1
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Wamser R, Zhang X, Kuropka B, Arkona C, Rademann J. Protein-Templated Ugi Reactions versus In-Situ Ligation Screening: Two Roads to the Identification of SARS-CoV-2 Main Protease Inhibitors. Chemistry 2024; 30:e202303940. [PMID: 38246870 DOI: 10.1002/chem.202303940] [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] [Received: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Protein-templated fragment ligation was established as a method for the rapid identification of high affinity ligands, and multicomponent reactions (MCR) such as the Ugi four-component reaction (Ugi 4CR) have been efficient in the synthesis of drug candidates. Thus, the combination of both strategies should provide a powerful approach to drug discovery. Here, we investigate protein-templated Ugi 4CR quantitatively using a fluorescence-based enzyme assay, HPLC-QTOF mass spectrometry (MS), and native protein MS with SARS-CoV-2 main protease as template. Ugi reactions were analyzed in aqueous buffer at varying pH and fragment concentration. Potent inhibitors of the protease were formed in presence of the protein via Ugi 4CR together with Ugi three-component reaction (Ugi 3CR) products. Binding of inhibitors to the protease was confirmed by native MS and resulted in the dimerization of the protein target. Formation of Ugi products was, however, more efficient in the non-templated reaction, apparently due to interactions of the protein with the isocyanide and imine fragments. Consequently, in-situ ligation screening of Ugi 4CR products was identified as a superior approach to the discovery of SARS-CoV-2 protease inhibitors.
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Affiliation(s)
- Rebekka Wamser
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Xinting Zhang
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Benno Kuropka
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Christoph Arkona
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
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2
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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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3
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. Angew Chem Int Ed Engl 2022; 61:e202211510. [PMID: 36112310 PMCID: PMC9827864 DOI: 10.1002/anie.202211510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 01/12/2023]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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4
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202211510. [PMID: 38505687 PMCID: PMC10947266 DOI: 10.1002/ange.202211510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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5
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Rademann J, Ahsanullah A, Hassan A, Ansari FL. Integration of C-Acylation in the Solid-Phase Synthesis of Peptides and Peptidomimetics Employing Meldrum’s Acid, Phosphorus, and Sulfur Ylides. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1667-3648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe modification of native peptides to peptidomimetics is an important goal in medicinal chemistry and requires, in many cases, the integration of C-acylation steps involving amino acids with classical peptide synthesis. Many classical C-acylation protocols involving Claisen condensations and the use of ylides are not compatible with peptide synthesis, mostly due to the requirements for strong bases leading to epimerization or deprotection of peptides. Meldrum’s acid as well as several specific phosphorus and sulfur ylides, however, are acidic enough to provide reactive C-nucleophiles under mildly basic conditions tolerated during peptide synthesis. This review provides an overview of peptide-compatible C-acylations using Meldrum’s acid and phosphorus and sulfur ylides, and their application in the medicinal chemistry of peptides.1 Introduction2 C-Acylation of Meldrum’s Acid2.1 C-Acylation of Meldrum’s Acid on Solid Phase3 Ylides as Substrates for C-Acylation3.1 C-Acylation of Phosphorus Ylides in Solution Phase3.2 C-Acylation of Solid-Supported Phosphorus Ylides3.3 C-Acylation of Sulfur Ylides3.4 C-Acylation of Solid-Supported Sulfur Ylides4 Miscellaneous Ylides as Acyl Anion Equivalents5 Summary
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Affiliation(s)
- Jörg Rademann
- Institut für Pharmazie, Medizinische Chemie, Freie Universität Berlin
| | | | - Abbas Hassan
- Department of Chemistry, Quaid-i-Azam University
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6
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Yu L, Liu A, Zhang B, Kuang J, Guo X, Tian C, Lu Y. Dipolar coupling-based electron paramagnetic resonance method for protease enzymatic characterization and inhibitor screening. Chem Commun (Camb) 2021; 57:9602-9605. [PMID: 34546243 DOI: 10.1039/d1cc03301h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we report an EPR-based method for protease enzymatic characterization and inhibitor screening. This method utilizes dual paramagnetically-labeled probes consisting of a nitroxide spin probe and a Gd3+ ion flanking a peptide that could be specifically cleaved by protease caspase-3. Distance-dependent dipolar coupling between the two paramagnetic centers can be modulated by the protease cleavage activity, thus providing a straightforward and convenient method for protease activity detection using EPR spectroscopy under ambient conditions. Moreover, time-course monitoring of the protease-catalyzed cleavage reaction demonstrated that this EPR-based method could not only allow a direct quantitative enzymatic kinetic assessment, but also could be used for protease inhibitor screening, thus holding great potential in drug discovery studies.
