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Simoben CV, Babiaka SB, Moumbock AFA, Namba-Nzanguim CT, Eni DB, Medina-Franco JL, Günther S, Ntie-Kang F, Sippl W. Challenges in natural product-based drug discovery assisted with in silico-based methods. RSC Adv 2023; 13:31578-31594. [PMID: 37908659 PMCID: PMC10613855 DOI: 10.1039/d3ra06831e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The application of traditional medicine by humans for the treatment of ailments as well as improving the quality of life far outdates recorded history. To date, a significant percentage of humans, especially those living in developing/underprivileged communities still rely on traditional medicine for primary healthcare needs. In silico-based methods have been shown to play a pivotal role in modern pharmaceutical drug discovery processes. The application of these methods in identifying natural product (NP)-based hits has been successful. This is very much observed in many research set-ups that use rationally in silico-based methods in combination with experimental validation techniques. The combination has rendered the use of in silico-based approaches even more popular and successful in the investigation of NPs. However, identifying and proposing novel NP-based hits for experimental validation comes with several challenges such as the availability of compounds by suppliers, the huge task of separating pure compounds from complex mixtures, the quantity of samples available from the natural source to be tested, not to mention the potential ecological impact if the natural source is exhausted. Because most peer-reviewed publications are biased towards "positive results", these challenges are generally not discussed in publications. In this review, we highlight and discuss these challenges. The idea is to give interested scientists in this field of research an idea of what they can come across or should be expecting as well as prompting them on how to avoid or fix these issues.
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Affiliation(s)
- Conrad V Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Smith B Babiaka
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen 72076 Tübingen Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Cyril T Namba-Nzanguim
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - Donatus Bekindaka Eni
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000 Mexico City 04510 Mexico
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
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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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Truong N, Goodis CC, Cottingham AL, Shaw JR, Fletcher S, Pearson RM. Modified Suberoylanilide Hydroxamic Acid Reduced Drug-Associated Immune Cell Death and Organ Damage under Lipopolysaccharide Inflammatory Challenge. ACS Pharmacol Transl Sci 2022; 5:1128-1141. [PMID: 36407956 PMCID: PMC9667537 DOI: 10.1021/acsptsci.2c00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 11/29/2022]
Abstract
Histone deacetylase inhibitors (HDACi) induce potent anti-inflammatory responses when used to treat inflammatory diseases. Suberoylanilide hydroxamic acid (SAHA), a pan-HDACi, decreases pro-inflammatory cytokine levels and attenuates cytokine storm in sepsis; however, its toxicity profile toward immune cells has limited its use as a sepsis therapeutic. Here, we developed a modification to SAHA by para-hydroxymethylating the capping group to generate SAHA-OH. We discovered that SAHA-OH provides a favorable improvement to the toxicity profile compared to SAHA. SAHA-OH significantly reduced primary macrophage apoptosis and splenic B cell death as well as mitigated organ damage using a lipopolysaccharide (LPS)-induced endotoxemia mouse model. Furthermore, SAHA-OH retained anti-inflammatory responses similar to SAHA as measured by reductions in LPS-induced proinflammatory cytokine secretions in vitro and in vivo. These effects were attributed to a decreased selectivity of HDAC1, 2, 3, 8 and an increased selectivity for HDAC6 for SAHA-OH as determined by IC50 values. Our results support the potential for SAHA-OH to modulate acute proinflammatory responses while mitigating SAHA-associated drug toxicity for use in the treatment of inflammation-associated diseases and conditions.
