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Grenier D, Audebert S, Preto J, Guichou JF, Krimm I. Linkers in fragment-based drug design: an overview of the literature. Expert Opin Drug Discov 2023; 18:987-1009. [PMID: 37466331 DOI: 10.1080/17460441.2023.2234285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION In fragment-based drug design, fragment linking is a popular strategy where two fragments binding to different sub-pockets of a target are linked together. This attractive method remains challenging especially due to the design of ideal linkers. AREAS COVERED The authors review the types of linkers and chemical reactions commonly used to the synthesis of linkers, including those utilized in protein-templated fragment self-assembly, where fragments are directly linked in the presence of the protein. Finally, they detail computational workflows and software including generative models that have been developed for fragment linking. EXPERT OPINION The authors believe that fragment linking offers key advantages for compound design, particularly for the design of bivalent inhibitors linking two distinct pockets of the same or different subunits. On the other hand, more studies are needed to increase the potential of protein-templated approaches in FBDD. Important computational tools such as structure-based de novo software are emerging to select suitable linkers. Fragment linking will undoubtedly benefit from developments in computational approaches and machine learning models.
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Affiliation(s)
- Dylan Grenier
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
| | - Solène Audebert
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Jordane Preto
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
| | - Jean-François Guichou
- Centre de Biologie Structurale, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Isabelle Krimm
- Team Small Molecules for Biological Targets, Centre de Recherche En Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France
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2
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Zhan F, Zhu J, Xie S, Xu J, Xu S. Advances of bioorthogonal coupling reactions in drug development. Eur J Med Chem 2023; 253:115338. [PMID: 37037138 DOI: 10.1016/j.ejmech.2023.115338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Currently, bioorthogonal coupling reactions have garnered considerable interest due to their high substrate selectivity and less restrictive reaction conditions. During recent decades, bioorthogonal coupling reactions have emerged as powerful tools in drug development. This review describes the current applications of bioorthogonal coupling reactions in compound library building mediated by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and in situ click chemistry or conjunction with other techniques; druggability optimization with 1,2,3-triazole groups; and intracellular self-assembly platforms with ring tension reactions, which are presented from the viewpoint of drug development. There is a reasonable prospect that bioorthogonal coupling reactions will accelerate the screening of lead compounds, the designing strategies of small molecules and expand the variety of designed compounds, which will be a new trend in drug development in the future.
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3
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [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: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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4
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Lossouarn A, Puteaux C, Bailly L, Tognetti V, Joubert L, Renard P, Sabot C. Metalloenzyme‐Mediated Thiol‐Yne Addition Towards Photoisomerizable Fluorescent Dyes. Chemistry 2022; 28:e202202180. [DOI: 10.1002/chem.202202180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Alexis Lossouarn
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Chloé Puteaux
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Laetitia Bailly
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Vincent Tognetti
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Laurent Joubert
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Pierre‐Yves Renard
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
| | - Cyrille Sabot
- Normandie Univ, CNRS, UNIROUEN, INSA Rouen, COBRA (UMR 6014) Rouen 76000 France
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5
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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6
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Rodríguez DF, Moglie Y, Ramírez-Sarmiento CA, Singh SK, Dua K, Zacconi FC. Bio-click chemistry: a bridge between biocatalysis and click chemistry. RSC Adv 2022; 12:1932-1949. [PMID: 35425264 PMCID: PMC8979012 DOI: 10.1039/d1ra08053a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/28/2021] [Indexed: 11/21/2022] Open
Abstract
The fields of click chemistry and biocatalysis have rapidly grown over the last two decades. The development of robust and active biocatalysts and the widespread use of straightforward click reactions led to significant interactions between these two fields. Therefore the name bio-click chemistry seems to be an accurate definition of chemoenzymatic reactions cooperating with click transformations. Bio-click chemistry can be understood as the approach towards molecules of high-value using a green and sustainable approach by exploiting the potential of biocatalytic enzyme activity combined with the reliable nature of click reactions. This review summarizes the principal bio-click chemistry reactions reported over the last two decades, with a special emphasis on small molecules. Contributions to the field of bio-click chemistry are manifold, but the synthesis of chiral molecules with applications in medicinal chemistry and sustainable syntheses will be especially highlighted.
