1
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Jha T, Jana R, Banerjee S, Baidya SK, Amin SA, Gayen S, Ghosh B, Adhikari N. Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:367-389. [PMID: 38757181 DOI: 10.1080/1062936x.2024.2350504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.
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Affiliation(s)
- T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - R Jana
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - B Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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2
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Dewaker V, Srivastava PN, Verma S, Srivastava AK, Prabhakar YS. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:13432-13455. [PMID: 34662251 DOI: 10.1080/07391102.2021.1989037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Designing an inhibitor having strong affinity in the active site pocket is the cherished goal of structure based drug designing. To achieve this, it is considerably important to predict which structural scaffold is better suited for change to increase affinity. We have explored five HDAC2 co-crystals having PDB ligand code-SHH (vorinostat), LLX, 20Y, IWX (BRD4884) and 6EZ (BRD7232). For analyzing protein-ligand interaction at an atomistic level, we have employed the NAMD molecular dynamics (MD) package. The obtained 100 ns long MD trajectories were subjected to quantitative estimations of non-bonding energies (NBEs) for inferring their interactions with the whole protein or its composite active site (CAS). In addition, relative ΔGbind was calculated to rank the inhibitors. These inhibitors' NBEs reveal that the phenyl moieties are the major structural scaffold where modifications should be attempted. We designed new compounds (NCs) via introducing hydroxyl groups at 4,5 position of the phenyl moiety of 6EZ, called NC1. Improvement in NC1 further encouraged us for CAP modification by isochromane and isoindoline moieties in place of oxabicyclooctane in NC1, resulting in NC2 and NC3. We also explored trifluoromethyl oxadiazole in 6EZ (NC4 and NC5) and SHH (NC6 and NC7). This moiety acts as a ZBG in NC4 while acting as a part of the foot-pocket in the rest. NC2 and NC6 have highest favorable NBEs among all studied ligands due increased favorable electrostatic contribution. We expect these NBEs data will provide atomistic level insights and benefit in designing new and improved HDAC2 inhibitors. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varun Dewaker
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Pratik Narain Srivastava
- Molecular Parasitology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saroj Verma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India.,College of Pharmacy, Shree Guru Gobind Singh Tricentenary University, Gurugram, Haryana, India
| | - Ajay K Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Yenamandra S Prabhakar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, India
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3
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Tinkov OV, Grigorev VY, Grigoreva LD, Osipov VN. HDAC1 PREDICTOR: a simple and transparent application for virtual screening of histone deacetylase 1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:915-931. [PMID: 36548122 DOI: 10.1080/1062936x.2022.2147996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Histone deacetylases play an important role in regulating gene expression by modifying histones and changing chromatin conformation. HDAC dysregulation is involved in many diseases, such as cancer, autoimmune and neurodegenerative diseases. Histone deacetylase 1 (HDAC1) inhibitors represent an important class of drugs. Quantitative Structure-Activity Relationship (QSAR) classification models were developed using 2D RDKit molecular descriptors; ECPF4 (Extended Connectivity Fingerprint) circular fingerprints; and the Random Forest, Gradient Boosting, and Support Vector Machine methods. The developed models were integrated into the HDAC1 PREDICTOR application, which is freely available at the link https://ovttiras-hdac1-inhibitors-hdac1-predictor-app-z3mrbr.streamlitapp.com. The HDAC1 PREDICTOR web application allows one to reveal the compounds for which the predicted activity to inhibit HDAC1 is higher than that of the reference Vorinostat compound (IC50 = 11.08 nM). The algorithm implemented in HDAC1 PREDICTOR for determining the contributions of molecular fragments to the inhibitory activity can be used to find the molecule segments that increase or decrease the activity, enabling the researcher to conduct a rational molecular design of new highly active HDAC1 inhibitors. The developed QSAR models and the code for their construction in the Python programming language are freely available on the GitHub platform at https://github.com/ovttiras/HDAC1-inhibitors.
