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Dascalu AE, Furman C, Landrieu I, Cantrelle FX, Mortelecque J, Grolaux G, Gillery P, Tessier F, Lipka E, Billamboz M, Boulanger E, Ghinet A. Development of Receptor for Advanced Glycation End Products (RAGE) ligands through target directed dynamic combinatorial chemistry: a novel class of possible antagonists. Chemistry 2024; 30:e202303255. [PMID: 38317623 DOI: 10.1002/chem.202303255] [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: 10/04/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
Abstract
RAGE is a transmembrane receptor of immunoglobulin family that can bind various endogenous and exogenous ligands, initiating the inflammatory downstream signaling pathways, including inflammaging. Therefore, RAGE represents an attractive drug target for age-related diseases. For the development of small-molecule RAGE antagonists, we employed protein-templated dynamic combinatorial chemistry (ptDCC) using RAGE's VC1 domain as a template, the first application of this approach in the context of RAGE. The affinities of DCC hits were validated using microscale thermophoresis. Subsequent screening against AGE2 (glyceraldehyde-modified AGE)-sRAGE (solubleRAGE) (AGE2-BSA/sRAGE) interaction using ELISA tests led to the identification of antagonists with micromolar potency. Our findings not only demonstrate the successful application of ptDCC on RAGE but also highlight its potential to address the pressing need for alternative strategies for the development of small-molecule RAGE antagonists, an area of research that has experienced a slowdown in recent years.
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Affiliation(s)
- Anca-Elena Dascalu
- Junia, Health and Environment, Laboratory of Sustainable Chemistry and Health, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- 'Alexandru Ioan Cuza' University of Iasi, Faculty of Chemistry, Bd. Carol I, Nr. 11, 700506, Iasi, Romania
| | - Christophe Furman
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- Univ. Lille, UFR Pharmacie, BP 83, F-59006, Lille, France
| | - Isabelle Landrieu
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France
| | - François-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France
| | - Justine Mortelecque
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- CNRS EMR9002 Integrative Structural Biology, F-59000, Lille, France
| | - Gaëlle Grolaux
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
| | - Philippe Gillery
- Univ. Reims Champagne-Ardenne, Laboratory of Biochemistry and Molecular Biology CNRS/URCA UMR 7369 MEDyC, Faculty of Medicine, F-51095, Reims, France
| | - Frédéric Tessier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- Univ. Lille, UFR Pharmacie, BP 83, F-59006, Lille, France
| | - Emmanuelle Lipka
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- Univ. Lille, UFR Pharmacie, BP 83, F-59006, Lille, France
| | - Muriel Billamboz
- Junia, Health and Environment, Laboratory of Sustainable Chemistry and Health, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
| | - Eric Boulanger
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
| | - Alina Ghinet
- Junia, Health and Environment, Laboratory of Sustainable Chemistry and Health, F-59000, Lille, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France
- 'Alexandru Ioan Cuza' University of Iasi, Faculty of Chemistry, Bd. Carol I, Nr. 11, 700506, Iasi, Romania
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Chung HH, Kao CY, Wang TSA, Chu J, Pei J, Hsu CC. Reaction Tracking and High-Throughput Screening of Active Compounds in Combinatorial Chemistry by Tandem Mass Spectrometry Molecular Networking. Anal Chem 2021; 93:2456-2463. [PMID: 33416326 DOI: 10.1021/acs.analchem.0c04481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combinatorial synthesis has been widely used as an efficient strategy to screen for active compounds. Mass spectrometry is the method of choice in the identification of hits resulting from high-throughput screenings due to its high sensitivity, specificity, and speed. However, manual data processing of mass spectrometry data, especially for structurally diverse products in combinatorial chemistry, is extremely time-consuming and one of the bottlenecks in this process. In this study, we demonstrated the effectiveness of a tandem mass spectrometry molecular networking-based strategy for product identification, reaction dynamics monitoring, and active compound targeting in combinatorial synthesis. Molecular networking connects compounds with similar tandem mass spectra into a cluster and has been widely used in natural products analysis. We show that both the expected and side products can be readily characterized using molecular networking based on their mass spectrometry fragmentation patterns. Additionally, time-dependent molecular networking was integrated to track reaction dynamics to determine the optimal reaction time to maximize target product yields. We also present a proof-of-concept experiment that successfully identified and isolated active molecules from a dynamic combinatorial library. These results demonstrated the potential of using molecular networking for identifying, tracking, and high-throughput screening of active compounds in combinatorial synthesis.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chih-Yao Kao
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - John Chu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Jiying Pei
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.,School of Marine Sciences, Guangxi University, No.100, East Daxue Rd., Nanning City, Guangxi 530015, China
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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Kieffer M, Bilbeisi RA, Thoburn JD, Clegg JK, Nitschke JR. Guest Binding Drives Host Redistribution in Libraries of Co II 4 L 4 Cages. Angew Chem Int Ed Engl 2020; 59:11369-11373. [PMID: 32243707 PMCID: PMC7383889 DOI: 10.1002/anie.202004627] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Two CoII 4 L4 tetrahedral cages prepared from similar building blocks showed contrasting host-guest properties. One cage did not bind guests, whereas the second encapsulated a series of anions, due to electronic and geometric effects. When the building blocks of both cages were present during self-assembly, a library of five CoII LA x LB 4-x cages was formed in a statistical ratio in the absence of guests. Upon incorporation of anions able to interact preferentially with some library members, the products obtained were redistributed in favor of the best anion binders. To quantify the magnitudes of these templation effects, ESI-MS was used to gauge the effect of each template upon library redistribution.
