism controlling gene expression and is, thus, associated with disease etiology and progression. Interfering pharmacologically with HDAC activity can correct abnormalities in cell proliferation, migration, vascularization, and death. RECENT ADVANCES Histone deacetylase inhibitors (HDACi) represent a new class of cytostatic agents that interfere with the function of HDACs and are able to increase gene expression by indirectly inducing histone acetylation. Several HDACi, alone or in combination with DNA-demethylating agents, chemopreventive, or classical chemotherapeutic drugs, are currently being used in clinical trials for solid and hematological malignancies, and are, thus, promising candidates for cancer therapy. CRITICAL ISSUES (i) Non-specific (off-target) HDACi effects due to activities unassociated with HDAC inhibition. (ii) Advantages/disadvantages of non-selective or isoform-directed HDACi. (iii) Limited number of response-predictive biomarkers. (iv) Toxicity leading to dysfunction of critical biological processes. FUTURE DIRECTIONS Selective HDACi could achieve enhanced clinical utility by reducing or eliminating the serious side effects associated with current first-generation non-selective HDACi. Isoform-selective and pan-HDACi candidates might benefit from the identification of biomarkers, enabling better patient stratification and prediction of response to treatment.
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Affiliation(s)
- Rosaria Benedetti
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy
| | - Mariarosaria Conte
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy
| | - Lucia Altucci
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy .,2 Istituto di Genetica e Biofisica "Adriano Buzzati-Traverso," Napoli, Italy
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Design, synthesis, 3D pharmacophore, QSAR, and docking studies of carboxylic acid derivatives as Histone Deacetylase inhibitors and cytotoxic agents. Bioorg Chem 2014; 57:65-82. [DOI: 10.1016/j.bioorg.2014.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/12/2014] [Accepted: 08/24/2014] [Indexed: 11/23/2022]
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24
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Dissecting histone deacetylase role in pulmonary arterial smooth muscle cell proliferation and migration. Biochem Pharmacol 2014; 91:181-90. [PMID: 25063234 DOI: 10.1016/j.bcp.2014.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 11/24/2022]
Abstract
Pulmonary Arterial Hypertension (PAH) is a rare and devasting condition characterized by elevated pulmonary vascular resistance and pulmonary artery pressure leading to right-heart failure and premature death. Pathologic alterations in proliferation, migration and survival of all cell types composing the vascular tissue play a key role in the occlusion of the vascular lumen. In the current study, we initially investigated the action of selective class I and class II HDAC inhibitors on the proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) after exposure to Platelet Derived Growth Factor (PDGF). Class I HDAC inhibitors were able to counteract the hyperproliferative response to PDGF, reducing both proliferation and migration in PASMCs, while class II were ineffective. Selective silencing with siRNAs targeted against different HDACs revealed a major role of class I, and within this class, of HDAC1 in mediating PDGF-induced Akt Phosphorylation and Cyclin D1 (CycD1) expression. These results from these combinatorial approaches were further confirmed by the ability of a specific HDAC1 inhibitor to antagonize the PDGF action. The finding that HDAC1 is a major conductor of PDGF-induced patterning in PAH-PASMCs prompts the development of novel selective inhibitors of this member of class I HDACs as a potential tool to control lung vascular homeostasis in PAH.
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Stolfa DA, Marek M, Lancelot J, Hauser AT, Walter A, Leproult E, Melesina J, Rumpf T, Wurtz JM, Cavarelli J, Sippl W, Pierce RJ, Romier C, Jung M. Molecular basis for the antiparasitic activity of a mercaptoacetamide derivative that inhibits histone deacetylase 8 (HDAC8) from the human pathogen schistosoma mansoni. J Mol Biol 2014; 426:3442-53. [PMID: 24657767 DOI: 10.1016/j.jmb.2014.03.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 10/25/2022]
Abstract
Schistosomiasis, caused by the parasitic flatworm Schistosoma mansoni and related species, is a tropical disease that affects over 200 million people worldwide. A new approach for targeting eukaryotic parasites is to tackle their dynamic epigenetic machinery that is necessary for the extensive phenotypic changes during the life cycle of the parasite. Recently, we identified S. mansoni histone deacetylase 8 (smHDAC8) as a potential target for antiparasitic therapy. Here, we present results on the investigations of a focused set of HDAC (histone deacetylase) inhibitors on smHDAC8. Besides several active hydroxamates, we identified a thiol-based inhibitor that inhibited smHDAC8 activity in the micromolar range with unexpected selectivity over the human isotype, which has not been observed so far. The crystal structure of smHDAC8 complexed with the thiol derivative revealed that the inhibitor is accommodated in the catalytic pocket, where it interacts with both the catalytic zinc ion and the essential catalytic tyrosine (Y341) residue via its mercaptoacetamide warhead. To our knowledge, this is the first complex crystal structure of any HDAC inhibited by a mercaptoacetamide inhibitor, and therefore, this finding offers a rationale for further improvement. Finally, an ester prodrug of the thiol HDAC inhibitor exhibited antiparasitic activity on cultured schistosomes in a dose-dependent manner.