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Affiliation(s)
- Diego F Rodríguez
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile Chile
| | - Yanina Moglie
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET Argentina
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile Santiago Chile.,ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio) Santiago Chile
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara 144411 Punjab India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney NSW 2007 Australia.,Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney Ultimo Australia
| | - Flavia C Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile Chile .,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile Santiago Chile.,Centro de Investigaciones en Nanotecnología y Materiales Avanzados, CIEN-UC, Pontificia Universidad Católica de Chile Santiago Chile
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7
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Deprez B, Bosc D, Charton J, Couturier C, Deprez-Poulain R, Flipo M, Leroux F, Villemagne B, Willand N. Molecular Design in Practice: A Review of Selected Projects in a French Research Institute That Illustrates the Link between Chemical Biology and Medicinal Chemistry. Molecules 2021; 26:6083. [PMID: 34641626 PMCID: PMC8512331 DOI: 10.3390/molecules26196083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/19/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical biology and drug discovery are two scientific activities that pursue different goals but complement each other. The former is an interventional science that aims at understanding living systems through the modulation of its molecular components with compounds designed for this purpose. The latter is the art of designing drug candidates, i.e., molecules that act on selected molecular components of human beings and display, as a candidate treatment, the best reachable risk benefit ratio. In chemical biology, the compound is the means to understand biology, whereas in drug discovery, the compound is the goal. The toolbox they share includes biological and chemical analytic technologies, cell and whole-body imaging, and exploring the chemical space through state-of-the-art design and synthesis tools. In this article, we examine several tools shared by drug discovery and chemical biology through selected examples taken from research projects conducted in our institute in the last decade. These examples illustrate the design of chemical probes and tools to identify and validate new targets, to quantify target engagement in vitro and in vivo, to discover hits and to optimize pharmacokinetic properties with the control of compound concentration both spatially and temporally in the various biophases of a biological system.
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Affiliation(s)
- Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Cyril Couturier
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
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8
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Zhou Y, Shen W, Peng J, Deng Y, Li X. Identification of isoform/domain-selective fragments from the selection of DNA-encoded dynamic library. Bioorg Med Chem 2021; 45:116328. [PMID: 34364223 DOI: 10.1016/j.bmc.2021.116328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged to be a powerful ligand screening technology in drug discovery. Recently, we reported a DNA-encoded dynamic library (DEDL) approach that combines the principle of traditional dynamic combinatorial library (DCL) with DEL. DEDL has shown excellent potential in fragment-based ligand discovery with a variety of protein targets. Here, we further tested the utility of DEDL in identifying low molecular weight fragments that are selective for different isoforms or domains of the same protein family. A 10,000-member DEDL was selected against sirtuin-1, 2, and 5 (SIRT1, 2, 5) and the BD1 and BD2 domains of bromodomain 4 (BRD4), respectively. Albeit with modest potency, a series of isoform/domain-selective fragments were identified and the corresponding inhibitors were derived by fragment linking.
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Innovation and Technology Commission, Hong Kong Special Administrative Region
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9
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Molęda Z, Zawadzka A, Czarnocki Z, Monjas L, Hirsch AKH, Budzianowski A, Maurin JK. "Clicking" fragment leads to novel dual-binding cholinesterase inhibitors. Bioorg Med Chem 2021; 42:116269. [PMID: 34130217 DOI: 10.1016/j.bmc.2021.116269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
Cholinesterase inhibitors are potent therapeutics in the treatment of Alzheimer's disease. Among them, dual binding ligands have recently gained a lot of attention. We discovered novel dual-binding cholinesterase inhibitors, using "clickable" fragments, which bind to either catalytic active site (CAS) or peripheral anionic site (PAS) of the enzyme. Copper(I)-catalyzed azide-alkyne cycloaddition allowed to effectively synthesize a series of final heterodimers, and modeling and kinetic studies confirmed their ability to bind to both CAS and PAS. A potent acetylcholinesterase inhibitor with IC50 = 18 nM (compound 23g) was discovered. A target-guided approach to link fragments by the enzyme itself was tested using butyrylcholinesterase.