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Affiliation(s)
- Lu Yu
- The Anhui Provincial Key Laboratory of High Field Magnetic Resonance Image, High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui 230031, P. R. China.
| | - Aokun Liu
- The Anhui Provincial Key Laboratory of High Field Magnetic Resonance Image, High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui 230031, P. R. China. .,The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bingbo Zhang
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Tongji University Cancer Center, The Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Jian Kuang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xiaoqi Guo
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Changlin Tian
- The Anhui Provincial Key Laboratory of High Field Magnetic Resonance Image, High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui 230031, P. R. China. .,The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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7
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Kant R, Yang MH, Tseng CH, Yen CH, Li WY, Tyan YC, Chen M, Tzeng CC, Chen WC, You K, Wang WC, Chen YL, Chen YMA. Discovery of an Orally Efficacious MYC Inhibitor for Liver Cancer Using a GNMT-Based High-Throughput Screening System and Structure-Activity Relationship Analysis. J Med Chem 2021; 64:8992-9009. [PMID: 34132534 DOI: 10.1021/acs.jmedchem.1c00093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Glycine-N-methyl transferase (GNMT) downregulation results in spontaneous hepatocellular carcinoma (HCC). Overexpression of GNMT inhibits the proliferation of liver cancer cell lines and prevents carcinogen-induced HCC, suggesting that GNMT induction is a potential approach for anti-HCC therapy. Herein, we used Huh7 GNMT promoter-driven screening to identify a GNMT inducer. Compound K78 was identified and validated for its induction of GNMT and inhibition of Huh7 cell growth. Subsequently, we employed structure-activity relationship analysis and found a potent GNMT inducer, K117. K117 inhibited Huh7 cell growth in vitro and xenograft in vivo. Oral administration of a dosage of K117 at 10 mpk (milligrams per kilogram) can inhibit Huh7 xenograft in a manner equivalent to the effect of sorafenib at a dosage of 25 mpk. A mechanistic study revealed that K117 is an MYC inhibitor. Ectopic expression of MYC using CMV promoter blocked K117-mediated MYC inhibition and GNMT induction. Overall, K117 is a potential lead compound for HCC- and MYC-dependent cancers.
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Affiliation(s)
- Rajni Kant
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Ming-Hui Yang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
| | - Chih-Hua Tseng
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Hung Yen
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,Research Center for Natural Products and Drug Development, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Wei-You Li
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Yu-Chang Tyan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Marcelo Chen
- Department of Urology, Mackay Memorial Hospital, Taipei 10449, Taiwan
| | - Cherng-Chyi Tzeng
- Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Wei-Cheng Chen
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Kaiting You
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan
| | - Yeh-Long Chen
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yi-Ming Arthur Chen
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
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8
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Hegedüs Z, Hóbor F, Shoemark DK, Celis S, Lian LY, Trinh CH, Sessions RB, Edwards TA, Wilson AJ. Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci 2021; 12:2286-2293. [PMID: 34163995 PMCID: PMC8179271 DOI: 10.1039/d0sc05694d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Affiliation(s)
- Zsófia Hegedüs
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Deborah K Shoemark
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Sergio Celis
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Lu-Yun Lian
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 3BX UK
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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9
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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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10
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Bancet A, Raingeval C, Lomberget T, Le Borgne M, Guichou JF, Krimm I. Fragment Linking Strategies for Structure-Based Drug Design. J Med Chem 2020; 63:11420-11435. [DOI: 10.1021/acs.jmedchem.0c00242] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Bancet
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Claire Raingeval
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Thierry Lomberget
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | - Marc Le Borgne
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | | | - Isabelle Krimm
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, 69008 Lyon, France
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11
