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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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2
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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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3
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Greenwood SOR, Chan AWE, Hansen DF, Marson CM. Potent non-hydroxamate inhibitors of histone deacetylase-8: Role and scope of an isoindolin-2-yl linker with an α-amino amide as the zinc-binding unit. Bioorg Med Chem Lett 2020; 30:126926. [PMID: 31952961 DOI: 10.1016/j.bmcl.2019.126926] [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: 09/26/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/24/2022]
Abstract
A series of potent inhibitors of histone deacetylase-8 (HDAC8) is described that contains an α-amino amide zinc-binding unit and a substituted isoindolinyl capping group. The presence of a 2,4-dichlorophenyl unit located in the acetate-release cavity was shown to confer a gain of approx. 4.3 kJ mol-1 in binding energy compared to a phenyl group, and the isoindoline linker has approx. 5.8 kJ mol-1 greater binding energy than the corresponding tetrahydroisoquinoline ring system. In a series of 5-substituted isoindolin-2-yl inhibitors, a 5-acetylamino derivative was found to be more potent than the 5-unsubstituted lead HDAC8 inhibitor (increase in binding energy of 2.0 kJ mol-1, ascribed to additional binding interactions within the Nε-acetyl-l-lysine binding tunnel in HDAC8, including hydrogen bonding to Asp101. Tolerance of a 5-substituent (capping group) on the isoindoline ring has been demonstrated, and which in some cases confers improved enzyme inhibition, the HDAC8 substrate-binding region providing a platform for additional interactions.
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Affiliation(s)
- Simon O R Greenwood
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H OAJ, UK; Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - A W Edith Chan
- Wolfson Institute of Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK
| | - D Flemming Hansen
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Charles M Marson
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H OAJ, UK.
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4
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Zwinderman MRH, de Weerd S, Dekker FJ. Targeting HDAC Complexes in Asthma and COPD. EPIGENOMES 2019; 3:19. [PMID: 34968229 PMCID: PMC8594684 DOI: 10.3390/epigenomes3030019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein acetylation. Over a thousand proteins are reversibly acetylated, and acetylation critically influences aberrant intracellular signaling pathways in asthma and COPD. The diverse set of selective and non-selective HDAC inhibitors used in pre-clinical models of airway inflammation show promising results, but several challenges still need to be overcome. One such challenge is the design of HDAC inhibitors with unique selectivity profiles, such as selectivity towards specific HDAC complexes. Novel strategies to disrupt HDAC complexes should be developed to validate HDACs further as targets for new anti-inflammatory pulmonary treatments.
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Affiliation(s)
| | | | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, The Netherlands (M.R.H.Z.) (S.d.W.)
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5
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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Du J, Liu L, Guo LZ, Yao XJ, Yang JM. Molecular basis of P450 OleT JE: an investigation of substrate binding mechanism and major pathways. J Comput Aided Mol Des 2017; 31:483-495. [PMID: 28342136 DOI: 10.1007/s10822-017-0013-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/23/2017] [Indexed: 02/02/2023]
Abstract
Cytochrome P450 OleTJE has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJE for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleTJE Compound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleTJE and valuable information for rational enzyme design for short chain fatty acid decarboxylation.