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Affiliation(s)
- Diana A Stolfa
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Martin Marek
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Julien Lancelot
- Center for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, 1 rue Professeur Calmette, F-59019 Lille Cedex, France
| | - Alexander-Thomas Hauser
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Alexandra Walter
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany; German Cancer Consortium (DKTK), Freiburg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Emeline Leproult
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Jelena Melesina
- Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle/Saale, Germany
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Jean-Marie Wurtz
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle/Saale, Germany
| | - Raymond J Pierce
- Center for Infection and Immunity of Lille, INSERM U1019-CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, 1 rue Professeur Calmette, F-59019 Lille Cedex, France
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, INSERM, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France.
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany.
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26
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Marek M, Kannan S, Hauser AT, Moraes Mourão M, Caby S, Cura V, Stolfa DA, Schmidtkunz K, Lancelot J, Andrade L, Renaud JP, Oliveira G, Sippl W, Jung M, Cavarelli J, Pierce RJ, Romier C. Structural basis for the inhibition of histone deacetylase 8 (HDAC8), a key epigenetic player in the blood fluke Schistosoma mansoni. PLoS Pathog 2013; 9:e1003645. [PMID: 24086136 PMCID: PMC3784479 DOI: 10.1371/journal.ppat.1003645] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/04/2013] [Indexed: 11/19/2022] Open
Abstract
The treatment of schistosomiasis, a disease caused by blood flukes parasites of the Schistosoma genus, depends on the intensive use of a single drug, praziquantel, which increases the likelihood of the development of drug-resistant parasite strains and renders the search for new drugs a strategic priority. Currently, inhibitors of human epigenetic enzymes are actively investigated as novel anti-cancer drugs and have the potential to be used as new anti-parasitic agents. Here, we report that Schistosoma mansoni histone deacetylase 8 (smHDAC8), the most expressed class I HDAC isotype in this organism, is a functional acetyl-L-lysine deacetylase that plays an important role in parasite infectivity. The crystal structure of smHDAC8 shows that this enzyme adopts a canonical α/β HDAC fold, with specific solvent exposed loops corresponding to insertions in the schistosome HDAC8 sequence. Importantly, structures of smHDAC8 in complex with generic HDAC inhibitors revealed specific structural changes in the smHDAC8 active site that cannot be accommodated by human HDACs. Using a structure-based approach, we identified several small-molecule inhibitors that build on these specificities. These molecules exhibit an inhibitory effect on smHDAC8 but show reduced affinity for human HDACs. Crucially, we show that a newly identified smHDAC8 inhibitor has the capacity to induce apoptosis and mortality in schistosomes. Taken together, our biological and structural findings define the framework for the rational design of small-molecule inhibitors specifically interfering with schistosome epigenetic mechanisms, and further support an anti-parasitic epigenome targeting strategy to treat neglected diseases caused by eukaryotic pathogens. Schistosomiasis, a neglected parasitic disease caused by flatworms of the genus Schistosoma, is responsible for hundreds of thousands of deaths yearly. Its treatment currently depends on a single drug, praziquantel, with reports of drug-resistant parasites. Human epigenetic enzymes, in particular histone deacetylases (HDACs), are predominantly attractive inhibitory targets for anti-cancer therapies. Validated scaffolds against these enzymes could also be used as leads in the search for novel specific drugs against schistosomiasis. In our study, we show that Schistosoma mansoni histone deacetylase 8 (smHDAC8) is a functional acetyl-L-lysine deacetylase that plays an important role in parasite infectivity and is therefore a relevant target for drug discovery. The determination of the atomic structures of smHDAC8 in complex with generic HDAC inhibitors revealed that the architecture of the smHDAC8 active site pocket differed significantly from its human counterparts and provided a framework for the development of inhibitors selectively interfering with schistosome epigenetic mechanisms. In agreement, this information enabled us to identify several small-molecule scaffolds that possess specific inhibitory effects on smHDAC8 and cause mortality in schistosomes. Our results provide the proof of concept that targeting epigenetic enzymes is a valid approach to treat neglected diseases caused by eukaryotic pathogens.