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Wong EL, Nawrotzky E, Arkona C, Kim BG, Beligny S, Wang X, Wagner S, Lisurek M, Carstanjen D, Rademann J. The transcription factor STAT5 catalyzes Mannich ligation reactions yielding inhibitors of leukemic cell proliferation. Nat Commun 2019; 10:66. [PMID: 30622248 PMCID: PMC6325109 DOI: 10.1038/s41467-018-07923-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Protein-templated fragment ligations have been established as a powerful method for the assembly and detection of optimized protein ligands. Initially developed for reversible ligations, the method has been expanded to irreversible reactions enabling the formation of super-additive fragment combinations. Here, protein-induced Mannich ligations are discovered as a biocatalytic reaction furnishing inhibitors of the transcription factor STAT5. STAT5 protein catalyzes multicomponent reactions of a phosphate mimetic, formaldehyde, and 1H-tetrazoles yielding protein ligands with greatly increased binding affinity and ligand efficiency. Reactions are induced under physiological conditions selectively by native STAT5 but not by other proteins. Formation of ligation products and (auto-)inhibition of the reaction are quantified and the mechanism is investigated. Inhibitors assembled by STAT5 block specifically the phosphorylation of this protein in a cellular model of acute myeloid leukemia (AML), DNA-binding of STAT5 dimers, expression of downstream targets of the transcription factor, and the proliferation of cancer cells in mice. The oncogene STAT5 is involved in cancer cell proliferation. Here, the authors use STAT5 protein to assemble its own small molecule inhibitors via Mannich ligation (three-component-reactions) and show that the resultant ligands can inhibit the proliferation of cancer cells in a mouse model.
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Affiliation(s)
- Ee Lin Wong
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Eric Nawrotzky
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Arkona
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Boo Geun Kim
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Samuel Beligny
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Xinning Wang
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Stefan Wagner
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Michael Lisurek
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Dirk Carstanjen
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany. .,Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
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12
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Craven GB, Affron DP, Allen CE, Matthies S, Greener JG, Morgan RML, Tate EW, Armstrong A, Mann DJ. High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery. Angew Chem Int Ed Engl 2018; 57:5257-5261. [PMID: 29480525 PMCID: PMC5947712 DOI: 10.1002/anie.201711825] [Citation(s) in RCA: 46] [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: 11/17/2017] [Revised: 01/16/2018] [Indexed: 01/10/2023]
Abstract
Cysteine‐reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high‐quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan‐reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine‐reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2‐selective allosteric (type IV) kinase inhibitor whose novel mode‐of‐action could be exploited therapeutically.
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Affiliation(s)
- Gregory B. Craven
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Dominic P. Affron
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Charlotte E. Allen
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Stefan Matthies
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Joe G. Greener
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Rhodri M. L. Morgan
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Edward W. Tate
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - Alan Armstrong
- Department of ChemistryImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
| | - David J. Mann
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonSW7 2AZUK
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13
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Craven GB, Affron DP, Allen CE, Matthies S, Greener JG, Morgan RML, Tate EW, Armstrong A, Mann DJ. High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gregory B. Craven
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Dominic P. Affron
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Charlotte E. Allen
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Stefan Matthies
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Joe G. Greener
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Rhodri M. L. Morgan
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Edward W. Tate
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Alan Armstrong
- Department of Chemistry; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - David J. Mann
- Department of Life Sciences; Imperial College London; South Kensington Campus London SW7 2AZ UK
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Abstract
Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs' chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- BEROCEUTICA GmbH, c/o Universität Potsdam, August-Bebel-Strasse 89, 14482, Potsdam, Germany.
