1
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Yoshida S, Sako Y, Nikaido E, Ueda T, Kozono I, Ichihashi Y, Nakahashi A, Onishi M, Yamatsu Y, Kato T, Nishikawa J, Tachibana Y. Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β-Herpesvirus Proteases. ACS Med Chem Lett 2023; 14:1558-1566. [PMID: 37974946 PMCID: PMC10641906 DOI: 10.1021/acsmedchemlett.3c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
Viral proteases, the key enzymes that regulate viral replication and assembly, are promising targets for antiviral drug discovery. Herpesvirus proteases are enzymes with no crystallographically confirmed noncovalent active-site binders, owing to their shallow and polar substrate-binding pockets. Here, we applied our previously reported "Peptide-to-Small Molecule" strategy to generate novel inhibitors of β-herpesvirus proteases. Rapid selection with a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease (HCMVPro) with high affinity, and pharmacophore queries were defined based on the results of subsequent intermolecular interaction analyses. Membrane-permeable small molecule 19, designed de novo according to this hypothesis, exhibited enzyme inhibitory activity (IC50 = 10-6 to 10-7 M) against β-herpesvirus proteases, and the design concept was proved by X-ray cocrystal analysis.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Sako
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Eiji Nikaido
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Taichi Ueda
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Ichihashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsufumi Nakahashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Motoyasu Onishi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yukiko Yamatsu
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Teruhisa Kato
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Junichi Nishikawa
- PeptiDream
Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Yuki Tachibana
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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2
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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Eberhardt J, Forli S. WaterKit: Thermodynamic Profiling of Protein Hydration Sites. J Chem Theory Comput 2023; 19:2535-2556. [PMID: 37094087 PMCID: PMC10732097 DOI: 10.1021/acs.jctc.2c01087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the most recent decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models) to more computationally expensive and accurate ones, mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show an unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well-suited to be integrated in high-throughput pipelines such as molecular docking.
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Affiliation(s)
- Jerome Eberhardt
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
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4
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Sakyi PO, Kwofie SK, Tuekpe JK, Gwira TM, Broni E, Miller WA, Wilson MD, Amewu RK. Inhibiting Leishmania donovani Sterol Methyltransferase to Identify Lead Compounds Using Molecular Modelling. Pharmaceuticals (Basel) 2023; 16:ph16030330. [PMID: 36986430 PMCID: PMC10054574 DOI: 10.3390/ph16030330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
The recent outlook of leishmaniasis as a global public health concern coupled with the reportage of resistance and lack of efficacy of most antileishmanial drugs calls for a concerted effort to find new leads. The study combined In silico and in vitro approaches to identify novel potential synthetic small-molecule inhibitors targeting the Leishmania donovani sterol methyltransferase (LdSMT). The LdSMT enzyme in the ergosterol biosynthetic pathway is required for the parasite’s membrane fluidity, distribution of membrane proteins, and control of the cell cycle. The lack of LdSMT homologue in the human host and its conserved nature among all Leishmania parasites makes it a viable target for future antileishmanial drugs. Initially, six known inhibitors of LdSMT with IC50 < 10 μM were used to generate a pharmacophore model with a score of 0.9144 using LigandScout. The validated model was used to screen a synthetic library of 95,630 compounds obtained from InterBioScreen limited. Twenty compounds with pharmacophore fit scores above 50 were docked against the modelled three-dimensional structure of LdSMT using AutoDock Vina. Consequently, nine compounds with binding energies ranging from −7.5 to −8.7 kcal/mol were identified as potential hit molecules. Three compounds comprising STOCK6S-06707, STOCK6S-84928, and STOCK6S-65920 with respective binding energies of −8.7, −8.2, and −8.0 kcal/mol, lower than 22,26-azasterol (−7.6 kcal/mol), a known LdSMT inhibitor, were selected as plausible lead molecules. Molecular dynamics simulation studies and molecular mechanics Poisson–Boltzmann surface area calculations showed that the residues Asp25 and Trp208 were critical for ligand binding. The compounds were also predicted to have antileishmanial activity with reasonable pharmacological and toxicity profiles. When the antileishmanial activity of the three hits was evaluated in vitro against the promastigotes of L. donovani, mean half-maximal inhibitory concentrations (IC50) of 21.9 ± 1.5 μM (STOCK6S-06707), 23.5 ± 1.1 μM (STOCK6S-84928), and 118.3 ± 5.8 μM (STOCK6S-65920) were obtained. Furthermore, STOCK6S-84928 and STOCK6S-65920 inhibited the growth of Trypanosoma brucei, with IC50 of 14.3 ± 2.0 μM and 18.1 ± 1.4 μM, respectively. The identified compounds could be optimised to develop potent antileishmanial therapeutic agents.