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Affiliation(s)
- Martin Marek
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France
| | | | - Alexander-Thomas Hauser
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marina Moraes Mourão
- Genomics and Computational Biology Group, Center for Excellence in Bioinformatics, National Institute of Science and Technology in Tropical Diseases, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Stéphanie Caby
- Center for Infection and Immunity of Lille (CIIL), INSERM U1019 – CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France
| | - Diana A. Stolfa
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Karin Schmidtkunz
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Julien Lancelot
- Center for Infection and Immunity of Lille (CIIL), INSERM U1019 – CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
| | - Luiza Andrade
- Genomics and Computational Biology Group, Center for Excellence in Bioinformatics, National Institute of Science and Technology in Tropical Diseases, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Jean-Paul Renaud
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, Center for Excellence in Bioinformatics, National Institute of Science and Technology in Tropical Diseases, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Wolfgang Sippl
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- Freiburg Institute of Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Freiburg Institute of Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France
| | - Raymond J. Pierce
- Center for Infection and Immunity of Lille (CIIL), INSERM U1019 – CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
- * E-mail: (RJP); (CR)
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France
- * E-mail: (RJP); (CR)
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Elaut G, Török G, Papeleu P, Vanhaecke T, Laus G, Tourwé D, Rogiers V. Rat hepatocyte suspensions as a suitable in vitro model for studying the biotransformation of histone deacetylase inhibitors. Altern Lab Anim 2013; 32 Suppl 1A:105-12. [PMID: 23577441 DOI: 10.1177/026119290403201s16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This paper focuses on the use of liver-derived in vitro systems for biotransformation studies during early drug development, as exemplified by the two molecules recently studied in our laboratory: Trichostatin A (TSA) and its structural analogue 5-(4-dimethylaminobenzoyl)aminovaleric acid hydroxamide (4-Me2N-BAVAH). Phase I biotransformation of TSA, a histone deacetylase inhibitor with promising antifibrotic and antitumoural properties, was investigated in liver microsomal (rat and human) and in hepatocyte (rat) suspensions. Within 40 minutes, 50 microM of TSA was completely metabolised by 2 x 10(6) hepatocytes/ml. Reduction of the hydroxamic acid function to its corresponding amide and N-demethylation were the two major phase I biotransformation pathways, while hydrolysis products of TSA were minor metabolites. Lower concentrations of TSA (5 microM and 25 microM) were N-demethylated faster. Liver microsomes, however, metabolised TSA incompletely with the formation of two major metabolites, N-mono- and N-didemethylated TSA. Unlike TSA, 4-Me2N-BAVAH (50 microM) could still be detected after 3 hours of incubation with 2 x 10(6) rat hepatocytes/ml suspension. Hydrolysis and reduction of the hydroxamic acid function to its corresponding acid and amide, respectively, were shown to be the major phase I biotransformation pathways. Lower concentrations of 4-Me2N-BAVAH were hydrolysed more readily. 4-Me2N-BAVAH and its metabolites were less subjected to N-demethylation than TSA.
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Affiliation(s)
- Greetje Elaut
- Department of Toxicology, Vrije Universiteit Brussel, Brussels, Belgium.
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Synthesis and evaluation of N⁸-acetylspermidine analogues as inhibitors of bacterial acetylpolyamine amidohydrolase. Bioorg Med Chem 2013; 21:4530-40. [PMID: 23790721 DOI: 10.1016/j.bmc.2013.05.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/14/2013] [Accepted: 05/18/2013] [Indexed: 12/23/2022]
Abstract
Polyamines are small essential polycations involved in many biological processes. Enzymes of polyamine metabolism have been extensively studied and are attractive drug targets. Nevertheless, the reversible acetylation of polyamines remains poorly understood. Although eukaryotic N(8)-acetylspermidine deacetylase activity has already been detected and studied, the specific enzyme responsible for this activity has not yet been identified. However, a zinc deacetylase from Mycoplana ramosa, acetylpolyamine amidohydrolase (APAH), has been reported to use various acetylpolyamines as substrates. The recently solved crystal structure of this polyamine deacetylase revealed the formation of an 'L'-shaped active site tunnel at the dimer interface, with ideal dimensions and electrostatic properties for accommodating narrow, flexible, cationic polyamine substrates. Here, we report the design, synthesis, and evaluation of N(8)-acetylspermidine analogues bearing different zinc binding groups as potential inhibitors of APAH. Most of the synthesized compounds exhibit modest potency, with IC₅₀ values in the mid-micromolar range, but compounds bearing hydroxamate or trifluoromethylketone zinc binding groups exhibit enhanced inhibitory potency in the mid-nanomolar range. These inhibitors will enable future explorations of acetylpolyamine function in both prokaryotes and eukaryotes.
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Kalyaanamoorthy S, Chen YPP. Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:317-28. [DOI: 10.1016/j.bbapap.2012.08.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Amide-based derivatives of β-alanine hydroxamic acid as histone deacetylase inhibitors: Attenuation of potency through resonance effects. Bioorg Med Chem Lett 2012; 22:6200-4. [DOI: 10.1016/j.bmcl.2012.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/23/2012] [Accepted: 08/01/2012] [Indexed: 01/27/2023]
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31
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Banno K, Kisu I, Yanokura M, Masuda K, Ueki A, Kobayashi Y, Susumu N, Aoki D. Epigenetics and genetics in endometrial cancer: new carcinogenic mechanisms and relationship with clinical practice. Epigenomics 2012; 4:147-62. [PMID: 22449187 DOI: 10.2217/epi.12.13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endometrial cancer is the seventh most common cancer worldwide among females. An increased incidence and a younger age of patients are also predicted to occur, and therefore elucidation of the pathological mechanisms is important. However, several aspects of the mechanism of carcinogenesis in the endometrium remain unclear. Associations with genetic mutations of cancer-related genes have been shown, but these do not provide a complete explanation. Therefore, epigenetic mechanisms have been examined. Silencing of genes by DNA hypermethylation, hereditary epimutation of DNA mismatch repair genes and regulation of gene expression by miRNAs may underlie carcinogenesis in endometrial cancer. New therapies include targeting epigenetic changes using histone deacetylase inhibitors. Some cases of endometrial cancer may also be hereditary. Thus, patients with Lynch syndrome which is a hereditary disease, have a higher risk for developing endometrial cancer than the general population. Identification of such disease-related genes may contribute to early detection and prevention of endometrial cancer.