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Affiliation(s)
- Zuzanna Molęda
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland.
| | - Anna Zawadzka
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Zbigniew Czarnocki
- University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Leticia Monjas
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | | | - Jan K Maurin
- National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; National Centre for Nuclear Research, 05-400 Otwock-Świerk, Poland
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10
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Prasher P, Sharma M, Zacconi F, Gupta G, Aljabali AA, Mishra V, Tambuwala MM, Kapoor DN, Negi P, Andreoli Pinto TDJ, Singh I, Chellappan DK, Dua K. Synthesis and Anticancer Properties of ‘Azole’ Based Chemotherapeutics as Emerging Chemical Moieties: A Comprehensive Review. CURR ORG CHEM 2021. [DOI: 10.2174/1385272824999200820152501] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Azole frameworks serve as privileged scaffolds in the contemporary drug design
paradigm owing to their unique physicochemical profile that promotes the development
of highly selective, physiological benevolent chemotherapeutics. Several azole nuclei
function as bioisostere in medicinal chemistry and prompt the development of tailored
therapeutics for targeting the desired biological entities. Besides, the azole scaffold forms
an integral part in the advanced drug designing methodologies, such as target template insitu
drug synthesis, that assists in rapid identification of the hit molecules form a diverse
pool of leads; and direct biomolecule-drug conjugation, along with bioorthogonal strategies
that ensure localization, and superior target specificity of the directed therapeutic.
Lastly, the structural diversity of azole framework and high yielding click synthetic methods
provide a comprehensive Structure-Activity Relationship analysis for design optimization of the potential
drug molecules by fine-tuning the placement of different substituents critical for the activity. This review provides
a comprehensive analysis of the synthesis and anticancer potential of azole based chemotherapeutics.
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Affiliation(s)
- Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Dehradun 248007, India
| | - Mousmee Sharma
- Department of Chemistry, Uttaranchal University, Arcadia Grant, Dehradun 248007, India
| | - Flavia Zacconi
- Departamento de Quimica Organica, Facultad de Quimica y de Farmacia, Pontificia Universidad Catolica de Chile, Av. Vicuna Mackenna 4860, Macul, Santiago 7820436, Chile
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302 017, Jaipur, India
| | - Alaa A.A. Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid, Jordan
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland BT52 1SA, United Kingdom
| | - Deepak N. Kapoor
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Post box no. 9, Solan, Himachal Pradesh 173 229, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Post box no. 9, Solan, Himachal Pradesh 173 229, India
| | - Terezinha de Jesus Andreoli Pinto
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Professor Lineu Prestes Street, São Paulo 05508-000, Brazil
| | - Inderbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Dinesh K. Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
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11
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Lossouarn A, Renard PY, Sabot C. Tailored Bioorthogonal and Bioconjugate Chemistry: A Source of Inspiration for Developing Kinetic Target-Guided Synthesis Strategies. Bioconjug Chem 2020; 32:63-72. [PMID: 33232599 DOI: 10.1021/acs.bioconjchem.0c00568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Kinetic target-guided synthesis (KTGS) is a promising tool for the discovery of biologically active compounds. It relies on the identification of potent ligands that are covalently assembled by the biological targets themselves from a pool of reagents. Significant effort is devoted to developing new KTGS strategies; however, only a handful of biocompatible reactions are available, which may be insufficient to meet the specificities (stability, dynamics, active site topology, etc.) of a wide range of biological targets with therapeutic potential. This Topical Review proposes a retrospective analysis of existing KTGS ligation tools, in terms of their kinetics and analogy with other biocompatible reactions, and provides new clues to expand the KTGS toolkit. By way of examples, a nonexhaustive selection of such chemical ligation tools belonging to different classes of reactions as promising candidate reactions for KTGS are suggested.