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Affiliation(s)
- O V Tinkov
- Department of Pharmacology and Pharmaceutical Chemistry, Medical Faculty, Shevchenko Transnistria State University, Tiraspol, Moldova
| | - V Y Grigorev
- Department of Computer-aided Molecular Design, Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), Chernogolovka, Russia
| | - L D Grigoreva
- Department of Fundamental Physicochemical Engineering, Moscow State University, Moscow, Russia
| | - V N Osipov
- Department of Chemical Synthesis, Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
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4
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Shioiri T, Ishihara K, Matsugi M. Cutting edge of diphenyl phosphorazidate (DPPA) as a synthetic reagent – A fifty-year odyssey. Org Chem Front 2022. [DOI: 10.1039/d2qo00403h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent developments of diphenyl phosphorazidate (DPPA, (C6H5O)2P(O)N3) has been reviewed.
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Affiliation(s)
- Takayuki Shioiri
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tempaku, Nagoya 468-8502, Japan
| | - Kotaro Ishihara
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tempaku, Nagoya 468-8502, Japan
| | - Masato Matsugi
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tempaku, Nagoya 468-8502, Japan
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5
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Nencetti S, Cuffaro D, Nuti E, Ciccone L, Rossello A, Fabbi M, Ballante F, Ortore G, Carbotti G, Campelli F, Banti I, Gangemi R, Marshall GR, Orlandini E. Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines. J Enzyme Inhib Med Chem 2021; 36:34-47. [PMID: 33100043 PMCID: PMC7594840 DOI: 10.1080/14756366.2020.1835883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Uveal melanoma (UM) represents an aggressive type of cancer and currently, there is no effective treatment for this metastatic disease. In the last years, histone deacetylase inhibitors (HDACIs) have been studied as a possible therapeutic treatment for UM, alone or in association with other chemotherapeutic agents. Here we synthesised a series of new HDACIs based on the SAHA scaffold bearing an (arylidene)aminoxy moiety. Their HDAC inhibitory activity was evaluated on isolated human HDAC1, 3, 6, and 8 by fluorometric assay and their binding mode in the catalytic site of HDACs was studied by molecular docking. The most promising hit was the quinoline derivative VS13, a nanomolar inhibitor of HDAC6, which exhibited a good antiproliferative effect on UM cell lines at micromolar concentration and a capability to modify the mRNA levels of HDAC target genes similar to that of SAHA.
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Affiliation(s)
| | | | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| | - Lidia Ciccone
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy.,Research Center "E. Piaggio", Università di Pisa, Pisa, Italy
| | - Marina Fabbi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | - Irene Banti
- Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| | | | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Elisabetta Orlandini
- Research Center "E. Piaggio", Università di Pisa, Pisa, Italy.,Dipartimento di Scienze della Terra, Università di Pisa, Pisa, Italy
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6
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Chen Y, Gao Y, He Y, Zhang G, Wen H, Wang Y, Wu QP, Cui H. Determining Essential Requirements for Fluorophore Selection in Various Fluorescence Applications Taking Advantage of Diverse Structure-Fluorescence Information of Chromone Derivatives. J Med Chem 2020; 64:1001-1017. [PMID: 33307695 DOI: 10.1021/acs.jmedchem.0c01508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we report our work exploring the essential requirements for fluorophore selection during the development of various fluorescence applications. We assembled a library of chromone-derived fluorophores with diverse structure-fluorescence properties, which allowed us to choose the fluorophore pairs with similar structures but differing fluorescence properties and compared the performance of the selected fluorophore pairs in three types of commonly used fluorescence applications. We found that the selection standard of a suitable fluorophore is variable depending on the application. (1) In fluorescence imaging, fluorophores with strong and constant fluorescence under various conditions, such as a large pH range, are preferred. Notably, (2) in the detection of bioactive species, fluorophores with relatively lower fluorescence quantum yield favor the detection sensitivity. Furthermore, (3) in enzymatic assays employing fluorescence, the key parameter is the binding affinity between the fluorophore and the enzyme.