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Affiliation(s)
- Kouji Banno
- Department of Obstetrics & Gynecology, School of Medicine, Keio University, Shinanomachi 35 Shinjuku-ku, Tokyo 160-8582, Japan.
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32
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Li X, Liu JL, Yang XH, Lu X, Zhao TT, Gong HB, Zhu HL. Synthesis, biological evaluation and molecular docking studies of 3-(1,3-diphenyl-1H-pyrazol-4-yl)-N-phenylacrylamide derivatives as inhibitors of HDAC activity. Bioorg Med Chem 2012; 20:4430-6. [DOI: 10.1016/j.bmc.2012.05.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/14/2012] [Accepted: 05/14/2012] [Indexed: 10/28/2022]
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33
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Synthesis of 2-quinolinecarboxamide derivatives as potential HDAC inhibitors. Chem Heterocycl Compd (N Y) 2011. [DOI: 10.1007/s10593-011-0825-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Yeung A, Bhargava RK, Ahn R, Bahna S, Kang NH, Lacoul A, Niles LP. HDAC inhibitor M344 suppresses MCF-7 breast cancer cell proliferation. Biomed Pharmacother 2011; 66:232-6. [PMID: 22436652 DOI: 10.1016/j.biopha.2011.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 06/05/2011] [Indexed: 11/17/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors represent a novel class of drugs that selectively induce cell cycle arrest and apoptosis in transformed cells. This study examined, for the first time, the effects of the relatively new HDAC inhibitor, M344 [4-dimethylamino-N-(6-hydroxycarbamoylhexyl)-benzamide], on the proliferation of MCF-7 breast cancer cells. MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assays revealed significant concentration- and time-dependent decreases in MCF-7 cell proliferation following treatment with M344 (1-100μM). In contrast to the significant induction of p21(waf1/cip1) mRNA expression following treatment with M344 (10μM) for 1 or 3 days, there was a significant decrease in p53 mRNA expression, although p53 protein levels were unchanged. Similar treatment with M344 also induced expression of the pro-apoptotic genes, Puma and Bax, together with the morphological features of apoptosis, in MCF-7 cells. The results of this study reinforce previous findings indicating that HDAC inhibitors are an important group of oncostatic drugs, and show that M344 is a potent suppressor of breast cancer cell proliferation.
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Affiliation(s)
- Angie Yeung
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
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Li X, Kaplun A, Lonardo F, Heath E, Sarkar FH, Irish J, Sakr W, Sheng S. HDAC1 inhibition by maspin abrogates epigenetic silencing of glutathione S-transferase pi in prostate carcinoma cells. Mol Cancer Res 2011; 9:733-45. [PMID: 21622623 PMCID: PMC3612175 DOI: 10.1158/1541-7786.mcr-10-0505] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Both maspin and glutathione S-transferase pi (GSTp) are implicated as tumor suppressors and downregulated in human prostate cancer. It is well established that GSTp downregulation is through DNA methylation-based silencing. We report here that maspin expression in prostate cancer cell line DU145 reversed GSTp DNA methylation, as measured by methylation- specific PCR, MethyLight assay, and bisulfite sequencing. The effect of maspin on GSTp expression was similar to that of the combination of a synthetic histone deacetylase (HDAC) inhibitor and DNA methylation inhibitor 5-aza-2'-deoxycytidine. Maspin expression also led to an increased level of acetylated histone 3, decreased level of methyl transferase, and methyl-CpG-binding domain proteins at the site of demethylated GSTp promoter DNA. Earlier, we have shown that maspin inhibits HDAC1. In PC3 cells, where both maspin and GSTp are expressed at a reduced level, maspin knockdown led to a significant reduction in GSTp expression, whereas dual knockdown of maspin and HDAC1 barely increased the level of GSTp expression. Thus, HDAC1 may play an essential role in cellular response to maspin-mediated GSTp desilencing. Maspin has been shown to increase tumor cell sensitivity to drug-induced apoptosis. Interestingly, GSTp reexpression in the absence of maspin expression perturbation blocked the phosphorylation of histone 2A.X, the induction of hypoxia-induced factor 1α (HIF-1α), and cell death of LNCaP cells under oxidative stress. Because DNA hypermethylation-based silencing may couple with and depend on histone deacetylation, our study suggests that endogenous HDAC inhibition by maspin may prevent pathologic gene silencing in prostate tumor progression.
