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Bülbül EF, Melesina J, Ibrahim HS, Abdelsalam M, Vecchio A, Robaa D, Zessin M, Schutkowski M, Sippl W. Docking, Binding Free Energy Calculations and In Vitro Characterization of Pyrazine Linked 2-Aminobenzamides as Novel Class I Histone Deacetylase (HDAC) Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082526. [PMID: 35458724 PMCID: PMC9032825 DOI: 10.3390/molecules27082526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/16/2022]
Abstract
Class I histone deacetylases, HDAC1, HDAC2, and HDAC3, represent potential targets for cancer treatment. However, the development of isoform-selective drugs for these enzymes remains challenging due to their high sequence and structural similarity. In the current study, we applied a computational approach to predict the selectivity profile of developed inhibitors. Molecular docking followed by MD simulation and calculation of binding free energy was performed for a dataset of 2-aminobenzamides comprising 30 previously developed inhibitors. For each HDAC isoform, a significant correlation was found between the binding free energy values and in vitro inhibitory activities. The predictive accuracy and reliability of the best preforming models were assessed on an external test set of newly designed and synthesized inhibitors. The developed binding free-energy models are cost-effective methods and help to reduce the time required to prioritize compounds for further studies.
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Affiliation(s)
- Emre F. Bülbül
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
| | - Jelena Melesina
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
| | - Hany S. Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt
| | - Mohamed Abdelsalam
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Anita Vecchio
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
| | - Matthes Zessin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (M.Z.); (M.S.)
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (M.Z.); (M.S.)
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (E.F.B.); (J.M.); (H.S.I.); (M.A.); (A.V.); (D.R.)
- Correspondence:
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Brandmaier S, Tetko IV. ROBUSTNESS IN EXPERIMENTAL DESIGN: A STUDY ON THE RELIABILITY OF SELECTION APPROACHES. Cell 2018. [DOI: 10.1016/s0092-8674(18)90002-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ovchinnikova SI, Bykov AA, Tsivadze AY, Dyachkov EP, Kireeva NV. Supervised extensions of chemography approaches: case studies of chemical liabilities assessment. J Cheminform 2014; 6:20. [PMID: 24868246 PMCID: PMC4018504 DOI: 10.1186/1758-2946-6-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/28/2014] [Indexed: 12/04/2022] Open
Abstract
Chemical liabilities, such as adverse effects and toxicity, play a significant role in modern drug discovery process. In silico assessment of chemical liabilities is an important step aimed to reduce costs and animal testing by complementing or replacing in vitro and in vivo experiments. Herein, we propose an approach combining several classification and chemography methods to be able to predict chemical liabilities and to interpret obtained results in the context of impact of structural changes of compounds on their pharmacological profile. To our knowledge for the first time, the supervised extension of Generative Topographic Mapping is proposed as an effective new chemography method. New approach for mapping new data using supervised Isomap without re-building models from the scratch has been proposed. Two approaches for estimation of model's applicability domain are used in our study to our knowledge for the first time in chemoinformatics. The structural alerts responsible for the negative characteristics of pharmacological profile of chemical compounds has been found as a result of model interpretation.
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Affiliation(s)
- Svetlana I Ovchinnikova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
| | - Arseniy A Bykov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
| | - Aslan Yu Tsivadze
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
| | - Evgeny P Dyachkov
- Kurnakov Institute of General and Inorganic Chemistry RAS, Leninsky pr-t 31, 119071 Moscow, Russia
| | - Natalia V Kireeva
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
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Brandmaier S, Tetko IV. Robustness in experimental design: A study on the reliability of selection approaches. Comput Struct Biotechnol J 2013; 7:e201305002. [PMID: 24688738 PMCID: PMC3962228 DOI: 10.5936/csbj.201305002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 06/27/2013] [Accepted: 06/30/2013] [Indexed: 11/22/2022] Open
Abstract
The quality criteria for experimental design approaches in chemoinformatics are numerous. Not only the error performance of a model resulting from the selected compounds is of importance, but also reliability, consistency, stability and robustness against small variations in the dataset or structurally diverse compounds. We developed a new stepwise, adaptive approach, DescRep, combining an iteratively refined descriptor selection with a sampling based on the putatively most representative compounds. A comparison of the proposed strategy was based on statistical performance of models derived from such a selection to those derived by other popular and frequently used approaches, such as the Kennard-Stone algorithm or the most descriptive compound selection. We used three datasets to carry out a statistical evaluation of the performance, reliability and robustness of the resulting models. Our results indicate that stepwise and adaptive approaches have a better adaptability to changes within a dataset and that this adaptability results in a better error performance and stability of the resulting models.
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Affiliation(s)
- Stefan Brandmaier
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Structural Biology, Neuherberg D-85764, Germany
| | - Igor V Tetko
- Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Institute of Structural Biology, Neuherberg D-85764, Germany
- Chemistry Department, Faculty of Science, King Abdulaziz University, P. O. Box 80203, Jeddah 21589, Saudi Arabia
- eADMET GmbH, Ingolstaedter Landstrasse 1, Neuherberg D-85764, Germany
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