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Affiliation(s)
- Yikun Chen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 8 Liangxiang Donglu, Beijing 102488, China.,State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Yongxin Gao
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Yujun He
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Gang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Hui Wen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Yuchen Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
| | - Qin-Pei Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 8 Liangxiang Donglu, Beijing 102488, China
| | - Huaqing Cui
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xiannongtan Street, Beijing 100050, China
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7
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Cappellacci L, Perinelli DR, Maggi F, Grifantini M, Petrelli R. Recent Progress in Histone Deacetylase Inhibitors as Anticancer Agents. Curr Med Chem 2020; 27:2449-2493. [PMID: 30332940 DOI: 10.2174/0929867325666181016163110] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/29/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022]
Abstract
Histone Deacetylase (HDAC) inhibitors are a relatively new class of anti-cancer agents that play important roles in epigenetic or non-epigenetic regulation, inducing death, apoptosis, and cell cycle arrest in cancer cells. Recently, their use has been clinically validated in cancer patients resulting in the approval by the FDA of four HDAC inhibitors, vorinostat, romidepsin, belinostat and panobinostat, used for the treatment of cutaneous/peripheral T-cell lymphoma and multiple myeloma. Many more HDAC inhibitors are at different stages of clinical development for the treatment of hematological malignancies as well as solid tumors. Also, clinical trials of several HDAC inhibitors for use as anti-cancer drugs (alone or in combination with other anti-cancer therapeutics) are ongoing. In the intensifying efforts to discover new, hopefully, more therapeutically efficacious HDAC inhibitors, molecular modelingbased rational drug design has played an important role. In this review, we summarize four major structural classes of HDAC inhibitors (hydroxamic acid derivatives, aminobenzamide, cyclic peptide and short-chain fatty acids) that are in clinical trials and different computer modeling tools available for their structural modifications as a guide to discover additional HDAC inhibitors with greater therapeutic utility.
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Affiliation(s)
- Loredana Cappellacci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Diego R Perinelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Filippo Maggi
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Mario Grifantini
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Riccardo Petrelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
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8
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Zhang B, Ruan ZW, Luo D, Zhu Y, Ding T, Sui Q, Lei X. Unexpected Enhancement of HDACs Inhibition by MeS Substitution at C-2 Position of Fluoro Largazole. Mar Drugs 2020; 18:md18070344. [PMID: 32629787 PMCID: PMC7401273 DOI: 10.3390/md18070344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/23/2020] [Accepted: 06/28/2020] [Indexed: 12/21/2022] Open
Abstract
Given our previous finding that fluorination at the C18 position of largazole showed reasonably good tolerance towards inhibitory activity and selectivity of histone deacetylases (HDACs), further modification on the valine residue in the fluoro-largazole's macrocyclic moiety with S-Me l-Cysteine or Glycine residue was performed. While the Glycine-modified fluoro analog showed poor activity, the S-Me l-Cysteine-modified analog emerged to be a very potent HDAC inhibitor. Unlike all previously reported C2-modified compounds in the largazole family (including our recent fluoro-largazole analogs) where replacement of the Val residue has failed to provide any potency improvement, the S-Me l-Cysteine-modified analog displayed significantly enhanced (five-nine-fold) inhibition of all the tested HDACs while maintaining the selectivity of HDAC1 over HDAC6, as compared to largazole thiol. A molecular modeling study provided rational explanation and structural evidence for the enhanced inhibitory activity. This new finding will aid the design of novel potent HDAC inhibitors.