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Affiliation(s)
- Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
- Correspondence: (S.K.K.); (R.K.A.); Tel.: +233-203797922 (S.K.K.); +233-543823483 (R.K.A.)
| | - Julius K. Tuekpe
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Theresa M. Gwira
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra P.O. Box LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra P.O. Box LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Richard K. Amewu
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Correspondence: (S.K.K.); (R.K.A.); Tel.: +233-203797922 (S.K.K.); +233-543823483 (R.K.A.)
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Yoshida S, Uehara S, Kondo N, Takahashi Y, Yamamoto S, Kameda A, Kawagoe S, Inoue N, Yamada M, Yoshimura N, Tachibana Y. Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J Med Chem 2022; 65:10655-10673. [PMID: 35904556 DOI: 10.1021/acs.jmedchem.2c00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, ″Peptide-to-Small Molecule″, which is a combination of rapid identification of high-affinity macrocyclic peptides via peptide display screening followed by pharmacophore-guided de novo design of small molecules, and demonstrate the applicability using nicotinamide N-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide 1 that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided de novo design and further structure-based optimization resulted in highly potent and cell-active small molecule 14 (cell-free IC50 = 0.0011 μM, cell-based IC50 = 0.40 μM), indicating that this strategy could be a new option for drug discovery.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Noriyasu Kondo
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yu Takahashi
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shiho Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsushi Kameda
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Kawagoe
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Naoko Inoue
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Masami Yamada
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Norito Yoshimura
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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6
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Rebelo P, Pacheco JG, Voroshylova IV, Seguro I, Cordeiro MNDS, Delerue-Matos C. Computational Modelling and Sustainable Synthesis of a Highly Selective Electrochemical MIP-Based Sensor for Citalopram Detection. Molecules 2022; 27:3315. [PMID: 35630794 PMCID: PMC9143463 DOI: 10.3390/molecules27103315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/10/2022] [Accepted: 05/19/2022] [Indexed: 12/04/2022] Open
Abstract
A novel molecularly imprinted polymer (MIP) has been developed based on a simple and sustainable strategy for the selective determination of citalopram (CTL) using screen-printed carbon electrodes (SPCEs). The MIP layer was prepared by electrochemical in situ polymerization of the 3-amino-4 hydroxybenzoic acid (AHBA) functional monomer and CTL as a template molecule. To simulate the polymerization mixture and predict the most suitable ratio between the template and functional monomer, computational studies, namely molecular dynamics (MD) simulations, were carried out. During the experimental preparation process, essential parameters controlling the performance of the MIP sensor, including CTL:AHBA concentration, number of polymerization cycles, and square wave voltammetry (SWV) frequency were investigated and optimized. The electrochemical characteristics of the prepared MIP sensor were evaluated by both cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques. Based on the optimal conditions, a linear electrochemical response of the sensor was obtained by SWV measurements from 0.1 to 1.25 µmol L-1 with a limit of detection (LOD) of 0.162 µmol L-1 (S/N = 3). Moreover, the MIP sensor revealed excellent CTL selectivity against very close analogues, as well as high imprinting factor of 22. Its applicability in spiked river water samples demonstrated its potential for adequate monitoring of CTL. This sensor offers a facile strategy to achieve portability while expressing a willingness to care for the environment.
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Affiliation(s)
- Patrícia Rebelo
- REQUIMTE, LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (P.R.); (I.S.); (C.D.-M.)
- REQUIMTE, LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4619-007 Porto, Portugal;
| | - João G. Pacheco
- REQUIMTE, LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (P.R.); (I.S.); (C.D.-M.)
| | - Iuliia V. Voroshylova
- REQUIMTE, LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4619-007 Porto, Portugal;
| | - Isabel Seguro
- REQUIMTE, LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (P.R.); (I.S.); (C.D.-M.)
| | - Maria Natália D. S. Cordeiro
- REQUIMTE, LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4619-007 Porto, Portugal;
| | - Cristina Delerue-Matos
- REQUIMTE, LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida 431, 4200-072 Porto, Portugal; (P.R.); (I.S.); (C.D.-M.)
