1
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Ripa L, Sandmark J, Hughes G, Shamovsky I, Gunnarsson A, Johansson J, Llinas A, Collins M, Jung B, Novén A, Pemberton N, Mogemark M, Xiong Y, Li Q, Tångefjord S, Ek M, Åstrand A. Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism. J Med Chem 2023; 66:14188-14207. [PMID: 37797307 DOI: 10.1021/acs.jmedchem.3c01269] [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: 10/07/2023]
Abstract
Histone deacetylase 6 (HDAC6) is a unique member of the HDAC family mainly targeting cytosolic nonhistone substrates, such as α-tubulin, cortactin, and heat shock protein 90 to regulate cell proliferation, metastasis, invasion, and mitosis in tumors. We describe the identification and characterization of a series of 2-(difluoromethyl)-1,3,4-oxadiazoles (DFMOs) as selective nonhydroxamic acid HDAC6 inhibitors. By comparing structure-activity relationships and performing quantum mechanical calculations of the HDAC6 catalytic mechanism, we show that potent oxadiazoles are electrophilic substrates of HDAC6 and propose a mechanism for the bioactivation. We also observe that the inherent electrophilicity of the oxadiazoles makes them prone to degradation in water solution and the generation of potentially toxic products cannot be ruled out, limiting the developability for chronic diseases. However, the oxadiazoles demonstrate high oral bioavailability and low in vivo clearance and are excellent tools for studying the role of HDAC6 in vitro and in vivo in rats and mice.
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Affiliation(s)
- Lena Ripa
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jenny Sandmark
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Glyn Hughes
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Igor Shamovsky
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Julia Johansson
- Clinical Pharmacology and Safety Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Antonio Llinas
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Mia Collins
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Bomi Jung
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Anna Novén
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Nils Pemberton
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Mickael Mogemark
- Clinical Pharmacology and Safety Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Yao Xiong
- Pharmaron Beijing, Co. Ltd., No. 6, Taihe Road, BDA, Beijing 100176, China
| | - Qing Li
- Pharmaron Beijing, Co. Ltd., No. 6, Taihe Road, BDA, Beijing 100176, China
| | - Stefan Tångefjord
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Margareta Ek
- Discovery Sciences, Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Annika Åstrand
- Respiratory & Immunology (R&I), Research and Early Development, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
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Toro TB, Skripnikova EV, Bornes KE, Zhang K, Watt TJ. Endogenous expression of inactive lysine deacetylases reveals deacetylation-dependent cellular mechanisms. PLoS One 2023; 18:e0291779. [PMID: 37721967 PMCID: PMC10506724 DOI: 10.1371/journal.pone.0291779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
Acetylation of lysine residues is an important and common post-translational regulatory mechanism occurring on thousands of non-histone proteins. Lysine deacetylases (KDACs or HDACs) are a family of enzymes responsible for removing acetylation. To identify the biological mechanisms regulated by individual KDACs, we created HT1080 cell lines containing chromosomal point mutations, which endogenously express either KDAC6 or KDAC8 having single inactivated catalytic domain. Engineered HT1080 cells expressing inactive KDA6 or KDAC8 domains remained viable and exhibited enhanced acetylation on known substrate proteins. RNA-seq analysis revealed that many changes in gene expression were observed when KDACs were inactivated, and that these gene sets differed significantly from knockdown and knockout cell lines. Using GO ontology, we identified several critical biological processes associated specifically with catalytic activity and others attributable to non-catalytic interactions. Treatment of wild-type cells with KDAC-specific inhibitors Tubastatin A and PCI-34051 resulted in gene expression changes distinct from those of the engineered cell lines, validating this approach as a tool for evaluating in-cell inhibitor specificity and identifying off-target effects of KDAC inhibitors. Probing the functions of specific KDAC domains using these cell lines is not equivalent to doing so using previously existing methods and provides novel insight into the catalytic functions of individual KDACs by investigating the molecular and cellular changes upon genetic inactivation.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Elena V. Skripnikova
- Division of Basic and Pharmaceutical Sciences, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kiara E. Bornes
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Kun Zhang
- Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, United States of America
- Bioinformatics Core, Xavier University of Louisiana, New Orleans, LA, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States of America
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3
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Rajaraman S, Balakrishnan R, Deshmukh D, Ganorkar A, Biswas S, Pulya S, Ghosh B. HDAC8 as an emerging target in drug discovery with special emphasis on medicinal chemistry. Future Med Chem 2023; 15:885-908. [PMID: 37227732 DOI: 10.4155/fmc-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
HDAC8 catalyzes the deacetylation of both histones and nonhistone proteins. The abnormal expression of HDAC8 is associated with various pathological conditions causing cancer and other diseases like myopathies, Cornelia de Lange syndrome, renal fibrosis, and viral and parasitic infections. The substrates of HDAC8 are involved in diverse molecular mechanisms of cancer such as cell proliferation, invasion, metastasis and drug resistance. Based on the crystal structures and the key residues at the active site, HDAC8 inhibitors have been designed along the canonical pharmacophore. This article details the importance, recent advancements, and the structural and functional aspects of HDAC8 with special emphasis on the medicinal chemistry aspect of HDAC8 inhibitors that will help in developing novel epigenetic therapeutics.