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Affiliation(s)
- Bingbing Zhang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China; (B.Z.); (Z.-W.R.); (Y.Z.); (T.D.)
| | - Zhu-Wei Ruan
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China; (B.Z.); (Z.-W.R.); (Y.Z.); (T.D.)
| | - Dongdong Luo
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China;
| | - Yueyue Zhu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China; (B.Z.); (Z.-W.R.); (Y.Z.); (T.D.)
| | - Tingbo Ding
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China; (B.Z.); (Z.-W.R.); (Y.Z.); (T.D.)
| | - Qiang Sui
- China State Institute of Pharmaceutical Industry, No. 285 Gebaini Road, Pudong Zone, Shanghai 201203, China;
| | - Xinsheng Lei
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China; (B.Z.); (Z.-W.R.); (Y.Z.); (T.D.)
- Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- Correspondence: ; Tel.: +86-021-51980128
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9
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Zhang B, Liu J, Gao D, Yu X, Wang J, Lei X. A fluorine scan on the Zn2+-binding thiolate side chain of HDAC inhibitor largazole: Synthesis, biological evaluation, and molecular modeling. Eur J Med Chem 2019; 182:111672. [DOI: 10.1016/j.ejmech.2019.111672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/31/2019] [Accepted: 08/31/2019] [Indexed: 10/26/2022]
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10
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Zhang B, Shan G, Zheng Y, Yu X, Ruan ZW, Li Y, Lei X. Synthesis and Preliminary Biological Evaluation of Two Fluoroolefin Analogs of Largazole Inspired by the Structural Similarity of the Side Chain Unit in Psammaplin A. Mar Drugs 2019; 17:md17060333. [PMID: 31163697 PMCID: PMC6628159 DOI: 10.3390/md17060333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Largazole, isolated from a marine Cyanobacterium of the genus Symploca, is a potent and selective Class I HDAC (histone deacetylation enzymes) inhibitor. This natural 16-membered macrocyclic depsipeptide features an interesting side chain unit, namely 3-hydroxy-7-mercaptohept-4-enoic acid, which occurs in many other natural sulfur-containing HDAC inhibitors. Notably, one similar fragment, where the amide moiety replaces the trans alkene moiety, appears in Psammaplin A, another marine natural product with potent HDAC inhibitory activities. Inspired by such a structural similarity, we hypothesized the fluoroolefin moiety would mimic both the alkene moiety in Largazole and the amide moiety in Psammaplin A, and thus designed and synthesized two novel fluoro olefin analogs of Largazole. The preliminary biological assays showed that the fluoro analogs possessed comparable Class I HDAC inhibitory effects, indicating that this kind of modification on the side chain of Largazole was tolerable.
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Affiliation(s)
- Bingbing Zhang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
| | - Guangsheng Shan
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
| | - Yinying Zheng
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
| | - Xiaolin Yu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhu-Wei Ruan
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
| | - Yang Li
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
| | - Xinsheng Lei
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Pudong Zone, Shanghai 201203, China.
- Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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11
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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12
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Yu X, Zhang B, Shan G, Wu Y, Yang FL, Lei X. Synthesis of the molecular hybrid inspired by Largazole and Psammaplin A. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Chen QY, Chaturvedi PR, Luesch H. Process Development and Scale-up Total Synthesis of Largazole, a Potent Class I Histone Deacetylase Inhibitor. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.7b00352] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qi-Yin Chen
- Oceanyx
Pharmaceuticals, Inc., Sid Martin Biotechnology Incubator, 12085 Research
Drive, Alachua, Florida 32615, United States
| | - Pravin R. Chaturvedi
- Oceanyx
Pharmaceuticals, Inc., Sid Martin Biotechnology Incubator, 12085 Research
Drive, Alachua, Florida 32615, United States
| | - Hendrik Luesch
- Oceanyx
Pharmaceuticals, Inc., Sid Martin Biotechnology Incubator, 12085 Research
Drive, Alachua, Florida 32615, United States
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14
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Abstract
Covering: 2016. Previous review: Nat. Prod. Rep., 2017, 34, 235-294This review covers the literature published in 2016 for marine natural products (MNPs), with 757 citations (643 for the period January to December 2016) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1277 in 432 papers for 2016), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
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15