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Affiliation(s)
- Nhu Truong
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Christopher C. Goodis
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Andrea L. Cottingham
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jacob R. Shaw
- Department
of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland 21201, United States
| | - Steven Fletcher
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Ryan M. Pearson
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
- Department
of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland 21201, United States
- Marlene
and Stewart Greenbaum Comprehensive Cancer Center, School of Medicine, University of Maryland, Baltimore, Maryland 21201, United States
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Vanegas JAG, Pacule HB, Capitão RM, Correia CRD, Terra WC, Campos VP, Oliveira DF. Methyl Esters of ( E)-Cinnamic Acid: Activity against the Plant-Parasitic Nematode Meloidogyne incognita and In Silico Interaction with Histone Deacetylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6624-6633. [PMID: 35622462 DOI: 10.1021/acs.jafc.1c08142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
(E)-Cinnamaldehyde is very active against Meloidogyne incognita but has low persistence in soil. To circumvent this problem, esters of cinnamic acid were evaluated as a substitute for (E)-cinnamaldehyde. The best results under assays with M. incognita second-stage juveniles (J2) were obtained for the methyl esters of (E)-p-fluoro- (13), (E)-p-chloro- (14), and (E)-p-bromocinnamic acid (15), which showed lethal concentrations to 50% (LC50) J2 of 168, 95, and 216 μg/mL, respectively. Under the same conditions, the LC50 values for the nematicides carbofuran and fluensulfone were 160 and 34 μg/mL, respectively. Substances 13-15 were also active against nematode eggs, which account for most of the M. incognita population in the field. According to an in silico study, substances 13-15 can act against the nematode through inhibition of histone deacetylase. Therefore, esters 13-15 and histone deacetylase are potentially useful for the rational design of new nematicides for the control of M. incognita.
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Affiliation(s)
- Javier A G Vanegas
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
| | - Horácio B Pacule
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
| | - Rebeca M Capitão
- Laboratório de Química Orgânica, Departamento de Química, Universidade Estadual de Campinas, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Carlos R D Correia
- Laboratório de Química Orgânica, Departamento de Química, Universidade Estadual de Campinas, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Willian C Terra
- Laboratório de Nematologia, Departamento de Fitopatologia, Universidade Federal de Lavras, CEP 37200-900, Lavras, Minas Gerais, Brazil
| | - Vicente P Campos
- Laboratório de Nematologia, Departamento de Fitopatologia, Universidade Federal de Lavras, CEP 37200-900, Lavras, Minas Gerais, Brazil
| | - Denilson F Oliveira
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
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5
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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Pflieger M, Sönnichsen M, Horstick‐Muche N, Yang J, Schliehe‐Diecks J, Schöler A, Borkhardt A, Hamacher A, Kassack MU, Hansen FK, Bhatia S, Kurz T. Oxa Analogues of Nexturastat A Demonstrate Improved HDAC6 Selectivity and Superior Antileukaemia Activity. ChemMedChem 2021; 16:1798-1803. [PMID: 33629513 PMCID: PMC8251746 DOI: 10.1002/cmdc.202001011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/19/2021] [Indexed: 01/03/2023]
Abstract
The acetylome is important for maintaining the homeostasis of cells. Abnormal changes can result in the pathogenesis of immunological or neurological diseases, and degeneration can promote the manifestation of cancer. In particular, pharmacological intervention in the acetylome with pan-histone deacetylase (HDAC) inhibitors is clinically validated. However, these drugs exhibit an undesirable risk-benefit profile due to severe side effects. Selective HDAC inhibitors might promote patient compliance and represent a valuable opportunity in personalised medicine. Therefore, we envisioned the development of HDAC6-selective inhibitors. During our lead structure identification, we demonstrated that an alkoxyurea-based connecting unit proves to be beneficial for HDAC6 selectivity and established the synthesis of alkoxyurea-based hydroxamic acids. Herein, we report highly potent N-alkoxyurea-based hydroxamic acids with improved HDAC6 preference compared to nexturastat A. We further validated the biological activity of these oxa analogues of nexturastat A in a broad subset of leukaemia cell lines and demonstrated their superior anti-proliferative properties compared to nexturastat A.
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Affiliation(s)
- Marc Pflieger
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Nadine Horstick‐Muche
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Jing Yang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
- Department of MedicineYangzhou Polytechnic CollegeWest Wenchang Road 458Yangzhou225009P.R. China
| | - Julian Schliehe‐Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical FacultyLeipzig UniversityBrüderstraße 3404103LeipzigGermany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Matthias U. Kassack
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Finn K. Hansen
- Pharmaceutical and Cell Biological Chemistry, Pharmaceutical InstituteUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical FacultyHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
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Elmezayen AD, Al-Obaidi A, Yelekçi K. Discovery of novel isoform-selective histone deacetylases 5 and 9 inhibitors through combined ligand-based pharmacophore modeling, molecular mocking, and molecular dynamics simulations for cancer treatment. J Mol Graph Model 2021; 106:107937. [PMID: 34049193 DOI: 10.1016/j.jmgm.2021.107937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022]
Abstract
Class IIa histone deacetylases (HDACs) 5 and 9 play crucial roles in several human disorders such as cancer, making them important targets for drug design. Continuous research is pursed to overcome the cytotoxicity side effect that comes with the currently available broad-spectrum HDACs inhibitors. Herein, common features of active HDACs inhibitors in clinical trials and use have been calculated to generate the best pharmacophore hypothesis. Guner-Henry scoring system was used to validate the generated hypotheses. Hypo1 of HDAC5 and Hypo2 of HDAC9 exhibited the most statistically significance hypotheses. Compounds with fit value of 3 and more were examined by QuickVina 2 docking tool to calculate their binding affinity toward all class IIa HDACs. A total of 6 potential selective compounds were subjected to 100 molecular dynamics (MD) simulation to examine their binding modes. The free binding energy calculations were computed according to the MM-PBSA method. Proposed selective compounds displayed good stability with their targets and thus they may offer potent leads for the designing of HDAC5 and HDAC9 isoform selective inhibitors.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083, Istanbul, Turkey.
