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Wang L, Wang S, Yang H, Li S, Wang X, Zhou Y, Tian S, Liu L, Bai F. Conformational Space Profiling Enhances Generic Molecular Representation for AI-Powered Ligand-Based Drug Discovery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403998. [PMID: 39206753 DOI: 10.1002/advs.202403998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/25/2024] [Indexed: 09/04/2024]
Abstract
The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, and is an essential module applied across a wide range of artificial intelligence-driven drug discovery scenarios. However, current molecular representation models rarely consider the three-dimensional conformational space of molecules, losing sight of the dynamic nature of small molecules as well as the essence of molecular conformational space that covers the heterogeneity of molecule properties, such as the multi-target mechanism of action, recognition of different biomolecules, dynamics in cytoplasm and membrane. In this study, a new model named GeminiMol is proposed to incorporate conformational space profiles into molecular representation learning, which extracts the feature of capturing the complicated interplay between the molecular structure and the conformational space. Although GeminiMol is pre-trained on a relatively small-scale molecular dataset (39290 molecules), it shows balanced and superior performance not only on 67 molecular properties predictions but also on 73 cellular activity predictions and 171 zero-shot tasks (including virtual screening and target identification). By capturing the molecular conformational space profile, the strategy paves the way for rapid exploration of chemical space and facilitates changing paradigms for drug design.
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Affiliation(s)
- Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Shihang Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Hao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Shiwei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Xinyu Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Yongqi Zhou
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Siyuan Tian
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Lu Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, Information Science and Technology, Shanghai Tech University, Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
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Skwarecki AS, Nowak MG, Milewska MJ. Amino Acid and Peptide-Based Antiviral Agents. ChemMedChem 2021; 16:3106-3135. [PMID: 34254457 DOI: 10.1002/cmdc.202100397] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 01/10/2023]
Abstract
A significant number of antiviral agents used in clinical practice are amino acids, short peptides, or peptidomimetics. Among them, several HIV protease inhibitors (e. g. lopinavir, atazanavir), HCV protease inhibitors (e. g. grazoprevir, glecaprevir), and HCV NS5A protein inhibitors have contributed to a significant decrease in mortality from AIDS and hepatitis. However, there is an ongoing need for the discovery of new antiviral agents and the development of existing drugs; amino acids, both proteinogenic and non-proteinogenic in nature, serve as convenient building blocks for this purpose. The synthesis of non-proteinogenic amino acid components of antiviral agents could be challenging due to the need for enantiomerically or diastereomerically pure products. Herein, we present a concise review of antiviral agents whose structures are based on amino acids of both natural and unnatural origin. Special attention is paid to the synthetic aspects of non-proteinogenic amino acid components of those agents.
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Affiliation(s)
- Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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3
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Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Eur J Med Chem 2018; 160:171-182. [PMID: 30340140 PMCID: PMC6237192 DOI: 10.1016/j.ejmech.2018.09.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/07/2023]
Abstract
We describe the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors with carboxamide derivatives as the P2 ligands. We have specifically designed aminothiochromane and aminotetrahydronaphthalene-based carboxamide ligands to promote hydrogen bonding and van der Waals interactions in the active site of HIV-1 protease. Inhibitors 4e and 4j have shown potent enzyme inhibitory and antiviral activity. High resolution X-ray crystal structures of 4d- and 4k-bound HIV-1 protease revealed molecular insights into the ligand-binding site interactions.
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4
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Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016; 37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
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Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016; 59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Gary Prato
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
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6
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Motwani HV, De Rosa M, Odell LR, Hallberg A, Larhed M. Aspartic protease inhibitors containing tertiary alcohol transition-state mimics. Eur J Med Chem 2014; 90:462-90. [PMID: 25481814 DOI: 10.1016/j.ejmech.2014.11.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/12/2014] [Accepted: 11/19/2014] [Indexed: 11/30/2022]
Abstract
Aspartic proteases (APs) are a class of enzymes engaged in the proteolytic digestion of peptide substrates. APs play important roles in physiological and infectious pathways, making them plausible drug targets. For instance in the treatment of HIV infections, access to an efficient combination of protease and reverse transcriptase inhibitors have changed a terminal illness to a chronic but manageable disease. However, the benefits have been limited due to the emergence of drug resistant viral strains, poor pharmacokinetic properties of peptidomimetic inhibitors and adverse effects associated with the treatment. In the 1980s, D. Rich and co-workers proposed a novel strategy for the development of AP inhibitors by replacing the secondary hydroxyl group with a tertiary alcohol as part of the transition state (TS) mimicking moiety. This strategy has been extensively explored over the last decade with a common belief that masking of the polar group, e.g. by intramolecular hydrogen bonding, has the potential to enhance transcellular transport. This is the first review presenting the advances of AP inhibitors comprising a tertiary hydroxyl group. The inhibitors have been classified into different tert-hydroxy TS mimics and their design strategies, synthesis, biological activities, structure-activity-relationships and X-ray structures are discussed.