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7
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Rebelo P, Pacheco JG, Voroshylova IV, Melo A, Cordeiro MND, Delerue-Matos C. A simple electrochemical detection of atorvastatin based on disposable screen-printed carbon electrodes modified by molecularly imprinted polymer: Experiment and simulation. Anal Chim Acta 2022; 1194:339410. [DOI: 10.1016/j.aca.2021.339410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/10/2021] [Accepted: 12/27/2021] [Indexed: 12/28/2022]
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8
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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9
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Olson B, Cruz A, Chen L, Ghattas M, Ji Y, Huang K, Ayoub S, Luchko T, McKay DJ, Kurtzman T. An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. J Comput Aided Mol Des 2020; 34:1219-1228. [PMID: 32918236 PMCID: PMC7486166 DOI: 10.1007/s10822-020-00341-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid inhomogeneous solvation theory maps were generated using AmberTools cpptraj-GIST, 3D reference interaction site model maps were created with AmberTools rism3d.snglpnt and hydration site analysis maps were created using SSTMap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
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Affiliation(s)
- Brian Olson
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
- Department of Biology and Chemistry, County College of Morris, 214 Center Grove Rd, Randolph, NJ, 07869, USA
| | - Anthony Cruz
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Lieyang Chen
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Mossa Ghattas
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Yeonji Ji
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Kunhui Huang
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Steven Ayoub
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, 91330, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, Center for Biological Physics, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, 91330, USA
| | - Daniel J McKay
- Ventus Therapeutics, Frederick-Banting, Montreal, QC, H9S 2A1, Canada
| | - Tom Kurtzman
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd, Bronx, NY, 10468, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
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10
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Kim M, Park K, Kim W, Jung S, Cho AE. Target-Specific Drug Design Method Combining Deep Learning and Water Pharmacophore. J Chem Inf Model 2020; 61:36-45. [PMID: 33252229 DOI: 10.1021/acs.jcim.0c00757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Following identification of a target protein, hit identification, which finds small organic molecules that bind to the target, is an important first step of a structure-based drug design project. In this study, we demonstrate a target-specific drug design method that can autonomously generate a series of target-favorable compounds. This method utilizes the seq2seq model based on a deep learning algorithm and a water pharmacophore. Water pharmacophore models are used to screen compounds that are favorable to a given target in a large compound database, and seq2seq compound generators are used to train the screened compounds and generate entirely new compounds based on the training model. Our method was tested through binding energy calculation studies of six pharmaceutically relevant targets in the directory of useful decoys (DUD) set with docking. The compounds generated by our method had lower average binding energies than decoy compounds in five out of six cases and included a number of compounds that had lower binding energies than the average binding energies of the active compounds in four cases. The generated compound lists for these four cases featured compounds with lower binding energies than even the most active compounds.
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Affiliation(s)
- Minsup Kim
- inCerebro Co., Ltd. Drug Discovery Institute, Seoul Technopark, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea
| | - Kichul Park
- inCerebro Co., Ltd. Drug Discovery Institute, Seoul Technopark, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea.,Department of Bioinformatics, Korea University, Sejong 30019, Korea
| | - Wonsang Kim
- inCerebro Co., Ltd. Drug Discovery Institute, Seoul Technopark, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea
| | - Sangwon Jung
- SK Biopharmaceuticals Co., Ltd., 221 Pangyoyeok-ro, Seongnam-si, Gyeonggi-do 13494, Korea
| | - Art E Cho
- inCerebro Co., Ltd. Drug Discovery Institute, Seoul Technopark, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea.,Department of Bioinformatics, Korea University, Sejong 30019, Korea
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11
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Xing B, Zhao J, Pan Q, Yang H, Wang L, Qu W, Gu L, Wang H, Han P, Ma G. Green Preparation of Few‐Layer Graphene Sheet Materials Using Naturally Occurring Calcium Carbonate and Plant Leaves. ChemistrySelect 2020. [DOI: 10.1002/slct.202000731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Baoyan Xing
- School of Materials Science Taiyuan University of Technology Taiyuan 030024 China
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Jianguo Zhao
- School of Materials Science Taiyuan University of Technology Taiyuan 030024 China
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Qiliang Pan
- School of Materials Science Taiyuan University of Technology Taiyuan 030024 China
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Hui Yang
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Lihua Wang
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Wenshan Qu
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Ling Gu
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Haiqing Wang
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
| | - Peide Han
- School of Materials Science Taiyuan University of Technology Taiyuan 030024 China
| | - Guibin Ma
- Institute of Carbon Materials Science Shanxi Datong University Datong 037009 China