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15
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Su D, Hu X, Dong C, Ren J. Determination of Caspase-3 Activity and Its Inhibition Constant by Combination of Fluorescence Correlation Spectroscopy with a Microwell Chip. Anal Chem 2017; 89:9788-9796. [DOI: 10.1021/acs.analchem.7b01735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Di Su
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiaocai Hu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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16
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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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17
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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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18
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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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19
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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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20
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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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21
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Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments. Nat Commun 2016; 7:12761. [PMID: 27677239 PMCID: PMC5052702 DOI: 10.1038/ncomms12761] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/29/2016] [Indexed: 02/01/2023] Open
Abstract
Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors. A protein-binding nucleophile reacts reversibly with a bis-electrophilic warhead, thereby positioning the second electrophile in close proximity of the active site of a viral protease, resulting in the covalent de-activation of the enzyme. The concept is implemented for Coxsackie virus B3 3C protease, a pharmacological target against enteroviral infections. Using an aldehyde-epoxide as bis-electrophile, active fragment combinations are validated through measuring the protein inactivation rate and by detecting covalent protein modification in mass spectrometry. The structure of one enzyme-inhibitor complex is determined by X-ray crystallography. The presented warhead activation assay provides potent non-peptidic, broad-spectrum inhibitors of enteroviral proteases.
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22
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Mondal M, Radeva N, Fanlo-Virgós H, Otto S, Klebe G, Hirsch AKH. Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2016; 55:9422-6. [PMID: 27400756 PMCID: PMC5113778 DOI: 10.1002/anie.201603074] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/05/2016] [Indexed: 12/31/2022]
Abstract
Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
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23
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Mondal M, Radeva N, Fanlo‐Virgós H, Otto S, Klebe G, Hirsch AKH. Fragmentverknüpfung und ‐optimierung von Hemmstoffen der Aspartylprotease Endothiapepsin: Fragmentbasiertes Wirkstoffdesign beschleunigt durch dynamische kombinatorische Chemie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Milon Mondal
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Hugo Fanlo‐Virgós
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
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24
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Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates. Nat Commun 2014; 5:5170. [PMID: 25403979 DOI: 10.1038/ncomms6170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/08/2014] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease-fragment-pre-substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions.
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25
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Schmidt MF. Drug target miRNAs: chances and challenges. Trends Biotechnol 2014; 32:578-585. [PMID: 25304465 DOI: 10.1016/j.tibtech.2014.09.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
Abstract
miRNAs, short ribonucleic acid gene regulators, are increasingly popular drug targets. Traditionally 'undruggable' proteins can be targeted via their miRNA gene regulators, enabling the treatment of diseases that, at present, seem impossible to cure. However, addressing miRNAs requires innovation at the level of drug discovery. This review article outlines the potential of miRNAs as drug targets, focuses on the challenges of developing miRNA-targeting drugs, and surveys new advances. The aim is to provide an orientation guide for scientists, as well business analysts, to help them navigate the jungle of different approaches in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
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26
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Guo Z, Yan Z, Zhou X, Wang Q, Lu M, Liu W, Zhou H, Yang C, McClain EJ. Synthesis and biological evaluation of novel 1,2-benzisothiazol-3-one-derived 1,2,3-triazoles as caspase-3 inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1259-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Holland-Nell K, Fernández-Bachiller MI, Ahsanullah, Rademann J. Chemoselective Wittig and Michael Ligations of Unprotected Peptidyl Phosphoranes in Water Furnish Potent Inhibitors of Caspase-3. Org Lett 2014; 16:4428-31. [DOI: 10.1021/ol501910x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kai Holland-Nell
- Medicinal Chemistry, Free University Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
- Leibniz Institute for Molecular Pharmacology (FMP), Robert
Rössle-Strasse 10, 13125 Berlin, Germany
| | - María Isabel Fernández-Bachiller
- Medicinal Chemistry, Free University Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
- Leibniz Institute for Molecular Pharmacology (FMP), Robert
Rössle-Strasse 10, 13125 Berlin, Germany
| | - Ahsanullah
- Medicinal Chemistry, Free University Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
- Leibniz Institute for Molecular Pharmacology (FMP), Robert
Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jörg Rademann
- Medicinal Chemistry, Free University Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
- Leibniz Institute for Molecular Pharmacology (FMP), Robert
Rössle-Strasse 10, 13125 Berlin, Germany
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28
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Abstract
As microRNA silencing processes are mediated by the protein Argonaute 2 and for target RNA binding only a short sequence at the microRNA's 5' end (seed region) is crucial, we report a novel inhibitor class: the microRNA-specific Argonaute 2 protein inhibitors that not only block this short recognition sequence but also bind to the protein's active site. We developed a model for rational drug design, enabling the identification of Argonaute 2 active site binders and their linkage with a peptide nucleic acid sequence (PNA), which addresses the microRNA of interest. The designed inhibitors targeting microRNA-122, a hepatitis C virus drug target, had an IC50 of 100 nM, 10-fold more active than the simple PNA sequence (IC50 of 1 μM), giving evidence that the strategy has potential. Due to their lower molecular weight, these inhibitors may show better pharmacokinetic properties than reported oligonucleotide inhibitors, enabling them for potential therapeutic use.