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Poli G, Di Fabio R, Ferrante L, Summa V, Botta M. Largazole Analogues as Histone Deacetylase Inhibitors and Anticancer Agents: An Overview of Structure-Activity Relationships. ChemMedChem 2017; 12:1917-1926. [PMID: 29117473 DOI: 10.1002/cmdc.201700563] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/31/2017] [Indexed: 12/18/2022]
Abstract
Since the time of its identification, the natural compound largazole rapidly caught the attention of the medicinal chemistry community for its impressive potency as an inhibitor of histone deacetylases (HDACs) and its strong antiproliferative activity against a broad panel of cancer cell lines. The design of largazole analogues is an expanding field of study, due to their remarkable potential as novel anticancer therapeutics. At present, a large ensemble of largazole analogues has been reported, allowing the identification of important structure-activity relationships (SAR) that can guide the design of novel compounds with improved HDAC inhibitory profiles, anticancer activity, and pharmacokinetic properties. The aim of this review is to concisely summarize the information obtained by biological evaluations of the various largazole analogues reported to date, with particular attention given to the latest analogues, as well as to analyze the various SAR obtained from this data, with the purpose of providing useful guidelines for the development of novel potent and selective HDAC inhibitors to be used as anticancer agents.
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Affiliation(s)
- Giulio Poli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Romano Di Fabio
- Promidis, Via Olgettina 60, 20132, Milano, Italy.,IRBM Science Park, Via Pontina Km 30 600, 00070, Pomezia, Italy
| | | | - Vincenzo Summa
- IRBM Science Park, Via Pontina Km 30 600, 00070, Pomezia, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
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16
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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17
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Combinations of isoform-targeted histone deacetylase inhibitors and bryostatin analogues display remarkable potency to activate latent HIV without global T-cell activation. Sci Rep 2017; 7:7456. [PMID: 28785069 PMCID: PMC5547048 DOI: 10.1038/s41598-017-07814-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/05/2017] [Indexed: 12/26/2022] Open
Abstract
Current antiretroviral therapy (ART) for HIV/AIDS slows disease progression by reducing viral loads and increasing CD4 counts. Yet ART is not curative due to the persistence of CD4+ T-cell proviral reservoirs that chronically resupply active virus. Elimination of these reservoirs through the administration of synergistic combinations of latency reversing agents (LRAs), such as histone deacetylase (HDAC) inhibitors and protein kinase C (PKC) modulators, provides a promising strategy to reduce if not eradicate the viral reservoir. Here, we demonstrate that largazole and its analogues are isoform-targeted histone deacetylase inhibitors and potent LRAs. Significantly, these isoform-targeted HDAC inhibitors synergize with PKC modulators, namely bryostatin-1 analogues (bryologs). Implementation of this unprecedented LRA combination induces HIV-1 reactivation to unparalleled levels and avoids global T-cell activation within resting CD4+ T-cells.
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Structural insights of SmKDAC8 inhibitors: Targeting Schistosoma epigenetics through a combined structure-based 3D QSAR, in vitro and synthesis strategy. Bioorg Med Chem 2017; 25:2105-2132. [DOI: 10.1016/j.bmc.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 11/24/2022]
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Reddy DR, Ballante F, Zhou NJ, Marshall GR. Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors. Eur J Med Chem 2016; 127:531-553. [PMID: 28109947 DOI: 10.1016/j.ejmech.2016.12.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 11/30/2016] [Accepted: 12/16/2016] [Indexed: 12/24/2022]
Abstract
A comprehensive investigation was performed to identify new benzodiazepine (BZD) derivatives as potent and selective human lysine deacetylase inhibitors (hKDACis). A total of 108 BZD compounds were designed, synthesized and from that 104 compounds were biologically evaluated against human lysine deacetylases (hKDACs) 1, 3 and 8 (class I) and 6 (class IIb). The most active compounds showed mid-nanomolar potencies against hKDACs 1, 3 and 6 and micromolar activity against hKDAC8, while a promising compound (6q) showed selectivity towards hKDAC3 among the different enzyme isoforms. An hKDAC6 homology model, refined by molecular dynamics simulation was generated, and molecular docking studies performed to rationalize the dominant ligand-residue interactions as well as to define structure-activity-relationships. Experimental results confirmed the usefulness of the benzodiazepine moiety as capping group when pursuing hKDAC isoform-selectivity inhibition, suggesting its continued use when designing new hKDACis.