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Affiliation(s)
- Srinidhi Rajaraman
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Ranjani Balakrishnan
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Dhruv Deshmukh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Abhiram Ganorkar
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Swati Biswas
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Sravani Pulya
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
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Toro TB, Bornes KE, Watt TJ. Lysine Deacetylase Substrate Selectivity: Distinct Interaction Surfaces Drive Positive and Negative Selection for Residues Following Acetyllysine. Biochemistry 2023; 62:1464-1483. [PMID: 37043688 PMCID: PMC10157890 DOI: 10.1021/acs.biochem.3c00001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Lysine acetylation is a post-translational modification that is reversed by lysine deacetylases (KDACs). The goal of this work was to identify determinants of substrate specificity for KDACs, focusing on short-range interactions occurring with residues immediately following the acetyllysine. Using a fluorescence-based in vitro assay, we determined the activity for each enzyme with a limited panel of derivative substrate peptides, revealing a distinct reactivity profile for each enzyme. We mapped the interaction surface for KDAC6, KDAC8, and KDAC1 with the +1 and +2 substrate residues (with respect to acetyllysine) based on enzyme-substrate interaction pairs observed in molecular dynamics simulations. Characteristic residues in each KDAC interact preferentially with particular substrate residues and correlate with either enhanced or inhibited activity. Although nonpolar aromatic residues generally enhanced activity with all KDACs, the manner in which each enzyme interacted with these residues is distinct. Furthermore, each KDAC has distinctive interactions that correlate with lower activity, primarily ionic in nature. KDAC8 exhibited the most diverse and widest range of effects, while KDAC6 was sensitive only to the +1 position and KDAC1 selectivity was primarily driven by negative selection. The substrate preferences were validated for KDAC6 and KDAC8 using a set of peptides derived from known acetylated proteins. Overall, we determined how KDAC6, KDAC8, and KDAC1 achieve substrate specificity with residues following the acetyllysine. These new insights into KDAC specificity will be critical for identifying novel substrates of particular KDACs, designing KDAC-specific inhibitors, and demonstrate a general framework for understanding substrate specificity for other enzyme classes.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Kiara E Bornes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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5
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Toro TB, Swanier JS, Bezue JA, Broussard CG, Watt TJ. Lysine Deacetylase Substrate Selectivity: A Dynamic Ionic Interaction Specific to KDAC8. Biochemistry 2021; 60:2524-2536. [PMID: 34357750 DOI: 10.1021/acs.biochem.1c00384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lysine acetylation and deacetylation are critical for regulation of many cellular proteins. Despite the importance of this cycle, it is unclear how lysine deacetylase (KDAC) family members discriminate between acetylated proteins to react with a discrete set of substrates. Potential short-range interactions between KDAC8 and a known biologically relevant peptide substrate were identified using molecular dynamics (MD) simulations. Activity assays with a panel of peptides derived from this substrate supported a putative ionic interaction between arginine at the -1 substrate position and KDAC8 D101. Additional assays and MD simulations confirmed this novel interaction, which promotes deacetylation of substrates. Verification that a negatively charged residue at the 101 position is necessary for the ionic interaction and observed reactivity with the substrates was performed using KDAC8 derivatives. Notably, this interaction is specific to KDAC8, as KDAC1 and KDAC6 do not form this interaction and each KDAC has a different specificity profile with the peptide substrates, even though all KDACs could potentially form ionic interactions. When reacted with a panel of putative human KDAC substrates, KDAC8 preferentially deacetylated substrates containing an arginine at the -1 position. KDAC8 D101-R(-1) is a specific enzyme-substrate interaction that begins to explain how KDACs discriminate between potential substrates and how different KDAC family members can react with different subsets of acetylated proteins in cells. This multi-pronged approach will be extended to identify other critical interactions for KDAC8 substrate binding and determine critical interactions for other KDACs.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Jordan S Swanier
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Jada A Bezue
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Christian G Broussard
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125-1098, United States
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Shukla VK, Siemons L, Gervasio FL, Hansen DF. Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8. Chem Sci 2021; 12:9318-9327. [PMID: 34349901 PMCID: PMC8278956 DOI: 10.1039/d1sc01929e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and an important drug-target. High-resolution structures of HDAC8 in complex with substrates or inhibitors are available, which have provided insights into the bound state of HDAC8 and its function. Here, using long all-atom unbiased molecular dynamics simulations and Markov state modelling, we show a strong correlation between the conformation of aromatic side chains near the active site and opening and closing of the surrounding functional loops of HDAC8. We also investigated two mutants known to allosterically downregulate the enzymatic activity of HDAC8. Based on experimental data, we hypothesise that I19S-HDAC8 is unable to release the product, whereas both product release and substrate binding are impaired in the S39E-HDAC8 mutant. The presented results deliver detailed insights into the functional dynamics of HDAC8 and provide a mechanism for the substantial downregulation caused by allosteric mutations, including a disease causing one.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
| | - Lucas Siemons
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
| | - Francesco L Gervasio
- Department of Chemistry, University College London London WC1E 6BT UK
- Pharmaceutical Sciences, University of Geneva Geneva CH-1211 Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva Geneva CH-1211 Switzerland
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London London WC1E 6BT UK
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Fragment-Based Drug Design of Selective HDAC6 Inhibitors. Methods Mol Biol 2021; 2266:155-170. [PMID: 33759126 DOI: 10.1007/978-1-0716-1209-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Medicinal chemistry society has enough arguments to justify the usage of fragment-based drug design (FBDD) methodologies for the identification of lead compounds. Since the FDA approval of three kinase inhibitors - vemurafenib, venetoclax, and erdafitinib, FBDD has become a challenging alternative to high-throughput screening methods in drug discovery. The following protocol presents in silico drug design of selective histone deacetylase 6 (HDAC6) inhibitors through a fragment-based approach. To date, structural motifs that are important for HDAC inhibitory activity and selectivity are described as: surface recognition group (CAP group), aliphatic or aromatic linker, and zinc-binding group (ZBG). The main idea of this FBDD method is to identify novel and target-selective CAP groups by virtual scanning of publicly available fragment databases. Template structure used to search for novel heterocyclic and carbocyclic fragments is 1,8-naphthalimide (CAP group of scriptaid, a potent HDAC inhibitor). Herein, the design of HDAC6 inhibitors is based on linking the identified fragments with the aliphatic or aromatic linker and hydroxamic acid (ZBG) moiety. Final selection of potential selective HDAC6 inhibitors is based on combined structure-based (molecular docking) and ligand-based (three-dimensional quantitative structure-activity relationships, 3D-QSAR) techniques. Designed compounds are docked in the active site pockets of human HDAC1 and HDAC6 isoforms, and their docking conformations used to predict their HDAC inhibitory and selectivity profiles through two developed 3D-QSAR models (describing HDAC1 and HDAC6 inhibitory activities).
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Smalley JP, Cowley SM, Hodgkinson JT. Bifunctional HDAC Therapeutics: One Drug to Rule Them All? Molecules 2020; 25:E4394. [PMID: 32987782 PMCID: PMC7583022 DOI: 10.3390/molecules25194394] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylase (HDAC) enzymes play crucial roles in epigenetic gene expression and are an attractive therapeutic target. Five HDAC inhibitors have been approved for cancer treatment to date, however, clinical applications have been limited due to poor single-agent drug efficacy and side effects associated with a lack of HDAC isoform or complex selectivity. An emerging strategy aiming to address these limitations is the development of bifunctional HDAC therapeutics-single molecules comprising a HDAC inhibitor conjugated to another specificity targeting moiety. This review summarises the recent advancements in novel types of dual-targeting HDAC modulators, including proteolysis-targeting chimeras (PROTACs), with a focus on HDAC isoform and complex selectivity, and the future potential of such bifunctional molecules in achieving enhanced drug efficacy and therapeutic benefits in treating disease.