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Affiliation(s)
- Alexis Lossouarn
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
| | - Pierre-Yves Renard
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
| | - Cyrille Sabot
- Normandie Université, Centre National de la Recherche Scientifique, UNIROUEN, INSA Rouen, COBRA, UMR 6014 & FR 3038, 76000, Rouen, France
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12
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Mancini F, Unver MY, Elgaher WAM, Jumde VR, Alhayek A, Lukat P, Herrmann J, Witte MD, Köck M, Blankenfeldt W, Müller R, Hirsch AKH. Protein-Templated Hit Identification through an Ugi Four-Component Reaction*. Chemistry 2020; 26:14585-14593. [PMID: 32428268 PMCID: PMC7756422 DOI: 10.1002/chem.202002250] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Kinetic target-guided synthesis represents an efficient hit-identification strategy, in which the protein assembles its own inhibitors from a pool of complementary building blocks via an irreversible reaction. Herein, we pioneered an in situ Ugi reaction for the identification of novel inhibitors of a model enzyme and binders for an important drug target, namely, the aspartic protease endothiapepsin and the bacterial β-sliding clamp DnaN, respectively. Highly sensitive mass-spectrometry methods enabled monitoring of the protein-templated reaction of four complementary reaction partners, which occurred in a background-free manner for endothiapepsin or with a clear amplification of two binders in the presence of DnaN. The Ugi products we identified show low micromolar activity on endothiapepsin or moderate affinity for the β-sliding clamp. We succeeded in expanding the portfolio of chemical reactions and biological targets and demonstrated the efficiency and sensitivity of this approach, which can find application on any drug target.
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Affiliation(s)
- Federica Mancini
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - M. Yagiz Unver
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Walid A. M. Elgaher
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Varsha R. Jumde
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Alaa Alhayek
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Peer Lukat
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
| | - Jennifer Herrmann
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Martin D. Witte
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Matthias Köck
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigSpielmannstr. 738106BraunschweigGermany
| | - Rolf Müller
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
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13
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Wagh SB, Maslivetc V, La Clair JJ, Kornienko A. A fluorescent target-guided Paal-Knorr reaction. RSC Adv 2020; 10:37035-37039. [PMID: 34262697 PMCID: PMC8276889 DOI: 10.1039/d0ra06962k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It has become increasingly apparent that high-diversity chemical reactions play a significant role in the discovery of bioactive small molecules. Here, we describe an expanse of this paradigm, combining a 'target-guided synthesis' concept with Paal-Knorr chemistry applied to the preparation of fluorescent ligands for human prostaglandin-endoperoxide synthase (COX-2).
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | - Vladimir Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | | | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
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14
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Paul R, Dutta D, Paul R, Dash J. Target-Directed Azide-Alkyne Cycloaddition for Assembling HIV-1 TAR RNA Binding Ligands. Angew Chem Int Ed Engl 2020; 59:12407-12411. [PMID: 32329147 PMCID: PMC7687225 DOI: 10.1002/anie.202003461] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 01/05/2023]
Abstract
The highly conserved HIV-1 transactivation response element (TAR) binds to the trans-activator protein Tat and facilitates viral replication in its latent state. The inhibition of Tat-TAR interactions by selectively targeting TAR RNA has been used as a strategy to develop potent antiviral agents. Therefore, HIV-1 TAR RNA represents a paradigmatic system for therapeutic intervention. Herein, we have employed biotin-tagged TAR RNA to assemble its own ligands from a pool of reactive azide and alkyne building blocks. To identify the binding sites and selectivity of the ligands, the in situ cycloaddition has been further performed using control nucleotide (TAR DNA and TAR RNA without bulge) templates. The hit triazole-linked thiazole peptidomimetic products have been isolated from the biotin-tagged target templates using streptavidin beads. The major triazole lead generated by the TAR RNA presumably binds in the bulge region, shows specificity for TAR RNA over TAR DNA, and inhibits Tat-TAR interactions.
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Affiliation(s)
- Rakesh Paul
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Debasish Dutta
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Raj Paul
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata700 032India
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15
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Paul R, Dutta D, Paul R, Dash J. Target‐Directed Azide‐Alkyne Cycloaddition for Assembling HIV‐1 TAR RNA Binding Ligands. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Debasish Dutta
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Raj Paul
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
| | - Jyotirmayee Dash
- School of Chemical Sciences Indian Association for the Cultivation of Science Jadavpur Kolkata 700 032 India
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16
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Abstract
The use of an acetylene (ethynyl) group in medicinal chemistry coincides with the launch of the Journal of Medicinal Chemistry in 1959. Since then, the acetylene group has been broadly exploited in drug discovery and development. As a result, it has become recognized as a privileged structural feature for targeting a wide range of therapeutic target proteins, including MAO, tyrosine kinases, BACE1, steroid receptors, mGlu5 receptors, FFA1/GPR40, and HIV-1 RT. Furthermore, a terminal alkyne functionality is frequently introduced in chemical biology probes as a click handle to identify molecular targets and to assess target engagement. This Perspective is divided into three parts encompassing: (1) the physicochemical properties of the ethynyl group, (2) the advantages and disadvantages of the ethynyl group in medicinal chemistry, and (3) the impact of the ethynyl group on chemical biology approaches.