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Affiliation(s)
- Xiaohua Li
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Alexander Kaplun
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Fulvio Lonardo
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Elisabeth Heath
- Department of Internal Medicine, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Fazlul H. Sarkar
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Jonathan Irish
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Wael Sakr
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
| | - Shijie Sheng
- Department of Pathology, The Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201
- Address correspondence to: 313-993-4112 (Tel);313-993-4112 (Fax);
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36
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Synergetic effects of DNA demethylation and histone deacetylase inhibition in primary rat hepatocytes. Invest New Drugs 2011; 30:1715-24. [DOI: 10.1007/s10637-011-9659-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 03/15/2011] [Indexed: 12/16/2022]
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Preservation of hepatocellular functionality in cultures of primary rat hepatocytes upon exposure to 4-Me2N-BAVAH, a hydroxamate-based HDAC-inhibitor. Toxicol In Vitro 2010; 25:100-9. [PMID: 20932894 DOI: 10.1016/j.tiv.2010.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/25/2010] [Accepted: 09/27/2010] [Indexed: 01/27/2023]
Abstract
Great efforts are being put in the development/optimization of reliable and highly predictive models for high-throughput screening of efficacy and toxicity of promising drug candidates. The use of primary hepatocyte cultures, however, is still limited by the occurrence of phenotypic alterations, including loss of xenobiotic biotransformation capacity. In the present study, the differentiation-stabilizing effect of a new histone deacetylase inhibitor 5-(4-dimethylaminobenzoyl)-aminovaleric acid hydroxamide (4-Me(2)N-BAVAH), a structural Trichostatin A (TSA)-analogue with a more favourable pharmaco-toxicological profile, was studied at a genome-wide scale by means of microarray analysis. Several genes coding for xenobiotic biotransformation enzymes were found to be positively regulated upon exposure to 4-Me(2)N-BAVAH. For CYP1A1/2B1/3A2, these observations were confirmed by qRT-PCR and immunoblot analysis. In addition, significantly higher 7-ethoxyresorufin-O-deethylase and 7-pentoxyresorufin-O-dealkylase activity levels were measured. These effects were accompanied by an increased expression of CCAAT/enhancer binding protein alpha and hepatic nuclear factor (HNF)4α, but not of HNF1α. Finally, 4-Me(2)N-BAVAH was found to induce histone H3 acetylation at the proximal promoter of the albumin, CYP1A1 and CYP2B1 genes, suggesting that chromatin remodelling is directly involved in the transcriptional regulation of these genes. In conclusion, histone deacetylase inhibitors prove to be efficient agents for better maintaining a differentiated hepatic phenotype in rat hepatocyte cultures.
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38
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Casagrande M, Basilico N, Rusconi C, Taramelli D, Sparatore A. Synthesis, antimalarial activity, and cellular toxicity of new arylpyrrolylaminoquinolines. Bioorg Med Chem 2010; 18:6625-33. [PMID: 20797868 DOI: 10.1016/j.bmc.2010.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/29/2010] [Accepted: 08/02/2010] [Indexed: 10/19/2022]
Abstract
A set of nine new arylpyrrolyl derivatives of 7-chloro-4-aminoquinoline, characterized by different substituents on the phenyl ring or different distance between the pyrrolic nitrogen and the 4-aminoquinoline, has been synthesized and tested for their activity against D-10 (CQ-S) and W-2 (CQ-R) strains of Plasmodium falciparum. All compounds exhibited activity against the CQ-S strain in the low nM range, comparable to that of chloroquine. Some of them were also highly active against the CQ-R strain and not toxic against normal cells. The antimalarial activity of this new class of compounds seems to be related to the inhibition of heme detoxification process of parasites, as in the case of chloroquine.
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Affiliation(s)
- Manolo Casagrande
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Università degli Studi di Milano, Via Mangiagalli, 25, 20133 Milan, Italy
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39
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Dowling DP, Gattis SG, Fierke CA, Christianson DW. Structures of metal-substituted human histone deacetylase 8 provide mechanistic inferences on biological function . Biochemistry 2010; 49:5048-56. [PMID: 20545365 DOI: 10.1021/bi1005046] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The metal-dependent histone deacetylases (HDACs) adopt an alpha/beta protein fold first identified in rat liver arginase. Despite insignificant overall amino acid sequence identity, these enzymes share a strictly conserved metal binding site with divergent metal specificity and stoichiometry. HDAC8, originally thought to be a Zn(2+)-metallohydrolase, exhibits increased activity with Co(2+) and Fe(2+) cofactors based on k(cat)/K(M) (Gantt, S. L., Gattis, S. G., and Fierke, C. A. (2006) Biochemistry 45, 6170-6178). Here, we report the first X-ray crystal structures of metallo-substituted HDAC8, Co(2+)-HDAC8, D101L Co(2+)-HDAC8, D101L Mn(2+)-HDAC8, and D101L Fe(2+)-HDAC8, each complexed with the inhibitor M344. Metal content of protein samples in solution is confirmed by inductively coupled plasma mass spectrometry. For the crystalline enzymes, peaks in Bijvoet difference Fourier maps calculated from X-ray diffraction data collected near the respective elemental absorption edges confirm metal substitution. Additional solution studies confirm incorporation of Cu(2+); Fe(3+) and Ni(2+) do not bind under conditions tested. The metal dependence of the substrate K(M) values and the K(i) values of hydroxamate inhibitors that chelate the active site metal are consistent with substrate-metal coordination in the precatalytic Michaelis complex that enhances catalysis. Additionally, although HDAC8 binds Zn(2+) nearly 10(6)-fold more tightly than Fe(2+), the affinities for both metal ions are comparable to the readily exchangeable metal concentrations estimated in living cells, suggesting that HDAC8 could bind either or both Fe(2+) or Zn(2+) in vivo.