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Affiliation(s)
- Juan Du
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Liu
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Li Zhong Guo
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao Jun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Jian Ming Yang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
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7
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Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today 2017; 22:249-269. [DOI: 10.1016/j.drudis.2016.11.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022]
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8
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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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9
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Kurisaki I, Barberot C, Takayanagi M, Nagaoka M. Dewetting of S1-Pocket via Water Channel upon Thrombin–Substrate Association Reaction. J Phys Chem B 2015; 119:15807-12. [DOI: 10.1021/acs.jpcb.5b09581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ikuo Kurisaki
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Chantal Barberot
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Masayoshi Takayanagi
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate
School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency,
Honmachi, Kawaguchi 332-0012, Japan
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10
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Mottamal M, Zheng S, Huang TL, Wang G. Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules 2015; 20:3898-941. [PMID: 25738536 PMCID: PMC4372801 DOI: 10.3390/molecules20033898] [Citation(s) in RCA: 477] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 02/04/2023] Open
Abstract
Histone dacetylases (HDACs) are a group of enzymes that remove acetyl groups from histones and regulate expression of tumor suppressor genes. They are implicated in many human diseases, especially cancer, making them a promising therapeutic target for treatment of the latter by developing a wide variety of inhibitors. HDAC inhibitors interfere with HDAC activity and regulate biological events, such as cell cycle, differentiation and apoptosis in cancer cells. As a result, HDAC inhibitor-based therapies have gained much attention for cancer treatment. To date, the FDA has approved three HDAC inhibitors for cutaneous/peripheral T-cell lymphoma and many more HDAC inhibitors are in different stages of clinical development for the treatment of hematological malignancies as well as solid tumors. In the intensifying efforts to discover new, hopefully more therapeutically efficacious HDAC inhibitors, molecular modeling-based rational drug design has played an important role in identifying potential inhibitors that vary in molecular structures and properties. In this review, we summarize four major structural classes of HDAC inhibitors 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)
- Madhusoodanan Mottamal
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Shilong Zheng
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Tien L Huang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Guangdi Wang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
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11
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Deschamps N, Simões-Pires CA, Carrupt PA, Nurisso A. How the flexibility of human histone deacetylases influences ligand binding: an overview. Drug Discov Today 2015; 20:736-42. [PMID: 25597521 DOI: 10.1016/j.drudis.2015.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/12/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022]
Abstract
Over the past decade, human histone deacetylases (HDACs) have become interesting as therapeutic targets because of the benefits that their modulation might provide in aging-related disorders. Recently, studies using crystallography and computational chemistry have provided information on the structure and conformational changes related to HDAC-mediated recognition events. Through the description of the key mass and one-off movements observed in metal-dependent HDACs, here we highlight the impact of flexibility on drug-binding affinity and specificity. The collected information will be useful for not only a better understanding of the biological functions of HDACs, but also the conception of new selective binders.
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Affiliation(s)
- Nathalie Deschamps
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Claudia Avello Simões-Pires
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Pierre-Alain Carrupt
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Quai Ernest Ansermet, 30, CH-1211 Geneva 4, Switzerland.
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Vellore NA, Baron R. Epigenetic molecular recognition: a biomolecular modeling perspective. ChemMedChem 2014; 9:484-94. [PMID: 24616246 DOI: 10.1002/cmdc.201300510] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 01/23/2023]
Abstract
The abnormal regulation of epigenetic protein families is associated with the onset and progression of various human diseases. However, epigenetic processes remain relatively obscure at the molecular level, thus preventing the rational design of chemical therapeutics. An array of robust computational and modeling approaches can complement experiments to shed light on the complex mechanisms of epigenetic molecular recognition and can guide medicinal chemists in designing selective and potent drug molecules. Herein we present a review of studies focused on epigenetic molecular recognition from a biomolecular modeling viewpoint. Although the known epigenetic targets are numerous, this review focuses on the more limited protein families on which computational modeling has been successfully applied. Therefore, we review three main topics: 1) histone deacetylases, 2) histone demethylases, and 3) histone tail dynamics. A brief review of the biological background and biomedical relevance is presented for each topic, followed by a detailed discussion of the computational studies and their relevance.
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Affiliation(s)
- Nadeem A Vellore
- Department of Medicinal Chemistry, College of Pharmacy and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 (USA)
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13
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Wang F, Ganesan A. Fragment based electronic structural analysis of l-phenylalanine using calculated ionization spectroscopy and dual space analysis. RSC Adv 2014. [DOI: 10.1039/c4ra09146a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fragmentation schemes in phenylalanine revealed using ionization spectroscopy and dual space analysis.
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Affiliation(s)
- Feng Wang
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences
- Engineering and Technology
- Swinburne University of Technology
| | - Aravindhan Ganesan
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences
- Engineering and Technology
- Swinburne University of Technology
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