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Affiliation(s)
- Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
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17
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Masuda R, Kawasaki Y, Igawa K, Manabe Y, Fujii H, Kato N, Tomooka K, Ohkanda J. Copper‐Free Huisgen Cycloaddition for the 14‐3‐3‐Templated Synthesis of Fusicoccin‐Peptide Conjugates. Chem Asian J 2020; 15:742-747. [DOI: 10.1002/asia.202000042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Ryoma Masuda
- Academic AssemblyInstitute of AgricultureShinshu University 8304 Minami-Minowa Kami-Ina Nagano 399-4598 Japan
| | - Yuuya Kawasaki
- Institute for Materials Chemistry and EngineeringKyushu University Kasuga-koen 6–1 Kasuga Fukuoka 816-8580 Japan
| | - Kazunobu Igawa
- Institute for Materials Chemistry and EngineeringKyushu University Kasuga-koen 6–1 Kasuga Fukuoka 816-8580 Japan
| | - Yoshiyuki Manabe
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Hiroshi Fujii
- Academic AssemblyInstitute of AgricultureShinshu University 8304 Minami-Minowa Kami-Ina Nagano 399-4598 Japan
| | - Nobuo Kato
- The Institute of Scientific Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki Osaka 567-0047 Japan
| | - Katsuhiko Tomooka
- Institute for Materials Chemistry and EngineeringKyushu University Kasuga-koen 6–1 Kasuga Fukuoka 816-8580 Japan
| | - Junko Ohkanda
- Academic AssemblyInstitute of AgricultureShinshu University 8304 Minami-Minowa Kami-Ina Nagano 399-4598 Japan
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18
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Bosc D, Camberlein V, Gealageas R, Castillo-Aguilera O, Deprez B, Deprez-Poulain R. Kinetic Target-Guided Synthesis: Reaching the Age of Maturity. J Med Chem 2019; 63:3817-3833. [PMID: 31820982 DOI: 10.1021/acs.jmedchem.9b01183] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinetic target-guided synthesis (KTGS) is an original discovery strategy allowing a target to catalyze the irreversible synthesis of its own ligands from a pool of reagents. Although pioneered almost two decades ago, it only recently proved its usefulness in medicinal chemistry, as exemplified by the increasing number of protein targets used, the wider range of target and pocket types, and the diversity of therapeutic areas explored. In recent years, two new leads for in vivo studies were released. Amidations and multicomponent reactions expanded the armamentarium of reactions beyond triazole formation and two new examples of in cellulo KTGS were also disclosed. Herein, we analyze the origins and the chemical space of both KTGS ligands and warhead-bearing reagents. We review the KTGS timeline focusing on recent cases in order to give medicinal chemists the full scope of this strategy which has great potential for hit discovery and hit or lead optimization.
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Affiliation(s)
- Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Virgyl Camberlein
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Omar Castillo-Aguilera
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.,Institut Universitaire de France, F- 75005 Paris, France
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19
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SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase. Proc Natl Acad Sci U S A 2019; 116:18808-18814. [PMID: 31484779 DOI: 10.1073/pnas.1909972116] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Sulfur fluoride exchange (SuFEx) has emerged as the new generation of click chemistry. We report here a SuFEx-enabled, agnostic approach for the discovery and optimization of covalent inhibitors of human neutrophil elastase (hNE). Evaluation of our ever-growing collection of SuFExable compounds toward various biological assays unexpectedly revealed a selective and covalent hNE inhibitor: benzene-1,2-disulfonyl fluoride. Synthetic derivatization of the initial hit led to a more potent agent, 2-(fluorosulfonyl)phenyl fluorosulfate with IC50 0.24 μM and greater than 833-fold selectivity over the homologous neutrophil serine protease, cathepsin G. The optimized, yet simple benzenoid probe only modified active hNE and not its denatured form.