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Affiliation(s)
- Joshua P. Smalley
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, George Porter Building, University Road, Leicester LE1 7RH, UK;
| | - Shaun M. Cowley
- Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK;
| | - James T. Hodgkinson
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, George Porter Building, University Road, Leicester LE1 7RH, UK;
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Toro TB, Watt TJ. Critical review of non-histone human substrates of metal-dependent lysine deacetylases. FASEB J 2020; 34:13140-13155. [PMID: 32862458 DOI: 10.1096/fj.202001301rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal-dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large-scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC-substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non-catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell-based experimental strategies used to identify KDAC-substrate pairs and evaluate each for the purpose of directly identifying non-histone substrates of metal-dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non-histone substrate-KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well-established, while another thirteen pairs have both cell-based and in vitro evidence but lack independent replication and/or sufficient cell-based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
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Zhang M, Ying JB, Wang SS, He D, Zhu H, Zhang C, Tang L, Lin R, Zhang Y. Exploring the binding mechanism of HDAC8 selective inhibitors: Lessons from the modification of Cap group. J Cell Biochem 2020; 121:3162-3172. [DOI: 10.1002/jcb.29583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Min Zhang
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
- Gansu Health Center HospitalLanzhou China
| | - Jun Biao Ying
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
- College of Pharmaceutical SciencesZhejiang UniversityHangzhou China
| | - Song Song Wang
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
- The Second Hospital of Hebei Medical UniversityShijiazhuang China
| | - Dian He
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
- Gansu Health Center HospitalLanzhou China
| | - Hongtian Zhu
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
| | - Chenghong Zhang
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
| | - Lei Tang
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
| | - Ruili Lin
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
| | - Yang Zhang
- Materia Medica Development Group, Institute of Medicinal ChemistryLanzhou University School of PharmacyLanzhou China
- School of Pharmaceutical SciencesChongqing UniversityChongqing China
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Multitarget Anticancer Agents Based on Histone Deacetylase and Protein Kinase CK2 inhibitors. Molecules 2020; 25:molecules25071497. [PMID: 32218358 PMCID: PMC7180456 DOI: 10.3390/molecules25071497] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
The design of multitarget drugs (MTDs) has become an innovative approach for the search of effective treatments in complex diseases such as cancer. In this work, we communicate our efforts in the design of multi-targeting histone deacetylase (HDAC) and protein kinase CK2 inhibitors as a novel therapeutic strategy against cancer. Using tetrabromobenzotriazole (TBB) and 2-dimethylamino-4,5,6,7-tetrabromo-benzimidazole (DMAT) as scaffolds for CK2 inhibition, and a hydroxamate to coordinate the zinc atom present in the active site of HDAC (zinc binding group, ZBG), new multitarget inhibitors have been designed and synthesized. According to the in vitro assays, N-Hydroxy-6-(4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzo[d]imidazol-1-yl)hexanamide (11b) is the most interesting compound, with IC50 values of 0.66; 1.46 and 3.67 µM. for HDAC6; HDAC1 and CK2; respectively. Cellular assays on different cancer cell lines rendered promising results for N-Hydroxy-8-(4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzo[d]imidazol-1-yl)octanamide (11d). This inhibitor presented the highest cytotoxic activity, proapoptotic capability, and the best mitochondria-targeting and multidrug-circumventing properties, thus being the most promising drug candidate for further in vivo studies.
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de Sena M. Pinheiro P, Rodrigues DA, do Couto Maia R, Thota S, Fraga CA. The Use of Conformational Restriction in Medicinal Chemistry. Curr Top Med Chem 2019; 19:1712-1733. [DOI: 10.2174/1568026619666190712205025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/01/2019] [Accepted: 05/05/2019] [Indexed: 12/13/2022]
Abstract
During the early preclinical phase, from hit identification and optimization to a lead compound,
several medicinal chemistry strategies can be used to improve potency and/or selectivity. The
conformational restriction is one of these approaches. It consists of introducing some specific structural
constraints in a lead candidate to reduce the overall number of possible conformations in order to favor
the adoption of a bioactive conformation and, as a consequence, molecular recognition by the target receptor.
In this work, we focused on the application of the conformational restriction strategy in the last
five years for the optimization of hits and/or leads of several important classes of therapeutic targets in
the drug discovery field. Thus, we recognize the importance of several kinase inhibitors to the current
landscape of drug development for cancer therapy and the use of G-protein Coupled Receptor (GPCR)
modulators. Several other targets are also highlighted, such as the class of epigenetic drugs. Therefore,
the possibility of exploiting conformational restriction as a tool to increase the potency and selectivity
and promote changes in the intrinsic activity of some ligands intended to act on many different targets
makes this strategy of structural modification valuable for the discovery of novel drug candidates.
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Affiliation(s)
- Pedro de Sena M. Pinheiro
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Daniel A. Rodrigues
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Rodolfo do Couto Maia
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Sreekanth Thota
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Carlos A.M. Fraga
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902, Rio de Janeiro, RJ, Brazil
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13
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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14
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Gomes ID, Pflum MKH. Optimal Substrate-Trapping Mutants to Discover Substrates of HDAC1. Chembiochem 2019; 20:1444-1449. [PMID: 30701667 DOI: 10.1002/cbic.201800797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 11/11/2022]
Abstract
Histone deacetylase 1 (HDAC1) regulates transcription by deacetylating histones. In addition to histones, several non-histone proteins are HDAC1 substrates, which suggests a role for HDAC1 beyond epigenetics. Unfortunately, the identification of non-histone substrates has been largely serendipitous, which makes full characterization of HDAC1 functions difficult. To overcome this challenge, inactive "trapping" mutants were recently developed to identify HDAC1 substrates. To optimize substrate trapping, the relative trapping abilities of 17 inactive HDAC1 mutants was assessed. HDAC1 H141A, F150A, and C151A showed strong binding to substrates LSD1 and p53. Interestingly, each mutant preferentially trapped a different substrate. By combining several inactive mutants, the trapping strategy will facilitate the discovery of new HDAC1 substrates and shed light on the variety of HDAC1-related functions in cell biology.
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Affiliation(s)
- Inosha D Gomes
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, 48202, USA
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, 48202, USA
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15
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Zhang QC, Li X, Wang X, Li SJ, Qu LB, Lan Y, Wei D. Insights into highly selective ring expansion of oxaziridines under Lewis base catalysis: a DFT study. Org Chem Front 2019. [DOI: 10.1039/c8qo01370e] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The possible mechanism and stereoselectivity of the NHC-catalyzed ring expansion reaction of oxaziridines have been theoretically studied for the first time.