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Affiliation(s)
- Marion Kieffer
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Rana A. Bilbeisi
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of Civil and Environmental EngineeringAmerican University of BeirutBeirutLebanon
| | - John D. Thoburn
- Department of ChemistryRandolph-Macon CollegeAshlandVA23005USA
| | - Jack K. Clegg
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
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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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Wu F, Zhuo L, Wang F, Huang W, Hao G, Yang G. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead. iScience 2020; 23:101179. [PMID: 32498019 PMCID: PMC7267738 DOI: 10.1016/j.isci.2020.101179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Motivated by the growing demand for reducing the chemical optimization burden of H2L, we developed auto in silico ligand directing evolution (AILDE, http://chemyang.ccnu.edu.cn/ccb/server/AILDE), an efficient and general approach for the rapid identification of drug leads in accessible chemical space. This computational strategy relies on minor chemical modifications on the scaffold of a hit compound, and it is primarily intended for identifying new lead compounds with minimal losses or, in some cases, even increases in ligand efficiency. We also described how AILDE greatly reduces the chemical optimization burden in the design of mesenchymal-epithelial transition factor (c-Met) kinase inhibitors. We only synthesized eight compounds and found highly efficient compound 5g, which showed an ∼1,000-fold improvement in in vitro activity compared with the hit compound. 5g also displayed excellent in vivo antitumor efficacy as a drug lead. We believe that AILDE may be applied to a large number of studies for rapid design and identification of drug leads. AILDE was developed for the rapid identification of drug leads A potent drug lead targeted to c-Met was found by synthesizing only eight compounds
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Linsheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Gefei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, P. R. China.
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7
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van der Vlag R, Yagiz Unver M, Felicetti T, Twarda‐Clapa A, Kassim F, Ermis C, Neochoritis CG, Musielak B, Labuzek B, Dömling A, Holak TA, Hirsch AKH. Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination. ChemMedChem 2020; 15:370-375. [PMID: 31774938 PMCID: PMC7064911 DOI: 10.1002/cmdc.201900574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.
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Affiliation(s)
- Ramon van der Vlag
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - M. Yagiz Unver
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Tommaso Felicetti
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo 106123PerugiaItaly
| | | | - Fatima Kassim
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Cagdas Ermis
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Constantinos G. Neochoritis
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
- Chemistry departmentUniversity of Crete70013HeraklionGreece
| | - Bogdan Musielak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of 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
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Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J Comput Aided Mol Des 2019; 34:27-37. [PMID: 31773463 DOI: 10.1007/s10822-019-00251-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
Influenza epidemics are responsible for an average of 3-5 millions of severe cases and up to 500,000 deaths around the world. One of flu pandemic types is influenza A(H1N1)pdm09 virus (pdm09H1N1). Oseltamivir is the antiviral drug used to treat influenza targeting at neuraminidase (NA) located on the viral surface. Influenza virus undergoes high mutation rates and leads to drug resistance, and thus the development of more efficient drugs is required. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. The obtained results in terms of binding free energy and intermolecular interactions in the ligand-protein interface showed that the oseltamivir could not be well accommodated in the binding pocket of both NA mutants and the 150-loop moves out from oseltamivir as an "open" state. A greater number of water molecules accessible to the binding pocket could disrupt the oseltamivir binding with NA target as seen be high mobility of oseltamivir at the active site. Additionally, our finding could guide to the design and development of novel NA inhibitor drugs.