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20
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Gladysz R, Vrijdag J, Van Rompaey D, Lambeir A, Augustyns K, De Winter H, Van der Veken P. Efforts towards an On‐Target Version of the Groebke–Blackburn–Bienaymé (GBB) Reaction for Discovery of Druglike Urokinase (uPA) Inhibitors. Chemistry 2019; 25:12380-12393. [DOI: 10.1002/chem.201901917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/18/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Rafaela Gladysz
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Johannes Vrijdag
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
- Laboratory of Medical BiochemistryDepartment of, Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Dries Van Rompaey
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Anne‐Marie Lambeir
- Laboratory of Medical BiochemistryDepartment of, Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
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21
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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22
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Prasher P, Sharma M. Tailored therapeutics based on 1,2,3-1 H-triazoles: a mini review. MEDCHEMCOMM 2019; 10:1302-1328. [PMID: 31534652 DOI: 10.1039/c9md00218a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Contemporary drug discovery approaches rely on library synthesis coupled with combinatorial methods and high-throughput screening to identify leads. However, due to the multitude of components involved, a majority of optimization techniques face persistent challenges related to the efficiency of synthetic processes and the purity of compound libraries. These methods have recently found an upgradation as fragment-based approaches for target-guided synthesis of lead molecules with active involvement of their biological target. The click chemistry approach serves as a promising tool for tailoring the therapeutically relevant biomolecules of interest, improving their bioavailability and bioactivity and redirecting them as efficacious drugs. 1,2,3-1H-Triazole nucleus, being a planar and biologically acceptable scaffold, plays a crucial role in the design of biomolecular mimetics and tailor-made molecules with therapeutic relevance. This versatile scaffold also forms an integral part of the current fragment-based approaches for drug design, kinetic target guided synthesis and bioorthogonal methodologies.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ; .,Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India . ;
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23
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AlFadly ED, Elzahhar PA, Tramarin A, Elkazaz S, Shaltout H, Abu-Serie MM, Janockova J, Soukup O, Ghareeb DA, El-Yazbi AF, Rafeh RW, Bakkar NMZ, Kobeissy F, Iriepa I, Moraleda I, Saudi MN, Bartolini M, Belal AS. Tackling neuroinflammation and cholinergic deficit in Alzheimer's disease: Multi-target inhibitors of cholinesterases, cyclooxygenase-2 and 15-lipoxygenase. Eur J Med Chem 2019; 167:161-186. [DOI: 10.1016/j.ejmech.2019.02.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 12/31/2022]
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24
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Unver MY, Gierse RM, Ritchie H, Hirsch AKH. Druggability Assessment of Targets Used in Kinetic Target-Guided Synthesis. J Med Chem 2018; 61:9395-9409. [DOI: 10.1021/acs.jmedchem.8b00266] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Robin M. Gierse
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Harry Ritchie
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
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25
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Antti H, Sellstedt M. Cell-Based Kinetic Target-Guided Synthesis of an Enzyme Inhibitor. ACS Med Chem Lett 2018; 9:351-353. [PMID: 29670699 DOI: 10.1021/acsmedchemlett.7b00535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/04/2018] [Indexed: 12/22/2022] Open
Abstract
Finding a new drug candidate for a selected target is an expensive and time-consuming process. Target guided-synthesis, or in situ click chemistry, is a concept where the drug target is used to template the formation of its own inhibitors from reactive building blocks. This could simplify the identification of drug candidates. However, with the exception of one example of an RNA-target, target-guided synthesis has always employed purified targets. This limits the number of targets that can be screened by the method. By applying methods from the field of metabolomics, we demonstrate that target-guided synthesis with protein targets also can be performed directly in cell-based systems. These methods offer new possibilities to conduct screening for drug candidates of difficult protein targets in cellular environments.