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Affiliation(s)
- Qiao-Chu Zhang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xue Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Xinghua Wang
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Shi-Jun Li
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
| | - Yu Lan
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P.R. China
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16
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Bin B, Lee S, Bhin J, Irié T, Kim S, Seo J, Mishima K, Lee T, Hwang D, Fukada T, Cho E. The epithelial zinc transporter
ZIP
10 epigenetically regulates human epidermal homeostasis by modulating histone acetyltransferase activity. Br J Dermatol 2018; 180:869-880. [DOI: 10.1111/bjd.17339] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Affiliation(s)
- B.‐H. Bin
- Basic Research & Innovation Division AmorePacific R&D Unit Yongin 17014 Republic of Korea
- Department of Biological Sciences Ajou University Suwon 16499Republic of Korea
| | - S.‐H. Lee
- Biosolution Corporation Seoul 01811Republic of Korea
| | - J. Bhin
- Division of Molecular Carcinogenesis the Netherlands Cancer Institute Amsterdam 1066 CXthe Netherlands
| | - T. Irié
- Division of Pathology Department of Oral Diagnostic Sciences School of Dentistry Showa University Tokyo 142‐8666Japan
- Division of Anatomical and Cellular Pathology Department of Pathology Iwate Medical University Iwate 028‐3694Japan
| | - S. Kim
- Biosolution Corporation Seoul 01811Republic of Korea
| | - J. Seo
- Beauty in Longevity Science Research Division AmorePacific R&D Unit Yongin 17014 Republic of Korea
| | - K. Mishima
- Division of Pathology Department of Oral Diagnostic Sciences School of Dentistry Showa University Tokyo 142‐8666Japan
| | - T.R. Lee
- Basic Research & Innovation Division AmorePacific R&D Unit Yongin 17014 Republic of Korea
| | - D. Hwang
- Center for Systems Biology of Plant Senescence and Life History Institute for Basic Science Daegu 42988Republic of Korea
| | - T. Fukada
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Tokushima 770‐8055 Japan
| | - E.‐G. Cho
- Basic Research & Innovation Division AmorePacific R&D Unit Yongin 17014 Republic of Korea
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17
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Li X, Tang M, Wang Y, Wang Y, Li Z, Qu LB, Wei D. Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Intramolecular Cyclization of Aldimines: General Mechanism and Role of Catalyst. Chem Asian J 2018; 13:1710-1718. [PMID: 29667337 DOI: 10.1002/asia.201800313] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/02/2018] [Indexed: 12/14/2022]
Abstract
One of the most challenging questions in the Lewis base organocatalyst field is how to predict the most electrophilic carbon for the complexation of N-heterocyclic carbene (NHC) and reactant. This study provides a valuable case for this issue. Multiple mechanisms (A, B, C, D, and E) for the intramolecular cyclization of aldimine catalyzed by NHC were investigated by using density functional theory (DFT). The computed results reveal that the NHC energetically prefers attacking the iminyl carbon (AIC mode, which is associated with mechanisms A and C) rather than attacking the olefin carbon (AOC mode, which is associated with mechanisms B and D) or attacking the carbonyl carbon (ACC mode, which is associated with mechanism E) of aldimine. The calculated results based on the different reaction models indicate that mechanism A (AIC mode), which is associated with the formation of the aza-Breslow intermediate, is the most favorable pathway. For mechanism A, there are five steps: (1) nucleophilic addition of NHC to the iminyl carbon of aldimine; (2) [1,2]-proton transfer to form an aza-Breslow intermediate; (3) intramolecular cyclization; (4) the other [1,2]-proton transfer; and (5) regeneration of NHC. The analyses of reactivity indexes have been applied to explain the chemoselectivity, and the general principles regarding the possible mechanisms would be useful for the rational design of NHC-catalyzed chemoselective reactions.
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Affiliation(s)
- Xue Li
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Mingsheng Tang
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Yanyan Wang
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Yang Wang
- Department of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 100 Kexue Street, Zhengzhou, Henan, 450002, P. R. China
| | - Zhongjun Li
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Ling-Bo Qu
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering, Zhengzhou University, No. 100 Kexue Street, Zhengzhou, Henan, 450001, P. R. China
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18
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Vanaja GR, Ramulu HG, Kalle AM. Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6. Cell Commun Signal 2018; 16:20. [PMID: 29716651 PMCID: PMC5930436 DOI: 10.1186/s12964-018-0231-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/13/2018] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) are involved in epigenetic gene regulation via deacetylation of acetylated lysine residues of both histone and non-histone proteins. Among the 18 HDACs identified in humans, HDAC8, a class I HDAC, is best understood structurally and enzymatically. However, its precise subcellular location, function in normal cellular physiology, its protein partners and substrates still remain elusive. METHODS The subcellular localization of HDAC8 was studied using immunofluorescence and confocal imaging. The binding parterns were identified employing immunoprecipitation (IP) followed by MALDI-TOF analysis and confirmed using in-silico protein-protein interaction studies, HPLC-based in vitro deacetylation assay, intrinsic fluorescence spectrophotometric analysis, Circular dichroism (CD) and Surface Plasmon Resonance (SPR). Functional characterization of the binding was carried out using immunoblot and knockdown by siRNA. Using one way ANOVA statistical significance (n = 3) was determined. RESULTS Here, we show that HDAC8 and its phosphorylated form (pHDAC8) localized predominantly in the cytoplasm in cancerous, HeLa, and non-cancerous (normal), HEK293T, cells, although nucleolar localization was observed in HeLa cells. The study identified Alpha tubulin as a novel interacting partner of HDAC8. Further, the results indicated binding and deacetylation of tubulin at ac-lys40 by HDAC8. Knockdown of HDAC8 by siRNA, inhibition of HDAC8 and/or HDAC6 by PCI-34051 and tubastatin respectively, cell-migration, cell morphology and cell cycle analysis clearly explained HDAC8 as tubulin deacetylase in HeLa cells and HDAC6 in HEK 293 T cells. CONCLUSIONS HDAC8 shows functional redundancy with HDAC6 when overexpressed in cervical cancer cells, HeLa, and deacetylaes ac-lys40 of alpha tubulin leading to cervical cancer proliferation and progression.
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Affiliation(s)
- G R Vanaja
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, TS, 500046, India
| | | | - Arunasree M Kalle
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, TS, 500046, India.
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19
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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20
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Sixto-López Y, Bello M, Correa-Basurto J. Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking. J Biomol Struct Dyn 2018; 37:584-610. [PMID: 29447615 DOI: 10.1080/07391102.2018.1441072] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K+) in both sites (HDAC1k), a second with K+ only at site 1 (HDAC1ks1), a third with K+ only at site 2 (HDAC1ks2) and a fourth with no K+ (HDAC1wk). We found that the presence or absence of K+ not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.
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Affiliation(s)
- Yudibeth Sixto-López
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
| | - Martiniano Bello
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
| | - José Correa-Basurto
- a Laboratorio de Modelado Molecular, Bioinformática y Diseño de fármacos, Sección de Estudios de Posgrado e Investigación , Escuela Superior de Medicina, Instituto Politécnico Nacional , Mexico City 11340 , Mexico
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21
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Toro TB, Painter RG, Haynes RA, Glotser EY, Bratton MR, Bryant JR, Nichols KA, Matthew-Onabanjo AN, Matthew AN, Bratcher DR, Perry CD, Watt TJ. Purification of metal-dependent lysine deacetylases with consistently high activity. Protein Expr Purif 2018; 141:1-6. [PMID: 28843507 PMCID: PMC5624855 DOI: 10.1016/j.pep.2017.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/28/2017] [Accepted: 08/22/2017] [Indexed: 11/25/2022]
Abstract
Metal-dependent lysine deacetylases (KDACs) are involved in regulation of numerous biological and disease processes through control of post-translational acetylation. Characterization of KDAC activity and substrate identification is complicated by inconsistent activity of prepared enzyme and a range of multi-step purifications. We describe a simplified protocol based on two-step affinity chromatography. The purification method is appropriate for use regardless of expression host, and we demonstrate purification of several representative members of the KDAC family as well as a selection of mutated variants. The purified proteins are highly active and consistent across preparations.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Richard G Painter
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Rashad A Haynes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Elena Y Glotser
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Melyssa R Bratton
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Jenae R Bryant
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Kyara A Nichols
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Asia N Matthew-Onabanjo
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Ashley N Matthew
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Derek R Bratcher
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Chanel D Perry
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
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22
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Toro TB, Edenfield SA, Hylton BJ, Watt TJ. Chelatable trace zinc causes low, irreproducible KDAC8 activity. Anal Biochem 2018; 540-541:9-14. [PMID: 29100752 PMCID: PMC5712482 DOI: 10.1016/j.ab.2017.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/09/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022]
Abstract
Acetylation is an important regulatory mechanism in cells, and emphasis is being placed on identifying substrates and small molecule modulators of this post-translational modification. However, the reported in vitro activity of the lysine deacetylase KDAC8 is inconsistent across experimental setups, even with the same substrate, complicating progress in the field. We detected trace levels of zinc, a known inhibitor of KDAC8 when present in excess, even in high-quality buffer reagents, at concentrations that are sufficient to significantly inhibit the enzyme under common reaction conditions. We hypothesized that trace zinc in solution could account for the observed variability in KDAC8 activity. We demonstrate that addition of chelators, including BSA, EDTA, and citrate, and/or the use of a phosphate-based buffer instead of the more common tris-based buffer, eliminates the inhibition from low levels of zinc as well as the dependence of specific activity on enzyme concentration. This results in high KDAC8 activity that is consistent across buffer systems, even using low concentrations of enzyme. We report conditions that are suitable for several assays to increase both enzyme activity and reproducibility. Our results have significant implications for approaches used to identify substrates and small molecule modulators of KDAC8 and interpretation of existing data.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Samantha A Edenfield
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Brandon J Hylton
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, LA 70125-1098, USA.