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Binding Free Energy (BFE) Calculations and Quantitative Structure-Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 ( smHDAC8) Inhibitors. Molecules 2021; 26:molecules26092584. [PMID: 33925246 PMCID: PMC8125515 DOI: 10.3390/molecules26092584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 01/02/2023] Open
Abstract
Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC50 values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.
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Linciano P, Benedetti R, Pinzi L, Russo F, Chianese U, Sorbi C, Altucci L, Rastelli G, Brasili L, Franchini S. Investigation of the effect of different linker chemotypes on the inhibition of histone deacetylases (HDACs). Bioorg Chem 2020; 106:104462. [PMID: 33213894 DOI: 10.1016/j.bioorg.2020.104462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Histone Deacetylases (HDACs) are among the most attractive and interesting targets in anticancer drug discovery. The clinical relevance of HDAC inhibitors (HDACIs) is testified by four FDA-approved drugs for cancer treatment. However, one of the main drawbacks of these drugs resides in the lack of selectivity against the different HDAC isoforms, resulting in severe side effects. Thus, the identification of selective HDACIs represents an exciting challenge for medicinal chemists. HDACIs are composed of a cap group, a linker region, and a metal-binding group interacting with the catalytic zinc ion. While the cap group has been extensively investigated, less information is available about the effect of the linker on isoform selectivity. To this aim, in this work, we explored novel linker chemotypes to direct isoform selectivity. A small library of 25 hydroxamic acids with hitherto unexplored linker chemotypes was prepared. In vitro tests demonstrated that, depending on the linker type, some candidates selectively inhibit HDAC1 over HDAC6 isoform or vice versa. Docking calculations were performed to rationalize the effect of the novel linker chemotypes on biologic activity. Moreover, four compounds were able to increase the levels of acetylation of histone H3 or tubulin. These compounds were also assayed in breast cancer MCF7 cells to test their antiproliferative effect. Three compounds showed a significant reduction of cancer proliferation, representing valuable starting points for further optimization.
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Affiliation(s)
- Pasquale Linciano
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Rosaria Benedetti
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Luca Pinzi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Fabiana Russo
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Ugo Chianese
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Claudia Sorbi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy.
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", via L. De Crecchio 7, 80138 Napoli, Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Livio Brasili
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Silvia Franchini
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy.
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10
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Histone deacetylases inhibitors as new potential drugs against Leishmania braziliensis, the main causative agent of new world tegumentary leishmaniasis. Biochem Pharmacol 2020; 180:114191. [PMID: 32777278 DOI: 10.1016/j.bcp.2020.114191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
The protozoan parasite Leishmania braziliensis is a major causative agent of the neglected tropical diseases Cutaneous and Mucocutaneous Leishmaniases in the New World. There are no vaccines to prevent the infection and the treatment relies on few drugs that often display high toxicity and costs. Thus, chemotherapeutic alternatives are required. Histone Deacetylases (HDACs) are epigenetic enzymes involved in the control of chromatin structure. In this work, we tested an in-house library of 78 hydroxamic acid derivatives as putative inhibitors of L. braziliensis HDACs (HDACi). The compounds were evaluated in relation to the toxicity to the host cell macrophage and to the leishmanicidal effect against L. braziliensis during in vitro infection. Eight HDACi showed significant leishmanicidal effects and the top 5 compounds showed effective concentrations (EC50) in the range of 4.38 to 10.21 μM and selectivity indexes (SI) from of 6 to 21.7. Analyses by Transmission Electron Microscopy (TEM) indicated induction of apoptotic cell death of L. braziliensis amastigotes with a necrotic phenotype. An altered chromatin condensation pattern and cellular disorganization of intracellular amastigotes was also observed. A tight connection between the mitochondrion and nuclear protrusions, presumably of endoplasmic reticulum origin, was found in parasites but not in the host cell. In flow cytometry (FC) analyses, HDACi promoted parasite cell cycle arrest in the G2-M phase and no changes were found in macrophages. In addition, the direct effect of HDACi against the promastigotes showed apoptosis as the main mechanism of cell death. The FC results corroborate the TEM analyses indicating that the HDACi lead to changes in the cell cycle and induction of apoptosis of L. braziliensis. The production of nitric oxide by the infected macrophages was not altered after treatment with the top 5 compounds. Taken together, our results evidenced new HDACi as promising agents for the development of new treatments for American Tegumentary Leishmaniasis caused by L. braziliensis.