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Affiliation(s)
- Marco F. Schmidt
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge,
United Kingdom
| | - Oliver Korb
- Cambridge Crystallographic Data Centre (CCDC), 12 Union Road, CB2 1EZ Cambridge,
United Kingdom
| | - Chris Abell
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge,
United Kingdom
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29
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Arkona C, Rademann J. Propargylamide als irreversible Inhibitoren von Cysteinproteasen - zur biologischen Reaktivität von Alkinen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Arkona C, Rademann J. Propargyl amides as irreversible inhibitors of cysteine proteases--a lesson on the biological reactivity of alkynes. Angew Chem Int Ed Engl 2013; 52:8210-2. [PMID: 23794491 DOI: 10.1002/anie.201303544] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Christoph Arkona
- Freie Universität Berlin, Institut für Pharmazie, Medizinische Chemie, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
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31
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Fernández-Bachiller MI, Horatscheck A, Lisurek M, Rademann J. Alzheimer's disease: identification and development of β-secretase (BACE-1) binding fragments and inhibitors by dynamic ligation screening (DLS). ChemMedChem 2013; 8:1041-56. [PMID: 23757181 DOI: 10.1002/cmdc.201300078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/25/2013] [Indexed: 11/12/2022]
Abstract
The application of dynamic ligation screening (DLS), a methodology for fragment-based drug discovery (FBDD), to the aspartic protease β-secretase (BACE-1) is reported. For this purpose, three new fluorescence resonance energy transfer (FRET) substrates were designed and synthesized. Their kinetic parameters (Vmax , KM , and kcat ) were determined and compared with a commercial substrate. Secondly, a peptide aldehyde was designed as a chemically reactive inhibitor (CRI) based on the Swedish mutation substrate sequence. Incubation of this CRI with the protease, a FRET substrate, and one amine per well taken from an amine library, which was assembled by a maximum common substructure (MCS) approach, revealed the fragment 3-(3-aminophenyl)-2H-chromen-2-one (1) to be a competitive BACE-1 inhibitor that enhanced the activity of the CRI. Irreversibly formed fragment combination products of 1 with the initial peptide sequence were active and confirmed the targeting of the active site through the ethane-1,2-diamine isostere. Finally, structure-assisted combination of fragment 1 with secondary fragments that target the S1 site in hit optimization yielded novel, entirely fragment-based BACE-1 inhibitors with up to 30-fold improved binding affinity. Interactions with the protein were explained by molecular modeling studies, which indicate that the new fragment combinations interact with the catalytic aspartic acid dyad, as well as with the adjacent binding sites required for potency.
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Affiliation(s)
- María Isabel Fernández-Bachiller
- Medicinal Chemistry Department, Leibniz Institut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch, Robert-Rössle Str. 10, 13125 Berlin, Germany
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Sun LX, Zhu LZ, Wang JK. N-[( E)-4-Bromobenzylidene]-3,4-dimethylaniline. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o631. [PMID: 23723798 PMCID: PMC3647832 DOI: 10.1107/s1600536813008143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 03/25/2013] [Indexed: 11/27/2022]
Abstract
In the title compound, C15H14BrN, the dihedral angle between the benzene rings is 6.4 (2)° and the molecule has an E conformation about the C=N bond. In the crystal, molecules are linked by C—H⋯π interactions, forming two-dimensional networks lying parallel to (001).
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Sun LX, Zhu LZ, Wang JK. N-[( E)-4-Bromobenzylidene]-2,3-dimethylaniline. Acta Crystallogr Sect E Struct Rep Online 2013; 69:o630. [PMID: 23723797 PMCID: PMC3647831 DOI: 10.1107/s1600536813008088] [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: 03/22/2013] [Accepted: 03/24/2013] [Indexed: 11/10/2022]
Abstract
The title compound, C15H14BrN, has an E conformation about the C=N bond and the dihedral angle between the benzene rings is 50.7 (2)°. In the crystal, molecules are linked via C—H⋯π interactions, forming columns propagating along [010].