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23
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Toro TB, Bryant JR, Watt TJ. Lysine Deacetylases Exhibit Distinct Changes in Activity Profiles Due to Fluorophore Conjugation of Substrates. Biochemistry 2017; 56:4549-4558. [PMID: 28749131 PMCID: PMC5937523 DOI: 10.1021/acs.biochem.7b00270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity. Here, we have compared the activity of several KDACs, representing all major classes of KDACs, with substrates in the presence and absence of AMC as well as peptides for which tryptophan has been substituted for AMC. Our results unequivocally demonstrate that AMC has a significant effect on activity for all KDACs tested. Furthermore, in neither the nature of the effect nor the magnitude is consistent across KDACs, making it impossible to predict the effect of AMC on a particular enzyme-substrate pair. AMC did not affect acetyllysine preference in a multiply acetylated substrate. In contrast, AMC significantly enhanced KDAC6 substrate affinity, greatly reduced Sirt1 activity, eliminated the substrate sequence specificity of KDAC4, and had no consistent effect with KDAC8 substrates. These results indicate that profiling of KDAC activity with labeled peptides is unlikely to produce biologically relevant data.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Jenae R. Bryant
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125-1098, United States
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24
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Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M. Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD). J Med Chem 2017; 61:1745-1766. [PMID: 28771357 DOI: 10.1021/acs.jmedchem.7b00115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) represents a serious public health issue, and discovery of new therapies is a pressing necessity. Alcohol exposure has been widely demonstrated to modulate epigenetic mechanisms, such as histone acetylation/deacetylation balance, in part via histone deacetylase (HDAC) inhibition. Epigenetic factors have been suggested to play a key role in AUD. To date, 18 different mammalian HDAC isoforms have been identified, and these have been divided into four classes. Since recent studies have suggested that both epigenetic mechanisms underlying AUD and the efficacy of HDAC inhibitors (HDACIs) in different animal models of AUD may involve class I HDACs, we herein report the development of class I HDACIs, including information regarding their structure, potency, and selectivity. More effort is required to improve the selectivity, pharmacokinetics, and toxicity profiles of HDACIs to achieve a better understanding of their efficacy in reducing addictive behavior.
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Affiliation(s)
- Erika Bourguet
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Katarzyna Ozdarska
- Institut de Chimie Moléculaire de Reims, UMR 7312-CNRS, UFR Pharmacie , Université de Reims Champagne-Ardenne , 51 rue Cognacq-Jay , 51096 Reims Cedex , France.,Department of Bioanalysis and Drugs Analysis , Medical University of Warsaw , S. Banacha 1 , 02-097 Warsaw , Poland
| | - Gautier Moroy
- Sorbonne Paris Cité, Molécules Thérapeutiques In Silico (MTi), INSERM UMR-S 973 , Université Paris Diderot , 35 rue Hélène Brion , 75013 Paris , France
| | - Jérôme Jeanblanc
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
| | - Mickaël Naassila
- INSERM ERi 24, Groupe de Recherche sur l'Alcool et les Pharmacodépendances (GRAP) , Université de Picardie Jules Verne, C.U.R.S. (Centre Universitaire de Recherche en Santé) , Chemin du Thil , 80000 Amiens , France.,Structure Fédérative de Recherche-Champagne Ardenne Picardie Santé (SFR-CAP Santé) , 51095 Reims Cedex , France
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25
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Rubio-Ruiz B, Weiss JT, Unciti-Broceta A. Efficient Palladium-Triggered Release of Vorinostat from a Bioorthogonal Precursor. J Med Chem 2016; 59:9974-9980. [DOI: 10.1021/acs.jmedchem.6b01426] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Belén Rubio-Ruiz
- Cancer Research
UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K
| | - Jason T. Weiss
- Cancer Research
UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K
| | - Asier Unciti-Broceta
- Cancer Research
UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K
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26
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Ingham O, Paranal RM, Smith WB, Escobar RA, Yueh H, Snyder T, Porco JA, Bradner JE, Beeler AB. Development of a Potent and Selective HDAC8 Inhibitor. ACS Med Chem Lett 2016; 7:929-932. [PMID: 27774131 PMCID: PMC5066159 DOI: 10.1021/acsmedchemlett.6b00239] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/19/2016] [Indexed: 12/19/2022] Open
Abstract
A novel, isoform-selective inhibitor of histone deacetylase 8 (HDAC8) has been discovered by the repurposing of a diverse compound collection. Medicinal chemistry optimization led to the identification of a highly potent (0.8 nM) and selective inhibitor of HDAC8.
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Affiliation(s)
- Oscar
J. Ingham
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ronald M. Paranal
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
| | - William B. Smith
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
| | - Randolph A. Escobar
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Han Yueh
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tracy Snyder
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John A. Porco
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - James E. Bradner
- Department
of Medical Oncology, Dana Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aaron B. Beeler
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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27
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de Lera AR, Ganesan A. Epigenetic polypharmacology: from combination therapy to multitargeted drugs. Clin Epigenetics 2016; 8:105. [PMID: 27752293 PMCID: PMC5062873 DOI: 10.1186/s13148-016-0271-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/21/2016] [Indexed: 12/20/2022] Open
Abstract
The modern drug discovery process has largely focused its attention in the so-called magic bullets, single chemical entities that exhibit high selectivity and potency for a particular target. This approach was based on the assumption that the deregulation of a protein was causally linked to a disease state, and the pharmacological intervention through inhibition of the deregulated target was able to restore normal cell function. However, the use of cocktails or multicomponent drugs to address several targets simultaneously is also popular to treat multifactorial diseases such as cancer and neurological disorders. We review the state of the art with such combinations that have an epigenetic target as one of their mechanisms of action. Epigenetic drug discovery is a rapidly advancing field, and drugs targeting epigenetic enzymes are in the clinic for the treatment of hematological cancers. Approved and experimental epigenetic drugs are undergoing clinical trials in combination with other therapeutic agents via fused or linked pharmacophores in order to benefit from synergistic effects of polypharmacology. In addition, ligands are being discovered which, as single chemical entities, are able to modulate multiple epigenetic targets simultaneously (multitarget epigenetic drugs). These multiple ligands should in principle have a lower risk of drug-drug interactions and drug resistance compared to cocktails or multicomponent drugs. This new generation may rival the so-called magic bullets in the treatment of diseases that arise as a consequence of the deregulation of multiple signaling pathways provided the challenge of optimization of the activities shown by the pharmacophores with the different targets is addressed.