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Affiliation(s)
- Henrik Antti
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
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26
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Fu S, Nie Q, Ma Y, Song P, Ren X, Luo C, Shang L, Yin Z. Target-guided screening of fragments (TGSOF) in the discovery of inhibitors against EV-A71 3C protease. Chem Commun (Camb) 2018; 54:2890-2893. [PMID: 29497732 DOI: 10.1039/c8cc00469b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Target-guided screening of fragments (TGSOF) was developed and employed in the identification of EV-A71 3C protease (3Cpro) inhibitors. We identified 4-acetylpyridine and 3-acetylpyridine as effective P3 fragments of an inhibitor and obtained the corresponding irreversible inhibitors 12c and 12fvia this method. Furthermore, based on 12c and 12f, we have obtained reversible inhibitors 17c and 17f. These results demonstrated that TGSOF is a useful strategy for identifying suitable fragments in developing leads in drug discovery.
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Affiliation(s)
- Shengjun Fu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China.
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27
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Galdeano C, Coquelle N, Cieslikiewicz-Bouet M, Bartolini M, Pérez B, Clos MV, Silman I, Jean L, Colletier JP, Renard PY, Muñoz-Torrero D. Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis. Molecules 2018. [PMID: 29534488 PMCID: PMC6017698 DOI: 10.3390/molecules23030634] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Symptomatic treatment of myasthenia gravis is based on the use of peripherally-acting acetylcholinesterase (AChE) inhibitors that, in some cases, must be discontinued due to the occurrence of a number of side-effects. Thus, new AChE inhibitors are being developed and investigated for their potential use against this disease. Here, we have explored two alternative approaches to get access to peripherally-acting AChE inhibitors as new agents against myasthenia gravis, by structural modification of the brain permeable anti-Alzheimer AChE inhibitors tacrine, 6-chlorotacrine, and huprine Y. Both quaternization upon methylation of the quinoline nitrogen atom, and tethering of a triazole ring, with, in some cases, the additional incorporation of a polyphenol-like moiety, result in more polar compounds with higher inhibitory activity against human AChE (up to 190-fold) and butyrylcholinesterase (up to 40-fold) than pyridostigmine, the standard drug for symptomatic treatment of myasthenia gravis. The novel compounds are furthermore devoid of brain permeability, thereby emerging as interesting leads against myasthenia gravis.
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Affiliation(s)
- Carles Galdeano
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
| | - Nicolas Coquelle
- Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Énergie Atomique (CEA) (UMR 5075), F-38054 Grenoble, France.
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - Monika Cieslikiewicz-Bouet
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy.
| | - Belén Pérez
- Department of Pharmacology, Therapeutics and Toxicology, Neuroscience Institute, Autonomous University of Barcelona, E-08193 Barcelona, Spain.
| | - M Victòria Clos
- Department of Pharmacology, Therapeutics and Toxicology, Neuroscience Institute, Autonomous University of Barcelona, E-08193 Barcelona, Spain.
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Ludovic Jean
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'Énergie Atomique (CEA) (UMR 5075), F-38054 Grenoble, France.
| | - Pierre-Yves Renard
- Laboratory COBRA (UMR 6014), Normandie Université, UNIROUEN, Institut National des Sciences Appliquées (INSA) Rouen, CNRS, 76000 Rouen, France.
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
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Anti-Hypertensive Peptides Derived from Caseins: Mechanism of Physiological Action, Production Bioprocesses, and Challenges for Food Applications. Appl Biochem Biotechnol 2018; 185:884-908. [DOI: 10.1007/s12010-018-2692-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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Roscales S, Plumet J. Metal-catalyzed 1,3-dipolar cycloaddition reactions of nitrile oxides. Org Biomol Chem 2018; 16:8446-8461. [DOI: 10.1039/c8ob02072h] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review recent advances in the metal-catalyzed 1,3-dipolar cycloaddition reactions of nitrile oxides are highlighted, covering references from the period 2000 until August 2018.