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Heise CE, Murray J, Augustyn KE, Bravo B, Chugha P, Cohen F, Giannetti AM, Gibbons P, Hannoush RN, Hearn BR, Jaishankar P, Ly CQ, Shah K, Stanger K, Steffek M, Tang Y, Zhao X, Lewcock JW, Renslo AR, Flygare J, Arkin MR. Mechanistic and structural understanding of uncompetitive inhibitors of caspase-6. PLoS One 2012; 7:e50864. [PMID: 23227217 PMCID: PMC3515450 DOI: 10.1371/journal.pone.0050864] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/25/2012] [Indexed: 01/13/2023] Open
Abstract
Inhibition of caspase-6 is a potential therapeutic strategy for some neurodegenerative diseases, but it has been difficult to develop selective inhibitors against caspases. We report the discovery and characterization of a potent inhibitor of caspase-6 that acts by an uncompetitive binding mode that is an unprecedented mechanism of inhibition against this target class. Biochemical assays demonstrate that, while exquisitely selective for caspase-6 over caspase-3 and -7, the compound's inhibitory activity is also dependent on the amino acid sequence and P1' character of the peptide substrate. The crystal structure of the ternary complex of caspase-6, substrate-mimetic and an 11 nM inhibitor reveals the molecular basis of inhibition. The general strategy to develop uncompetitive inhibitors together with the unique mechanism described herein provides a rationale for engineering caspase selectivity.
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Affiliation(s)
- Christopher E. Heise
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Jeremy Murray
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Katherine E. Augustyn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Brandon Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Preeti Chugha
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Frederick Cohen
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Anthony M. Giannetti
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Paul Gibbons
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Brian R. Hearn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Priyadarshini Jaishankar
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Cuong Q. Ly
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Kinjalkumar Shah
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Karen Stanger
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Micah Steffek
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Yinyan Tang
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Xianrui Zhao
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Joseph W. Lewcock
- Department of Neuroscience, Genentech, Inc., South San Francisco, California, United States of America
| | - Adam R. Renslo
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - John Flygare
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
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Richter M, Chakrabarti A, Ruttekolk IR, Wiesner B, Beyermann M, Brock R, Rademann J. Multivalent Design of Apoptosis-Inducing Bid-BH3 Peptide-Oligosaccharides Boosts the Intracellular Activity at Identical Overall Peptide Concentrations. Chemistry 2012; 18:16708-15. [DOI: 10.1002/chem.201202276] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Indexed: 11/08/2022]
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Horatscheck A, Wagner S, Ortwein J, Kim BG, Lisurek M, Beligny S, Schütz A, Rademann J. Benzoylphosphonat-basierte, photoaktive Phosphotyrosinpeptidmimetika zur funktionellen Modulierung von Proteintyrosinphosphatasen und hochspezifischen Markierung von SH2-Domänen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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37
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Horatscheck A, Wagner S, Ortwein J, Kim BG, Lisurek M, Beligny S, Schütz A, Rademann J. Benzoylphosphonate-based photoactive phosphopeptide mimetics for modulation of protein tyrosine phosphatases and highly specific labeling of SH2 domains. Angew Chem Int Ed Engl 2012; 51:9441-7. [PMID: 22907897 DOI: 10.1002/anie.201201475] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/31/2012] [Indexed: 11/09/2022]
Affiliation(s)
- André Horatscheck
- Abteilung für Medizinische Chemie, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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Zhu Q, Gao L, Chen Z, Zheng S, Shu H, Li J, Jiang H, Liu S. A novel class of small-molecule caspase-3 inhibitors prepared by multicomponent reactions. Eur J Med Chem 2012; 54:232-8. [PMID: 22652225 DOI: 10.1016/j.ejmech.2012.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/30/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
A series of tetra- and pentasubstituted polyfunctional dihydropyrroles 5 and 6 were synthesized via practical multicomponent reactions (MCRs) for research on their structure-activity relationship as caspase-3 inhibitors. Among 39 compounds evaluated, 14 of them exhibited inhibition against caspase-3 with IC(50) ranging from 5 to 20 μM. The inhibitory activities of 5 and 6 depend on the nature of substituents on different positions. 5 and 6 possess a different scaffold from those previously reported and are the first caspase-3 inhibitors prepared via MCRs. The most active compounds 5k (IC(50) = 5.27 μM) could therefore be used as a lead for the development of highly potent caspase-3 inhibitors as drug candidates for therapeutic agents by taking advantage of MCRs.