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Affiliation(s)
- Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IIS Galicia Sur, 36310 Vigo, Spain
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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28
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Barker C, Lukac I, Leach AG. Designing Hydroxamates and Reversed Hydroxamates to Inhibit Zinc-containing Proteases but not Cytochrome P450s: Insights from Quantum Mechanics and Protein-ligand Crystal Structures. Mol Inform 2016; 34:608-14. [PMID: 27490712 DOI: 10.1002/minf.201400171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/08/2015] [Indexed: 11/07/2022]
Abstract
The Hydroxamate is a useful functional group that binds to metals in a range of enzymes, notably zinc in matrix metalloproteases and histone deacetylases. The group is also able to form interactions with iron leading to inhibition of the cytochromes P450, particularly the 3A4 isoform. We have studied the available crystal structures of zinc-containing proteins bound to hydroxamates and compared the observed geometries with those found by quantum mechanical calculations. This has revealed the likely binding mode preferences for neutral and anionic protonation states and highlighted the importance of electrostatic complementarity. Calculations were also performed for the interaction of the hydroxamate with iron in a heme environment, as found in the cytochromes P450. These reveal that the preferred binding mode of hydroxamates in this environment involves the s-trans conformation. These calculations provide design guidelines for those interested in designing inhibitors of metalloenzymes that do not block metabolism of other drugs. The ability to predict the geometries and energies of binding modes that cannot be studied experimentally is an advantage offered by this kind of study.
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Affiliation(s)
- Charlotte Barker
- Charlotte Barker, Iva Lukac, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Iva Lukac
- Charlotte Barker, Iva Lukac, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Andrew G Leach
- Andrew G. Leach, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK phone:+44 (0)1512312404.
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29
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Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment. J Mol Graph Model 2016; 67:69-84. [DOI: 10.1016/j.jmgm.2016.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 12/13/2022]
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30
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Roche J, Bertrand P. Inside HDACs with more selective HDAC inhibitors. Eur J Med Chem 2016; 121:451-483. [PMID: 27318122 DOI: 10.1016/j.ejmech.2016.05.047] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 01/08/2023]
Abstract
Inhibitors of histone deacetylases (HDACs) are nowadays part of the therapeutic arsenal mainly against cancers, with four compounds approved by the Food and Drug Administration. During the last five years, several groups have made continuous efforts to improve this class of compounds, designing more selective compounds or compounds with multiple capacities. After a survey of the HDAC biology and structures, this review summarizes the results of the chemists working in this field, and highlights when possible the behavior of the molecules inside their targets.
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Affiliation(s)
- Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions, Equipe « SEVE Sucres & Echanges Végétaux-Environnement », Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Philippe Bertrand
- Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B28, F-86073 Poitiers Cedex 09, France; Réseau Epigénétique du Cancéropôle Grand Ouest, France.
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31
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Nechay MR, Gallup NM, Morgenstern A, Smith QA, Eberhart ME, Alexandrova AN. Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis. J Phys Chem B 2016; 120:5884-95. [DOI: 10.1021/acs.jpcb.6b00997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Nathan M. Gallup
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Amanda Morgenstern
- Molecular
Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Quentin A. Smith
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Mark E. Eberhart
- Molecular
Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- California NanoSystems Institute, Los Angeles, California 90095, United States
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32
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Krämer A, Herzer J, Overhage J, Meyer-Almes FJ. Substrate specificity and function of acetylpolyamine amidohydrolases from Pseudomonas aeruginosa. BMC BIOCHEMISTRY 2016; 17:4. [PMID: 26956223 PMCID: PMC4784309 DOI: 10.1186/s12858-016-0063-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/02/2016] [Indexed: 11/13/2022]
Abstract
Background Pseudomonas aeruginosa, a Gram-negative, aerobic coccobacillus bacterium is an opportunistic human pathogen and worldwide the fourth most common cause of hospital-acquired infections which are often high mortality such as ventilator-associated pneumoniae. The polyamine metabolism of P. aeruginosa and particularly the deacetylation of acetylpolyamines has been little studied up to now. Results with other bacterial pathogens e.g., Y. pestis suggest that polyamines may be involved in the formation of biofilms or confer resistance against certain antibiotics. Results To elucidate the role of acetylpolyamines and their enzymatic deacetylation in more detail, all three putative acetylpolyamine amidohydrolases (APAHs) from P. aeruginosa have been expressed in enzymatic active form. The APAHs PA0321 and PA1409 are shown to be true polyamine deacetylases, whereas PA3774 is not able to deacetylate acetylated polyamines. Every APAH can hydrolyze trifluoroacetylated lysine-derivatives, but only PA1409 and much more efficiently PA3774 can also process the plain acetylated lysine substrate. P. aeruginosa is able to utilize acetylcadaverine and acetylputrescine as a carbon source under glucose starvation. If either the PA0321 or the PA1409 but not the PA3774 gene is disrupted, the growth of P. aeruginosa is reduced and delayed. In addition, we were able to show that the APAH inhibitors SAHA and SATFMK induce biofilm formation in both PA14 and PAO1 wildtype strains. Conclusions P. aeruginosa has two functional APAHs, PA0321 and PA1409 which enable the utilization of acetylpolyamines for the metabolism of P. aeruginosa. In contrast, the physiological role of the predicted APAH, PA3774, remains to be elucidated. Its ability to deacetylate synthetic acetylated lysine substrates points to a protein deacetylation functionality with yet unknown substrates. Electronic supplementary material The online version of this article (doi:10.1186/s12858-016-0063-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Krämer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295, Darmstadt, Germany
| | - Jan Herzer
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, 76021, Karlsruhe, Germany
| | - Joerg Overhage
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces, 76021, Karlsruhe, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295, Darmstadt, Germany.
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33
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Gantt SML, Decroos C, Lee MS, Gullett LE, Bowman CM, Christianson DW, Fierke CA. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry 2016; 55:820-32. [PMID: 26806311 DOI: 10.1021/acs.biochem.5b01327] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Histone deacetylases (HDACs) regulate cellular processes such as differentiation and apoptosis and are targeted by anticancer therapeutics in development and in the clinic. HDAC8 is a metal-dependent class I HDAC and is proposed to use a general acid-base catalytic pair in the mechanism of amide bond hydrolysis. Here, we report site-directed mutagenesis and enzymological measurements to elucidate the catalytic mechanism of HDAC8. Specifically, we focus on the catalytic function of Y306 and the histidine-aspartate dyads H142-D176 and H143-D183. Additionally, we report X-ray crystal structures of four representative HDAC8 mutants: D176N, D176N/Y306F, D176A/Y306F, and H142A/Y306F. These structures provide a useful framework for understanding enzymological measurements. The pH dependence of kcat/KM for wild-type Co(II)-HDAC8 is bell-shaped with two pKa values of 7.4 and 10.0. The upper pKa reflects the ionization of the metal-bound water molecule and shifts to 9.1 in Zn(II)-HDAC8. The H142A mutant has activity 230-fold lower than that of wild-type HDAC8, but the pKa1 value is not altered. Y306F HDAC8 is 150-fold less active than the wild-type enzyme; crystal structures show that Y306 hydrogen bonds with the zinc-bound substrate carbonyl, poised for transition state stabilization. The H143A and H142A/H143A mutants exhibit activity that is >80000-fold lower than that of wild-type HDAC8; the buried D176N and D176A mutants have significant catalytic effects, with more subtle effects caused by D183N and D183A. These enzymological and structural studies strongly suggest that H143 functions as a single general base-general acid catalyst, while H142 remains positively charged and serves as an electrostatic catalyst for transition state stabilization.