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Affiliation(s)
- Daniel P Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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40
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Wang H, Lim ZY, Zhou Y, Ng M, Lu T, Lee K, Sangthongpitag K, Goh KC, Wang X, Wu X, Khng HH, Goh SK, Ong WC, Bonday Z, Sun ET. Acylurea connected straight chain hydroxamates as novel histone deacetylase inhibitors: Synthesis, SAR, and in vivo antitumor activity. Bioorg Med Chem Lett 2010; 20:3314-21. [DOI: 10.1016/j.bmcl.2010.04.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/01/2010] [Accepted: 04/10/2010] [Indexed: 10/19/2022]
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41
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Salmi-Smail C, Fabre A, Dequiedt F, Restouin A, Castellano R, Garbit S, Roche P, Morelli X, Brunel JM, Collette Y. Modified cap group suberoylanilide hydroxamic acid histone deacetylase inhibitor derivatives reveal improved selective antileukemic activity. J Med Chem 2010; 53:3038-47. [PMID: 20218673 DOI: 10.1021/jm901358y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of SAHA cap derivatives was designed and prepared in good-to-excellent yields that varied from 49% to 95%. These derivatives were evaluated for their antiproliferative activity in several human cancer cell lines. Antiproliferative activity was observed for concentrations varying from 0.12 to >100 microM, and a molecular modeling approach of selected SAHA derivatives, based on available structural information of human HDAC8 in complex with SAHA, was performed. Strikingly, two compounds displayed up to 10-fold improved antileukemic activity with respect to SAHA; however, these compounds displayed antiproliferative activity similar to SAHA when assayed against solid tumor-derived cell lines. A 10-fold improvement in the leukemic vs peripheral blood mononuclear cell therapeutic ratio, with no evident in vivo toxicity toward blood cells, was also observed. The herein-described compounds and method of synthesis will provide invaluable tools to investigate the molecular mechanism responsible for the reported selectively improved antileukemic activity.
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Affiliation(s)
- Chanaz Salmi-Smail
- Unite 891 INSERM, Centre de Recherche en Cancerologie de Marseille, 27 Bd Lei Roure, 13009 Marseille 09, France
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42
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Identification of type-specific anticancer histone deacetylase inhibitors: road to success. Cancer Chemother Pharmacol 2010; 66:625-33. [DOI: 10.1007/s00280-010-1324-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 04/01/2010] [Indexed: 10/19/2022]
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Pontiki E, Hadjipavlou-Litina D. Histone deacetylase inhibitors (HDACIs). Structure--activity relationships: history and new QSAR perspectives. Med Res Rev 2010; 32:1-165. [PMID: 20162725 DOI: 10.1002/med.20200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Histone deacetylase (HDAC) inhibition is a recent, clinically validated therapeutic strategy for cancer treatment. HDAC inhibitors (HDACIs) block angiogenesis, arrest cell growth, and lead to differentiation and apoptosis in tumor cells. In this article, a survey of published quantitative structure-activity relationships (QSARs) studies are presented and discussed in the hope of identifying the structural determinants for anticancer activity. Secondly a two-dimensional QSAR study was carried out on biological results derived from various types of HDACIs and from different assays using the C-QSAR program of Biobyte. The QSAR analysis presented here is an attempt to organize the knowledge on the HDACIs with the purpose of designing new chemical entities with enhanced inhibitory potencies and to study the mechanism of action of the compounds. This study revealed that lipophilicity is one of the most important determinants of activity. Additionally, steric factors such as the overall molar refractivity (CMR), molar volume (MgVol), the substituent's molar refractivity (MR) (linear or parabola), or the sterimol parameters B(1) and L are important. Electronic parameters indicated as σ(p), are found to be present only in one case.
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Affiliation(s)
- Eleni Pontiki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotelian University of Thessaloniki, Thessaloniki 54124, Greece.