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Asfaha Y, Schrenk C, Alves Avelar LA, Hamacher A, Pflieger M, Kassack MU, Kurz T. Recent advances in class IIa histone deacetylases research. Bioorg Med Chem 2019; 27:115087. [PMID: 31561937 DOI: 10.1016/j.bmc.2019.115087] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/25/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic control plays an important role in gene regulation through chemical modifications of DNA and post-translational modifications of histones. An essential post-translational modification is the histone acetylation/deacetylation-process which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The mammalian zinc dependent HDAC family is subdivided into three classes: class I (HDACs 1-3, 8), class II (IIa: HDACs 4, 5, 7, 9; IIb: HDACs 6, 10) and class IV (HDAC 11). In this review, recent studies on the biological role and regulation of class IIa HDACs as well as their contribution in neurodegenerative diseases, immune disorders and cancer will be presented. Furthermore, the development, synthesis, and future perspectives of selective class IIa inhibitors will be highlighted.
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Affiliation(s)
- Yodita Asfaha
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Christian Schrenk
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Leandro A Alves Avelar
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Marc Pflieger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Matthias U Kassack
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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Kozlov MV, Konduktorov KA, Shcherbakova AS, Kochetkov SN. Synthesis of N'-propylhydrazide analogs of hydroxamic inhibitors of histone deacetylases (HDACs) and evaluation of their impact on activities of HDACs and replication of hepatitis C virus (HCV). Bioorg Med Chem Lett 2019; 29:2369-2374. [PMID: 31201063 DOI: 10.1016/j.bmcl.2019.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 01/22/2023]
Abstract
N'-Propylhydrazide analogs of hydroxamic inhibitors of histone deacetylases (HDACs), including tubastatin A, vorinostat and belinostat, were synthesized. All prepared compounds inhibited HDAC1/2/3, but not HDAC6, except for one hydrazide analog of HDAC4/5/7 inhibitor that was completely inactive. A novel 4-substituted derivative of N'-propylbenzohydrazide with extremely high anti-HCV activity was discovered.
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Affiliation(s)
- Maxim V Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia.
| | - Konstantin A Konduktorov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia
| | - Anastasia S Shcherbakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia
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Lascano S, Lopez M, Arimondo PB. Natural Products and Chemical Biology Tools: Alternatives to Target Epigenetic Mechanisms in Cancers. CHEM REC 2018; 18:1854-1876. [PMID: 30537358 DOI: 10.1002/tcr.201800133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
DNA methylation and histone acetylation are widely studied epigenetic modifications. They are involved in numerous pathologies such as cancer, neurological disease, inflammation, obesity, etc. Since the discovery of the epigenome, numerous compounds have been developed to reverse DNA methylation and histone acetylation aberrant profile in diseases. Among them several were inspired by Nature and have a great interest as therapeutic molecules. In the quest of finding new ways to target epigenetic mechanisms, the use of chemical tools is a powerful strategy to better understand epigenetic mechanisms in biological systems. In this review we will present natural products reported as DNMT or HDAC inhibitors for anticancer treatments. We will then discuss the use of chemical tools that have been used in order to explore the epigenome.
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Affiliation(s)
- Santiago Lascano
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier-ENSCM, 240 avenue du Prof. E. Jeanbrau, 34296, Montpellier cedex 5, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, 28 rue du Docteur Roux, 75724, Paris cedex 15, France
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