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Affiliation(s)
- Sister M Lucy Gantt
- Departments of Chemistry and Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Christophe Decroos
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
| | - Matthew S Lee
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
| | - Laura E Gullett
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
| | - Christine M Bowman
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States.,Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Carol A Fierke
- Departments of Chemistry and Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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34
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Toro TB, Pingali S, Nguyen TP, Garrett DS, Dodson KA, Nichols KA, Haynes RA, Payton-Stewart F, Watt TJ. KDAC8 with High Basal Velocity Is Not Activated by N-Acetylthioureas. PLoS One 2016; 11:e0146900. [PMID: 26745872 PMCID: PMC4706426 DOI: 10.1371/journal.pone.0146900] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/24/2015] [Indexed: 12/04/2022] Open
Abstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Recently, a series of N-acetylthioureas were synthesized and reported to enhance the activity of KDAC8 with a fluorogenic substrate. To determine if the activation was general, we synthesized three of the most potent N-acetylthioureas and measured their effect with peptide substrates and the fluorogenic substrate under multiple reaction conditions and utilizing two enzyme purification approaches. No activation was observed for any of the three N-acetylthioureas under any assayed conditions. Further characterization of KDAC8 kinetics with the fluorogenic substrate yielded a kcat/KM of 164 ± 17 in the absence of any N-acetylthioureas. This catalytic efficiency is comparable to or higher than that previously reported when KDAC8 was activated by the N-acetylthioureas, suggesting that the previously reported activation effect may be due to use of an enzyme preparation that contains a large fraction of inactive enzyme. Further characterization with a less active preparation and additional substrates leads us to conclude that N-acetylthioureas are not true activators of KDAC8 and only increase activity if the enzyme preparation is below the maximal basal activity.
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Affiliation(s)
- Tasha B. Toro
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Subramanya Pingali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Thao P. Nguyen
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Destane S. Garrett
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Kyra A. Dodson
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Kyara A. Nichols
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Rashad A. Haynes
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Florastina Payton-Stewart
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
| | - Terry J. Watt
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Dr., New Orleans, Louisiana, United States of America
- * E-mail:
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35
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Ballante F, Marshall GR. An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design. J Chem Inf Model 2016; 56:54-72. [PMID: 26682916 DOI: 10.1021/acs.jcim.5b00603] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular docking is a widely used technique in drug design to predict the binding pose of a candidate compound in a defined therapeutic target. Numerous docking protocols are available, each characterized by different search methods and scoring functions, thus providing variable predictive capability on a same ligand-protein system. To validate a docking protocol, it is necessary to determine a priori the ability to reproduce the experimental binding pose (i.e., by determining the docking accuracy (DA)) in order to select the most appropriate docking procedure and thus estimate the rate of success in docking novel compounds. As common docking programs use generally different root-mean-square deviation (RMSD) formulas, scoring functions, and format results, it is both difficult and time-consuming to consistently determine and compare their predictive capabilities in order to identify the best protocol to use for the target of interest and to extrapolate the binding poses (i.e., best-docked (BD), best-cluster (BC), and best-fit (BF) poses) when applying a given docking program over thousands/millions of molecules during virtual screening. To reduce this difficulty, two new procedures called Clusterizer and DockAccessor have been developed and implemented for use with some common and "free-for-academics" programs such as AutoDock4, AutoDock4(Zn), AutoDock Vina, DOCK, MpSDockZn, PLANTS, and Surflex-Dock to automatically extrapolate BD, BC, and BF poses as well as to perform consistent cluster and DA analyses. Clusterizer and DockAccessor (code available over the Internet) represent two novel tools to collect computationally determined poses and detect the most predictive docking approach. Herein an application to human lysine deacetylase (hKDAC) inhibitors is illustrated.
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Affiliation(s)
- Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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36
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Abstract
SAHA (vorinostat, Merck) is a famous clinical drug for zinc-containing histone deacetylase (HDAC) targets against cancer and several other human disorders, whose inhibition mechanism (namely the protonation mechanism) upon binding to HDAC has been debated for more than ten years. It is very challenging to verify experimentally and is still controversial theoretically. The popular "Class-dependent" (namely "Tyr-dependent") hypothesis is that the deprotonation of SAHA is mostly regulated by the conserved Tyr308 in class I HDAC while it is replaced by the His843 in class IIa HDAC. Herein, by elaborate QM(DFT)/MM MD simulations, we exclude the prevalent "Class-dependent" mechanism and advance a novel "Metal-dependent" mechanism, where the remote second metal site (K(+) in most HDAC and Ca(2+) in HDAC2) determines the protonation of SAHA. This proof-of-principle "Metal-dependent" mechanism opens up a new avenue to utilize the second metal site for isoform-selective inhibitor design.
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Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China.
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37
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Gong W, Wu R, Zhang Y. Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J Comput Chem 2015; 36:2228-35. [PMID: 26452222 DOI: 10.1002/jcc.24203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/17/2015] [Accepted: 08/30/2015] [Indexed: 12/21/2022]
Abstract
Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs.