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Affiliation(s)
- Hitesh V Motwani
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Maria De Rosa
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Luke R Odell
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden.
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De Rosa M, Unge J, Motwani HV, Rosenquist Å, Vrang L, Wallberg H, Larhed M. Synthesis of P1'-functionalized macrocyclic transition-state mimicking HIV-1 protease inhibitors encompassing a tertiary alcohol. J Med Chem 2014; 57:6444-57. [PMID: 25054811 DOI: 10.1021/jm500434q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Seven novel tertiary alcohol containing linear HIV-1 protease inhibitors (PIs), decorated at the para position of the benzyl group in the P1' side with (hetero)aromatic moieties, were synthesized and biologically evaluated. To study the inhibition and antiviral activity effect of P1-P3 macrocyclization, 14- and 15-membered macrocyclic PIs were prepared by ring-closing metathesis of the corresponding linear PIs. The macrocycles were more active than the linear precursors and compound 10f, with a 2-thiazolyl group in the P1' position, was the most potent PI of this new series (Ki 2.2 nM, EC50 0.2 μM). Co-crystallized complexes of both linear and macrocyclic PIs with the HIV-1 protease enzyme were prepared and analyzed.
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Affiliation(s)
- Maria De Rosa
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University , P.O. Box 574, SE-751 23 Uppsala, Sweden
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Joshi A, Véron JB, Unge J, Rosenquist Å, Wallberg H, Samuelsson B, Hallberg A, Larhed M. Design and Synthesis of P1–P3 Macrocyclic Tertiary-Alcohol-Comprising HIV-1 Protease Inhibitors. J Med Chem 2013; 56:8999-9007. [DOI: 10.1021/jm400811d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Advait Joshi
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Jean-Baptiste Véron
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Johan Unge
- MAX IV-laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
| | | | - Hans Wallberg
- Medivir AB, P.O. Box 1086, SE-141
22 Huddinge, Sweden
| | | | - Anders Hallberg
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department
of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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Wu X, Ohrngren P, Joshi AA, Trejos A, Persson M, Arvela RK, Wallberg H, Vrang L, Rosenquist A, Samuelsson BB, Unge J, Larhed M. Synthesis, X-ray analysis, and biological evaluation of a new class of stereopure lactam-based HIV-1 protease inhibitors. J Med Chem 2012; 55:2724-36. [PMID: 22376008 PMCID: PMC3310203 DOI: 10.1021/jm201620t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
In an effort to identify a new class of druglike HIV-1
protease
inhibitors, four different stereopure β-hydroxy γ-lactam-containing
inhibitors have been synthesized, biologically evaluated, and cocrystallized.
The impact of the tether length of the central spacer (two or three
carbons) was also investigated. A compound with a shorter tether and
(3R,4S) absolute configuration exhibited
high activity with a Ki of 2.1 nM and
an EC50 of 0.64 μM. Further optimization by decoration
of the P1′ side chain furnished an even more potent HIV-1 protease
inhibitor (Ki = 0.8 nM, EC50 = 0.04 μM). According to X-ray analysis, the new class of
inhibitors did not fully succeed in forming two symmetric hydrogen
bonds to the catalytic aspartates. The crystal structures of the complexes
further explain the difference in potency between the shorter inhibitors
(two-carbon spacer) and the longer inhibitors (three-carbon spacer).
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Affiliation(s)
- Xiongyu Wu
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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Gising J, Odell LR, Larhed M. Microwave-assisted synthesis of small molecules targeting the infectious diseases tuberculosis, HIV/AIDS, malaria and hepatitis C. Org Biomol Chem 2012; 10:2713-29. [PMID: 22227602 DOI: 10.1039/c2ob06833h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The unique properties of microwave in situ heating offer unparalleled opportunities for medicinal chemists to speed up lead optimisation processes in early drug discovery. The technology is ideal for small-scale discovery chemistry because it allows full reaction control, short reaction times, high safety and rapid feedback. To illustrate these advantages, we herein describe applications and approaches in the synthesis of small molecules to combat four of the most prevalent infectious diseases; tuberculosis, HIV/AIDS, malaria and hepatitis C, using dedicated microwave instrumentation.
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Affiliation(s)
- Johan Gising
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
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