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Affiliation(s)
- Qiuhua Zhu
- School of Pharmaceutical Sciences, Southern Medical University, 1838 Northern Guangzhou Road, Guangzhou, Guangdong 510515, China
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Saavedra CJ, Boto A, Hernández R. Preparation of modified peptides: direct conversion of α-amino acids into β-amino aldehydes. Org Biomol Chem 2012; 10:4448-61. [DOI: 10.1039/c2ob25433f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Ahsanullah, Al-Gharabli SI, Rademann J. Soluble Peptidyl Phosphoranes for Metal-Free, Stereoselective Ligations in Organic and Aqueous Solution. Org Lett 2011; 14:14-7. [DOI: 10.1021/ol202627h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahsanullah
- Institute of Pharmacy, University of Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Chemical-Pharmaceutical Engineering, German-Jordanian University, 35247 Amman, Jordan
| | - Samer I. Al-Gharabli
- Institute of Pharmacy, University of Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Chemical-Pharmaceutical Engineering, German-Jordanian University, 35247 Amman, Jordan
| | - Jörg Rademann
- Institute of Pharmacy, University of Leipzig, Brüderstrasse 34, 04103 Leipzig, Germany, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Chemical-Pharmaceutical Engineering, German-Jordanian University, 35247 Amman, Jordan
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41
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Schmidt MF, Groves MR, Rademann J. Dynamic Substrate Enhancement for the Identification of Specific, Second-Site-Binding Fragments Targeting a Set of Protein Tyrosine Phosphatases. Chembiochem 2011; 12:2640-6. [DOI: 10.1002/cbic.201100414] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 11/08/2022]
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Abstract
We describe an intuitive and rapid procedure for analyzing experimental data by nonlinear least-squares fitting (NLSF) in the most widely used spreadsheet program. Experimental data in x/y form and data calculated from a regression equation are inputted and plotted in a Microsoft Excel worksheet, and the sum of squared residuals is computed and minimized using the Solver add-in to obtain the set of parameter values that best describes the experimental data. The confidence of best-fit values is then visualized and assessed in a generally applicable and easily comprehensible way. Every user familiar with the most basic functions of Excel will be able to implement this protocol, without previous experience in data fitting or programming and without additional costs for specialist software. The application of this tool is exemplified using the well-known Michaelis-Menten equation characterizing simple enzyme kinetics. Only slight modifications are required to adapt the protocol to virtually any other kind of dataset or regression equation. The entire protocol takes approximately 1 h.
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Schmidt MF, Rademann J. Dynamic template-assisted strategies in fragment-based drug discovery. Trends Biotechnol 2009; 27:512-21. [PMID: 19679363 PMCID: PMC7114311 DOI: 10.1016/j.tibtech.2009.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/16/2009] [Accepted: 06/17/2009] [Indexed: 11/27/2022]
Abstract
Fragment-based methods for drug discovery are increasingly popular because they provide drug leads with greater ligand efficiency than conventional high-throughput screening. However, established methods for fragment detection do not address the central question in fragment-based ligand discovery: how can a primary ligand be optimally extended by a secondary fragment? Dynamic screening methods solve this issue by using a protein target as a template for ligand assembly, thus yielding high-affinity binders from low-affinity fragments. This review summarizes recent work on dynamic screening methodology, which resulted in the development of several high-affinity binders for various targets. Strengths and limitations of the published approaches are discussed and possible contributions of dynamic screening methodology to the drug discovery process are highlighted.
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Affiliation(s)
- Marco F Schmidt
- Department of Medicinal Chemistry, Leibniz-Institute of Molecular Pharmacology, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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