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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 PMCID: PMC6748286 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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Hatai J, Schmuck C. Diverse Properties of Guanidiniocarbonyl Pyrrole-Based Molecules: Artificial Analogues of Arginine. Acc Chem Res 2019; 52:1709-1720. [PMID: 31150198 DOI: 10.1021/acs.accounts.9b00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The guanidinium moiety, which is present in active sites of many enzymes, plays an important role in the binding of anionic substrates. In addition, it was also found to be an excellent binding motif for supramolecular chemistry. Inspired by Nature, scientists have developed artificial receptors containing guanidinium scaffolds that bind to a variety of oxoanions through hydrogen bonding and charge pairing interactions. However, the majority of binding studies is restricted to organic solvents. Polyguanidinium based molecules can form efficient complexes in aqueous solvents due to strong electrostatic interactions. However, they only have moderate association constants, which are significantly decreased in the presence of competing anions and salts. Hence, to improve the binding affinity of the guanidinium moiety, our group developed the cationic guanidiniocarbonyl pyrrole (GCP) moiety. This rigid planar analogue binds efficiently to oxoanions, like carboxylates even in aqueous solvents. The lower p Ka value (7-8) of GCP compared to guanidinium derivatives (p Ka 13) favors the formation of strong, hydrogen bonded ion pairs. In addition, carboxylate binding is further enhanced by additional amide hydrogen bond donors located at the five position of the pyrrole core. Moreover, the design has allowed for introducing secondary interactions between receptor side chains and guest molecules, which allows for optimizing binding specificity and selectivity. The spectroscopic data confirmed stabilization of guanidiniocarbonyl pyrrole/oxoanion complexes through a combination of ion pairing and multiple hydrogen bonding interactions. The key role of the ionic interaction in a polar solvent, is demonstrated by a zwitterion derivative of the guanidiniocarbonyl pyrrole, which self-assembles in both dimethyl sulfoxide and pure water with association constants of K > 1010 M-1 and K = 170 M-1, respectively. In this Account, we discuss strategies for making GCP functionalized compounds, in order to boost their ability to bind oxoanions. Then we explore how these building blocks have been incorporated into different synthetic molecules and peptide sequences, highlighting examples that demonstrated the versatility of this binding scaffold. For instance, the high oxoanion binding property of GCP-based compounds was exploited to generate a detectable signal for sensing applications, thus improving selectivity and sensitivity in aqueous solution. Moreover, peptides and molecules containing GCP have shown excellent gene transfections properties. Furthermore, the self-assembly and zwitterionic behavior of zwitterionic GCP analogues was used to develop variety of supramolecular architectures such as stable supramolecular β-helix structure, linear supramolecular oligomers, one-dimensional rods or two-dimension sheets, fibers, vesicles, soft nanospheres, as well as stimuli responsive supramolecular gels.
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Affiliation(s)
- Joydev Hatai
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Carsten Schmuck
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
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Frei P, Hevey R, Ernst B. Dynamic Combinatorial Chemistry: A New Methodology Comes of Age. Chemistry 2018; 25:60-73. [DOI: 10.1002/chem.201803365] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Rachel Hevey
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Ekström AG, Wang JT, Bella J, Campopiano DJ. Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library. Org Biomol Chem 2018; 16:8144-8149. [DOI: 10.1039/c8ob01918e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.
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Affiliation(s)
| | | | - Juraj Bella
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
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13
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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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14
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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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15
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Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery. Molecules 2016; 21:molecules21070910. [PMID: 27438816 PMCID: PMC6273345 DOI: 10.3390/molecules21070910] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023] Open
Abstract
Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.
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16
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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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17
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Harnessing dynamic combinatorial chemistry in the search for new ligands for protein targets. Future Med Chem 2015; 7:2095-8. [DOI: 10.4155/fmc.15.146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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18
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Jiang QQ, Sicking W, Ehlers M, Schmuck C. Discovery of potent inhibitors of human β-tryptase from pre-equilibrated dynamic combinatorial libraries. Chem Sci 2014; 6:1792-1800. [PMID: 29163876 PMCID: PMC5644118 DOI: 10.1039/c4sc02943g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/05/2014] [Indexed: 01/07/2023] Open
Abstract
Pre-equilibrated combinatorial libraries based on multivalent peptide acyl hydrazones were used to find potent inhibitors of β-tryptase. The best inhibitors bind to the protein surface, and inhibit β-tryptase with nanomolar affinity (Kica. 10 nM) and high selectivity in a reversible and non-competitive way.