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44
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Preclinical studies of chemotherapy using histone deacetylase inhibitors in endometrial cancer. Obstet Gynecol Int 2010; 2010:923824. [PMID: 20169171 PMCID: PMC2821626 DOI: 10.1155/2010/923824] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 11/23/2009] [Accepted: 01/14/2010] [Indexed: 11/29/2022] Open
Abstract
Because epigenetic alterations are believed to be involved in the repression of tumor suppressor genes and promotion of tumorigenesis in endometrial cancers, novel compounds endowed with a histone deacetylase (HDAC) inhibitory activity are an attractive therapeutic approach. In this review, we discuss the biologic and therapeutic effects of HDAC inhibitors (HDACIs) in treating endometrial cancer. HDACIs were able to mediate inhibition of cell growth, cell cycle arrest, apoptosis, and the expression of genes related to the malignant phenotype in a variety of endometrial cancer cell lines. Furthermore, HDACIs were able to induce the accumulation of acetylated histones in the chromatin of the p21WAF1 gene in human endometrial carcinoma cells. In xenograft models, some HDACIs have demonstrated antitumor activity with only few side effects. In this review, we discuss the biologic and therapeutic effects of HDACIs in treating endometrial cancer, with a special focus on preclinical studies.
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45
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Zhu Y, Li HF, Lu S, Zheng YX, Wu Z, Tang WF, Zhou X, Lu T. Investigation on the isoform selectivity of histone deacetylase inhibitors using chemical feature based pharmacophore and docking approaches. Eur J Med Chem 2010; 45:1777-91. [PMID: 20153566 DOI: 10.1016/j.ejmech.2010.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 01/03/2010] [Accepted: 01/06/2010] [Indexed: 11/16/2022]
Abstract
A three dimensional (3D) chemical feature based pharmacophore model was developed for selective histone deacetylase 1 (HDAC1) inhibitors, which provides an efficient way to discuss the isoform selectivity of HDAC inhibitors. In contrast to the classical pan-HDAC pharmacophore, two hydrophobic features (HY and HYAr2) were found in the chemical feature based pharmacophore model, which might be responsible for the selectivity of HDAC1 inhibitions. Molecular docking also highlighted the two hydrophobic features, which are located in the internal cavity adjacent to the active site. The results contribute to our understanding of the molecular mechanism underlying the selectivity of HDAC1 inhibitors and suggest a possible target region to design novel selective HDAC1 inhibitors.
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Affiliation(s)
- Yong Zhu
- Department of Organic Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
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46
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A rationally designed histone deacetylase inhibitor with distinct antitumor activity against ovarian cancer. Neoplasia 2009; 11:552-63, 3 p following 563. [PMID: 19484144 DOI: 10.1593/neo.09204] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 12/26/2022] Open
Abstract
Histone deacetylase inhibitors (HDACIs) are a class of antineoplastic agents previously demonstrating preclinical chemosensitizing activity against drug-resistant cancer cells and mouse xenografts. However, whereas clinical studies have shown efficacy against human hematologic malignancies, solid tumor trials have proved disappointing. We previously developed a novel HDACI, "OSU-HDAC42," and herein examine its activity against ovarian cancer cell lines and xenografts. OSU-HDAC42, (i) unlike most HDACIs, elicited a more than five-fold increase in G(2)-phase cells, at 2.5 microM, with G(2) arrest followed by apoptosis; (ii) at 1.0 microM, completely repressed messenger RNA expression of the cell cycle progression gene cdc2; (iii) at low doses (0.25-1.0 microM for 24 hours), induced tumor cell epithelial differentiation, as evidenced by morphology changes and a more than five-fold up-regulation of epithelium-specific cytokeratins; (iv) potently abrogated the growth of numerous ovarian cancer cells, with IC(50) values of 0.5 to 1.0 microM, whereas also remaining eight-fold less toxic (IC(50) of 8.6 microM) to normal ovarian surface epithelial cells; and (v) chemosensitizated platinum-resistant mouse xenografts to cisplatin. Compared with the clinically approved HDACI suberoylanilide hydroxamic acid (vorinostat), 1.0 microM OSU-HDAC42 was more biochemically potent (i.e., enzyme-inhibitory), as suggested by greater gene up-regulation and acetylation of both histone and nonhistone proteins. In p53-dysfunctional cells, however, OSU-HDAC42 was two- to eight-fold less inductive of p53-regulated genes, whereas also having a two-fold higher IC(50) than p53-functional cells, demonstrating some interaction with p53 tumor-suppressive cascades. These findings establish OSU-HDAC42 as a promising therapeutic agent for drug-resistant ovarian cancer and justify its further investigation.