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Affiliation(s)
- D Rajasekhar Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Nancy J Zhou
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States.
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20
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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21
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Almaliti J, Al-Hamashi AA, Negmeldin AT, Hanigan CL, Perera L, Pflum MKH, Casero RA, Tillekeratne LMV. Largazole Analogues Embodying Radical Changes in the Depsipeptide Ring: Development of a More Selective and Highly Potent Analogue. J Med Chem 2016; 59:10642-10660. [PMID: 27809521 DOI: 10.1021/acs.jmedchem.6b01271] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A number of analogues of the marine-derived histone deacetylase inhibitor largazole incorporating major structural changes in the depsipeptide ring were synthesized. Replacing the thiazole-thiazoline fragment of largazole with a bipyridine group gave analogue 7 with potent cell growth inhibitory activity and an activity profile similar to that of largazole, suggesting that conformational change accompanying switching hybridization from sp3 to sp2 at C-7 is well tolerated. Analogue 7 was more class I selective compared to largazole, with at least 464-fold selectivity for class I HDAC proteins over class II HDAC6 compared to a 22-fold selectivity observed with largazole. To our knowledge 7 represents the first example of a potent and highly cytotoxic largazole analogue not containing a thiazoline ring. The elimination of a chiral center derived from the unnatural amino acid R-α-methylcysteine makes the molecule more amenable to chemical synthesis, and coupled with its increased class I selectivity, 7 could serve as a new lead compound for developing selective largazole analogues.
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Affiliation(s)
- Jehad Almaliti
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan , Amman, 11942, Jordan
| | - Ayad A Al-Hamashi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States
| | - Ahmed T Negmeldin
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Christin L Hanigan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine , Bunting/Blaustein Cancer Research Building 1, Room 551, 1650 Orleans Street, Baltimore, Maryland 21231, United States
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Robert A Casero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine , Bunting/Blaustein Cancer Research Building 1, Room 551, 1650 Orleans Street, Baltimore, Maryland 21231, United States
| | - L M Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, The University of Toledo , 2801, W. Bancroft Street, Toledo, Ohio 43606, United States
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22
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Halsall JA, Turner BM. Histone deacetylase inhibitors for cancer therapy: An evolutionarily ancient resistance response may explain their limited success. Bioessays 2016; 38:1102-1110. [PMID: 27717012 PMCID: PMC5091640 DOI: 10.1002/bies.201600070] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone deacetylase inhibitors (HDACi) are in clinical trials against a variety of cancers. Despite early successes, results against the more common solid tumors have been mixed. How is it that so many cancers, and most normal cells, tolerate the disruption caused by HDACi-induced protein hyperacetylation? And why are a few cancers so sensitive? Here we discuss recent results showing that human cells mount a coordinated transcriptional response to HDACi that mitigates their toxic effects. We present a hypothetical signaling system that could trigger and mediate this response. To account for the existence of such a response, we note that HDACi of various chemical types are made by a variety of organisms to kill or suppress competitors. We suggest that the resistance response in human cells is a necessary evolutionary consequence of exposure to environmental HDACi. We speculate that cancers sensitive to HDACi are those in which the resistance response has been compromised by mutation. Identifying such mutations will allow targeting of HDACi therapy to potentially susceptible cancers. Also see the video abstract here.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Bryan M Turner
- Chromatin and Gene Expression Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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23
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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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