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Affiliation(s)
- Wenjing Gong
- Department of Chemistry, New York University, New York, New York, 10003
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York, 10003.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
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38
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Toro TB, Watt TJ. KDAC8 substrate specificity quantified by a biologically relevant, label-free deacetylation assay. Protein Sci 2015; 24:2020-32. [PMID: 26402585 DOI: 10.1002/pro.2813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/21/2015] [Accepted: 09/20/2015] [Indexed: 01/25/2023]
Abstract
Analysis of the human proteome has identified thousands of unique protein sequences that contain acetylated lysine residues in vivo. These modifications regulate a variety of biological processes and are reversed by the lysine deacetylase (KDAC) family of enzymes. Despite the known prevalence and importance of acetylation, the details of KDAC substrate recognition are not well understood. While several methods have been developed to monitor protein deacetylation, none are particularly suited for identifying enzyme-substrate pairs of label-free substrates across the entire family of lysine deacetylases. Here, we present a fluorescamine-based assay which is more biologically relevant than existing methods and amenable to probing substrate specificity. Using this assay, we evaluated the activity of KDAC8 and other lysine deacetylases, including a sirtuin, for several peptides derived from known acetylated proteins. KDAC8 showed clear preferences for some peptides over others, indicating that the residues immediately surrounding the acetylated lysine play an important role in substrate specificity. Steady-state kinetics suggest that the sequence surrounding the acetylated lysine affects binding affinity and catalytic rate independently. Our results provide direct evidence that potential KDAC8 substrates previously identified through cell based experiments can be directly deacetylated by KDAC8. Conversely, the data from this assay did not correlate well with predictions from previous screens for KDAC8 substrates using less biologically relevant substrates and assay conditions. Combining results from our assay with mass spectrometry-based experiments and cell-based experiments will allow the identification of specific KDAC-substrate pairs and lead to a better understanding of the biological consequences of these interactions.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana, 70125
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana, 70125
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39
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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40
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Pietra F. Restoring Histone Deacetylase Activity by Waste Product Release. A View from Molecular Mechanics Simulations with Mammalian HDAC8. Chem Biodivers 2015; 12:503-12. [DOI: 10.1002/cbdv.201400314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Indexed: 11/05/2022]
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41
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Zhou J, Wu R, Wang B, Cao Z, Yan H, Mo Y. Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Zexing Cao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Honggao Yan
- Center
for Biological Modeling and Departments of Biochemistry and Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yirong Mo
- Department
of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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42
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Hou X, Du J, Liu R, Zhou Y, Li M, Xu W, Fang H. Enhancing the Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Customized ZBG Features: A Case Study Using Histone Deacetylase 8. J Chem Inf Model 2015; 55:861-71. [DOI: 10.1021/ci500762z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Jinan, Shandong 250117, China
| | - Renshuai Liu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yi Zhou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Wenfang Xu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
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43
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Histone deacetylases: structural determinants of inhibitor selectivity. Drug Discov Today 2015; 20:718-35. [PMID: 25687212 DOI: 10.1016/j.drudis.2015.01.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 12/22/2022]
Abstract
Histone deacetylases (HDACs) are epigenetic targets with an important role in cancer, neurodegeneration, inflammation, and metabolic disorders. Although clinically effective HDAC inhibitors have been developed, the design of inhibitors with the desired isoform(s) selectivity remains a challenge. Selective inhibitors could help clarify the function of each isoform, and provide therapeutic agents having potentially fewer adverse effects. Crystal structures of several HDACs have been reported, enabling structure-based drug design and providing important information to understand enzyme function. Here, we provide a comprehensive review of the structural information available on HDACs, discussing both conserved and isoform-specific structural and mechanistic features. We focus on distinctive aspects that help rationalize inhibitor selectivity, and provide structure-based recommendations for achieving the desired selectivity.
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Elbadawi MAA, Awadalla MKA, Hamid MMA, Mohamed MA, Awad TA. Valproic acid as a potential inhibitor of Plasmodium falciparum histone deacetylase 1 (PfHDAC1): an in silico approach. Int J Mol Sci 2015; 16:3915-31. [PMID: 25679451 PMCID: PMC4346934 DOI: 10.3390/ijms16023915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/30/2015] [Indexed: 11/25/2022] Open
Abstract
A new Plasmodium falciparum histone deacetylase1 (PfHDAC1) homology model was built based on the highest sequence identity available template human histone deacetylase 2 structure. The generated model was carefully evaluated for stereochemical accuracy, folding correctness and overall structure quality. All evaluations were acceptable and consistent. Docking a group of hydroxamic acid histone deacetylase inhibitors and valproic acid has shown binding poses that agree well with inhibitor-bound histone deacetylase-solved structural interactions. Docking affinity dG scores were in agreement with available experimental binding affinities. Further, enzyme-ligand complex stability and reliability were investigated by running 5-nanosecond molecular dynamics simulations. Thorough analysis of the simulation trajectories has shown that enzyme-ligand complexes were stable during the simulation period. Interestingly, the calculated theoretical binding energies of the docked hydroxamic acid inhibitors have shown that the model can discriminate between strong and weaker inhibitors and agrees well with the experimental affinities reported in the literature. The model and the docking methodology can be used in screening virtual libraries for PfHDAC1 inhibitors, since the docking scores have ranked ligands in accordance with experimental binding affinities. Valproic acid calculated theoretical binding energy suggests that it may inhibit PfHDAC1.
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Affiliation(s)
| | | | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan.
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan.
| | - Talal Ahmed Awad
- Medicinal and Aromatic Plants Research Institute, National Centre of Research, Khartoum 11111, Sudan.
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45
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Gleeson D, Gleeson MP. Application of QM/MM and QM methods to investigate histone deacetylase 8. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00471j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational chemistry plays an important supporting role in the early stages of drug discovery research.
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Affiliation(s)
- Duangkamol Gleeson
- Department of Chemistry
- Faculty of Science
- King Mongkut’s Institute of Technology Ladkrabang
- Bangkok 10520
- Thailand
| | - M. Paul Gleeson
- Department of Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok 10900
- Thailand
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46
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Martínez-González JÁ, Rodríguez A, Puyuelo MP, González M, Martínez R. Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Singh RK, Suzuki T, Mandal T, Balsubramanian N, Haldar M, Mueller DJ, Strode JA, Cook G, Mallik S, Srivastava DK. Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme. Biochemistry 2014; 53:7445-58. [PMID: 25407689 PMCID: PMC4263425 DOI: 10.1021/bi500711x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Among the different histone deacetylase
(HDAC) isozymes, HDAC8
is the most highly malleable enzyme, and it exhibits the potential
to accommodate structurally diverse ligands (albeit with moderate
binding affinities) in its active site pocket. To probe the molecular
basis of this feature, we performed detailed thermodynamic studies
of the binding of structurally similar ligands, which differed with
respect to the “cap”, “linker”, and “metal-binding”
regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore,
to HDAC8. The experimental data revealed that although the enthalpic
(ΔH°) and entropic (ΔS°) changes for the binding of individual SAHA analogues to HDAC8
were substantially different, their binding free energies (ΔG°) were markedly similar, conforming to a strong enthalpy–entropy
compensation effect. This effect was further observed in the temperature-dependent
thermodynamics of binding of all SAHA analogues to the enzyme. Notably,
in contrast to other metalloenzymes, our isothermal titration calorimetry
experiments (performed in different buffers of varying ionization
enthalpies) suggest that depending on the ligand, its zinc-binding
group may or may not be deprotonated upon the binding to HDAC8. Furthermore,
the heat capacity changes (ΔCp°) associated with the ligand binding
to HDAC8 markedly differed from one SAHA analogue to the other, and
such features could primarily be rationalized in light of the dynamic
flexibility in the enzyme structure in conjunction with the reorganization
of the active site resident water molecules. Arguments are presented
that although the binding thermodynamic features described above would
facilitate identification of weak to moderately tight-binding HDAC8
inhibitors (by a high-throughput and/or virtual screening of libraries
of small molecules), they would pose major challenges for the structure-based
rational design of highly potent and isozyme-selective inhibitors
of human HDAC8.
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Affiliation(s)
- Raushan K Singh
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
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Zhou J, Xie H, Liu Z, Luo HB, Wu R. Structure–Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. J Chem Inf Model 2014; 54:3162-71. [DOI: 10.1021/ci500513n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hujun Xie
- School
of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035 Zhejiang, P.R. China
| | - Zhihong Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 Guangdong, P.R. China
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