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12
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Olson B, Cruz A, Chen L, Ghattas M, Ji Y, Huang K, McKay DJ, Kurtzman T. An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.12275705.v1. [PMID: 32511289 PMCID: PMC7263766 DOI: 10.26434/chemrxiv.12275705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid Inhomogeneous Solvation Theory maps were generated using AmberTools cpptraj-GIST and Hydration Site Analysis maps were created using SSTmap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
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Affiliation(s)
- Brian Olson
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
- County College of Morris, Department of Biology and Chemistry, 214 Center Grove Rd, Randolph, NJ, United States of America, 07869
| | - Anthony Cruz
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Lieyang Chen
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Mossa Ghattas
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Yeonji Ji
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Kunhui Huang
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
| | - Daniel J McKay
- Ventus Therapeutics, 7150 Frederick-Banting Montreal, Quebec H9S 2A1
| | - Tom Kurtzman
- Lehman College Department of Chemistry, 205 W Bedford Park Blvd Bronx, NY, United States of America, 10468
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York New York, United States of America, 10016
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13
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Pharmacoinformatics and molecular dynamic simulation studies to identify potential small-molecule inhibitors of WNK-SPAK/OSR1 signaling that mimic the RFQV motifs of WNK kinases. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2020.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Schaller D, Šribar D, Noonan T, Deng L, Nguyen TN, Pach S, Machalz D, Bermudez M, Wolber G. Next generation 3D pharmacophore modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1468] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Dora Šribar
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Theresa Noonan
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Lihua Deng
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Trung Ngoc Nguyen
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - David Machalz
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Marcel Bermudez
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
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15
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Hüfner-Wulsdorf T, Klebe G. Role of Water Molecules in Protein–Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics. J Chem Inf Model 2020; 60:1818-1832. [DOI: 10.1021/acs.jcim.0c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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16
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Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase. Sci Rep 2019; 9:13587. [PMID: 31537874 PMCID: PMC6753110 DOI: 10.1038/s41598-019-49984-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/30/2019] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.
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17
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Darby JF, Hopkins AP, Shimizu S, Roberts SM, Brannigan JA, Turkenburg JP, Thomas GH, Hubbard RE, Fischer M. Water Networks Can Determine the Affinity of Ligand Binding to Proteins. J Am Chem Soc 2019; 141:15818-15826. [DOI: 10.1021/jacs.9b06275] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Adam P. Hopkins
- Demuris Ltd., The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne NE4 5BX, United Kingdom
| | | | | | | | | | | | - Roderick E. Hubbard
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, and Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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18
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Schaller D, Pach S, Wolber G. PyRod: Tracing Water Molecules in Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:2818-2829. [PMID: 31117512 DOI: 10.1021/acs.jcim.9b00281] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the drug design community. Including corresponding data into 3D pharmacophore modeling is essential for efficient high throughput virtual screening. Here, we present PyRod, a free and open-source Python software that allows for visualization of pharmacophoric binding pocket characteristics, identification of hot spots for ligand binding, and subsequent generation of pharmacophore features for virtual screening. The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. The described software was applied to 5 therapeutically relevant drug targets, and generated pharmacophores were evaluated using DUD-E benchmarking sets. The best performing pharmacophore was found for the HIV1 protease with an early enrichment factor of 54.6. PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. Since structural information about cocrystallized ligands is not needed, screening campaigns can be followed, for which less or no ligand information is available. PyRod is freely available at https://github.com/schallerdavid/pyrod .
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Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry , Freie Universität Berlin , Königin-Luise-Strasse 2+4 , 14195 Berlin , Germany
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19
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Pradhan MR, Nguyen MN, Kannan S, Fox SJ, Kwoh CK, Lane DP, Verma CS. Characterization of Hydration Properties in Structural Ensembles of Biomolecules. J Chem Inf Model 2019; 59:3316-3329. [DOI: 10.1021/acs.jcim.8b00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mohan R. Pradhan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Minh N. Nguyen
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Stephen J. Fox
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - David P. Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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