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Affiliation(s)
- Silvia Roscales
- Universidad Complutense
- Facultad de Química
- Departamento de Química Orgánica
- Ciudad Universitaria
- Madrid
| | - Joaquín Plumet
- Universidad Complutense
- Facultad de Química
- Departamento de Química Orgánica
- Ciudad Universitaria
- Madrid
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:7464-7485. [PMID: 32313319 PMCID: PMC7159557 DOI: 10.1002/ange.201610372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/28/2022]
Abstract
AbstractProteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery. Angew Chem Int Ed Engl 2017; 56:7358-7378. [PMID: 28117936 PMCID: PMC7159684 DOI: 10.1002/anie.201610372] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
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Jaegle M, Steinmetzer T, Rademann J. Protein-Templated Formation of an Inhibitor of the Blood Coagulation Factor Xa through a Background-Free Amidation Reaction. Angew Chem Int Ed Engl 2017; 56:3718-3722. [PMID: 28199769 PMCID: PMC5363247 DOI: 10.1002/anie.201611547] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Indexed: 11/16/2022]
Abstract
Protein‐templated reactions enable the target‐guided formation of protein ligands from reactive fragments, ideally with no background reaction. Herein, we investigate the templated formation of amides. A nucleophilic fragment that binds to the coagulation factor Xa was incubated with the protein and thirteen differentially activated dipeptides. The protein induced a non‐catalytic templated reaction for the phenyl and trifluoroethyl esters; the latter was shown to be a completely background‐free reaction. Starting from two fragments with millimolar affinity, a 29 nm superadditive inhibitor of factor Xa was obtained. The fragment ligation reaction was detected with high sensitivity by an enzyme activity assay and by mass spectrometry. The reaction progress and autoinhibition of the templated reaction by the formed ligation product were determined, and the structure of the protein–inhibitor complex was elucidated.
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Affiliation(s)
- Mike Jaegle
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany
| | - Torsten Steinmetzer
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35037, Marburg, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany
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Jaegle M, Steinmetzer T, Rademann J. Proteintemplat‐gesteuerte Bildung eines Inhibitors des Koagulationsfaktors Xa durch eine Amidierung ohne Hintergrundreaktion. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mike Jaegle
- Medizinische Chemie Institut für Pharmazie Freie Universität Berlin Königin-Luise-Straße 2+4 14195 Berlin Deutschland
| | - Torsten Steinmetzer
- Philipps-Universität Marburg Fachbereich Pharmazie Institut für Pharmazeutische Chemie Marbacher Weg 6 35037 Marburg Deutschland
| | - Jörg Rademann
- Medizinische Chemie Institut für Pharmazie Freie Universität Berlin Königin-Luise-Straße 2+4 14195 Berlin Deutschland
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Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Ther 2016; 167:28-37. [DOI: 10.1016/j.pharmthera.2016.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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Kinetic target-guided synthesis in drug discovery and chemical biology: a comprehensive facts and figures survey. Future Med Chem 2016; 8:381-404. [DOI: 10.4155/fmc-2015-0007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
For the last 15 years, kinetic target-guided syntheses, including in situ click chemistry, have been used as alternative methods to find ligands to therapeutically relevant proteins. In this review, a comprehensive survey of biological targets used in kinetic target-guided synthesis covers historical and recent examples. The chemical reactions employed and practical aspects, including controls, library sizes and product detection, are presented. A particular focus is on the reagents and warhead selection and design with a critical overview of the challenges encountered. As protein supply remains a key success factor, it appears that increased efforts should be taken toward miniaturization in order to expand the scope of this strategy and qualify it as a fully fledged drug discovery tool.
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Zhan P, Pannecouque C, De Clercq E, Liu X. Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends. J Med Chem 2015; 59:2849-78. [PMID: 26509831 DOI: 10.1021/acs.jmedchem.5b00497] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The early effectiveness of combinatorial antiretroviral therapy (cART) in the treatment of HIV infection has been compromised to some extent by rapid development of multidrug-resistant HIV strains, poor bioavailability, and cumulative toxicities, and so there is a need for alternative strategies of antiretroviral drug discovery and additional therapeutic agents with novel action modes or targets. From this perspective, we first review current strategies of antiretroviral drug discovery and optimization, with the aid of selected examples from the recent literature. We highlight the development of phosphate ester-based prodrugs as a means to improve the aqueous solubility of HIV inhibitors, and the introduction of the substrate envelope hypothesis as a new approach for overcoming HIV drug resistance. Finally, we discuss future directions for research, including opportunities for exploitation of novel antiretroviral targets, and the strategy of activation of latent HIV reservoirs as a means to eradicate the virus.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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