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47
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Li X, Chen BD. Histone Deacetylase Inhibitor M344 Inhibits Cell Proliferation and Induces Apoptosis in Human THP-1 Leukemia Cells. ACTA ACUST UNITED AC 2009; 1:352-363. [PMID: 20526416 DOI: 10.5099/aj090400352] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Histone acetylation plays an important role in the silencing and activation of genes involved in tumoregenesis. Trichostatin A, originally identified as an anti-fungal drug, is a potent inhibitor of histone deacetylase (HDAC) with potential anti-tumor activity. In this study, we investigated the effect of M344, an amide analogues of trichostatin A, on the growth and differentiation of THP-1 human leukemia cells. We showed that at low doses, (< 0.2 muM), M344 could inhibit the growth of THP-1 cells at G1 phase in vitro with low cytotoxic effect. Low dose of M344 exerted some differentiating effect on THP-1 cells as judged by the expression of c-fms proto-oncogene (M-CSF receptor) and appearance of adherent cells. Growth arrest induced by M344 is associated with increased levels of cyclin-dependent protein kinase inhibitor p21 and cyclin E, in agreement with G1 phase arrest. At higher doses (2 muM), M344 could induce THP-1 cells to undergo apoptosis, which was associated with the cleavage of PARP, cytochrome c release and activation of both caspases-8, -9, followed by the activation of caspase-3. In addition, M344 could increase the levels of pro-apoptotic protein Bax but decreased the levels of anti-apoptotic protein XIAP. M344 is a potent activator of NF-kappaB transcription factor. RT-PCR assay showed that the M344 could transiently increase IL-1 expression yet markedly decreased TNF-alpha expression. Our results show that M344 is a potent growth inhibitor and inducer of apoptosis in human leukemia cells and suggest potential therapeutic strategies of HDAC inhibitors for patients with leukemias.
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Affiliation(s)
- Xiaohua Li
- Department of Internal medicine and Karmanos Cancer Institute, Wayne State University School of Medicine, 550 E. Canfield, Detroit, MI 48201
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48
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Cragg GM, Grothaus PG, Newman DJ. Impact of natural products on developing new anti-cancer agents. Chem Rev 2009; 109:3012-43. [PMID: 19422222 DOI: 10.1021/cr900019j] [Citation(s) in RCA: 887] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gordon M Cragg
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, NCI-Frederick, Fairview Center, Suite 206, P.O. Box B, Frederick, Maryland 21702-1201, USA
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49
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Konsoula Z, Cao H, Velena A, Jung M. Pharmacokinetics-pharmacodynamics and antitumor activity of mercaptoacetamide-based histone deacetylase inhibitors. Mol Cancer Ther 2009; 8:2844-51. [PMID: 19789216 DOI: 10.1158/1535-7163.mct-09-0629] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Structurally diverse histone deacetylase inhibitors (HDACI) have emerged as chemotherapeutic agents. Here, we report the first mercaptoacetamide HDACIs (coded 6MAQH and 5MABMA) for use in treatment against prostate cancer cells in vitro and in vivo and correlate their plasma pharmacokinetics and tissue-pharmacodynamics with tumor sensitivity. HDACIs were assessed for in vitro microsomal stability and growth inhibition against prostate cancer and nonmalignant cells. Antitumor activity was determined following i.p. administration of 6MAQH and 5MABMA (0.5 and 5 mg/Kg) using mice bearing PC3 tumor xenografts (n = 10). The plasma pharmacokinetics of 6MAQH and 5MABMA and their effects on the acetylation of histone H4 in tissues were determined in athymic mice. Both HDACIs significantly inhibited the growth of cancer cells while exerting limited effect on nonmalignant cells. They exhibited stability in human, dog, and rat microsomes [t(1/2 (min)) = 83, 72, and 66 for 6MAQH and 68, 43, and 70 for 5MABMA, respectively]. Both HDACIs (0.5 mg/Kg) led to tumor regression (P < 0.01), which was sustained for at least 60 days. In vivo data show favorable plasma pharmacokinetics with the area under the curve of 4.97 +/- 0.6 micromol/L x h for 6MAQH and 4.23 +/- 0.43 micromol/L x h for 5MABMA. The clearance rates for 6MAQH and 5MABMA were 4.05 +/- 0.15 and 4.87 +/- 0.2 L/h, whereas the half-lives were 2.2 +/- 0.33 and 1.98 +/- 0.21 h, respectively. Both HDACIs markedly enhanced the acetylation of histone H4 within 30 minutes in tissues, including the brain, liver, and spleen. Taken together, the results provide a rationale for further investigation of these mercaptoacetamide HDACIs as potent anticancer agents.
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Affiliation(s)
- Zacharoula Konsoula
- Division of Radiation Biology, Department of Radiation Medicine, The Research Building, Room E-211, Georgetown University School of Medicine, Box 571482, 3970 Reservoir Road, Northwest, Washington, DC 20057-1482, USA
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50
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Tang H, Wang XS, Huang XP, Roth BL, Butler KV, Kozikowski AP, Jung M, Tropsha A. Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. J Chem Inf Model 2009; 49:461-76. [DOI: 10.1021/ci800366f] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hao Tang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Xiang S. Wang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Xi-Ping Huang
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Bryan L. Roth
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Kyle V. Butler
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Alan P. Kozikowski
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Mira Jung
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, and Carolina Exploratory Center for Cheminformatics Research, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, Biophysics Training Program, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 833 South Wood Street, Chicago, Illinois 60612, and Department of Radiation Medicine, Georgetown University Medical
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