Pre-equilibrated dynamic combinatorial libraries based on acyl hydrazone interchange of peptide-derived hydrazides and di- and tri-aldehydes have been used to discover potent inhibitors with nanomolar affinities for β-tryptase. To identify potent inhibitors the activity of the full library containing 95 members was compared with those of sub-libraries in which individual building blocks were missing. The most active library members contain a rigid central aromatic scaffold with three cationic peptide arms. The arms of the best inhibitors also contained a tailor-made GCP oxoanion binding motif attached to a lysine side chain. The most potent tri-armed hydrazones with peptide arms GKWR or GKWK(GCP) were shown to inhibit β-tryptase (Kica. 10–20 nM) reversibly, non-competitively and selectively (compared to related serine proteases, e.g. trypsin and chymotrypsin), most likely by binding to the protein surface, also in agreement with molecular modelling calculations. These new inhibitors are one order of magnitude more efficient than related tetravalent inhibitors obtained from previous work on a split-mix-combinatorial library and were identified with significantly less effort, demonstrating the usefulness of this approach for the identification of enzyme inhibitors in general.
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Affiliation(s)
- Qian-Qian Jiang
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Wilhelm Sicking
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Martin Ehlers
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Carsten Schmuck
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
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19
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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20
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Biased and unbiased strategies to identify biologically active small molecules. Bioorg Med Chem 2014; 22:4474-89. [DOI: 10.1016/j.bmc.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 12/20/2022]
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21
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Weber L. In vitro combinatorial chemistry to create drug candidates. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 1:261-7. [PMID: 24981494 DOI: 10.1016/j.ddtec.2004.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In vitro combinatorial chemistry represents a variety of technologies where the selection and synthesis of novel molecules is performed in one integrated process. In its application towards drug discovery, the biological target is used to select and/or to amplify compounds out of a large pool of potential combinatorial compound library members. Recent examples provide a first proof-of-concept that dynamic combinatorial libraries or 'click chemistry' are able to discover highly potent and selective small molecule inhibitors of target enzymes.:
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Affiliation(s)
- Lutz Weber
- Morphochem AG, Gmunder Street 37-37A, 81379 München, Germany.
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22
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Mondal M, Radeva N, Köster H, Park A, Potamitis C, Zervou M, Klebe G, Hirsch AKH. Strukturbasiertes Design von Hemmstoffen der Aspartylprotease Endothiapepsin mittels dynamischer kombinatorischer Chemie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309682] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Mondal M, Radeva N, Köster H, Park A, Potamitis C, Zervou M, Klebe G, Hirsch AKH. Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry. Angew Chem Int Ed Engl 2014; 53:3259-63. [PMID: 24532096 DOI: 10.1002/anie.201309682] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 12/19/2022]
Abstract
Structure-based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial chemistry (DCC) has emerged as a powerful strategy to identify bioactive ligands given that it enables the target to direct the synthesis of its strongest binder. We have designed a library of potential inhibitors (acylhydrazones) generated from five aldehydes and five hydrazides and used DCC to identify the best binder(s). After addition of the aspartic protease endothiapepsin, we characterized the protein-bound library member(s) by saturation-transfer difference NMR spectroscopy. Cocrystallization experiments validated the predicted binding mode of the two most potent inhibitors, thus demonstrating that the combination of de novo SBD and DCC constitutes an efficient starting point for hit identification and optimization.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands) http://www.rug.nl/research/bio-organic-chemistry/hirsch/
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24
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Misuraca MC, Moulin E, Ruff Y, Giuseppone N. Experimental and theoretical methods for the analyses of dynamic combinatorial libraries. NEW J CHEM 2014. [DOI: 10.1039/c4nj00304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Progresses in spatial and temporal analytical tools open new avenues for the study and control of increasingly complex chemical systems.
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Affiliation(s)
- Maria Cristina Misuraca
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Yves Ruff
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Nicolas Giuseppone
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
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25
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Ulrich S, Dumy P. Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry. Chem Commun (Camb) 2014; 50:5810-25. [DOI: 10.1039/c4cc00263f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Abdelrahim MYM, Tanc M, Winum JY, Supuran CT, Barboiu M. Dominant behaviours in the expression of human carbonic anhydrase hCA I activity. Chem Commun (Camb) 2014; 50:8043-6. [DOI: 10.1039/c4cc03289f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.
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Affiliation(s)
- M. Yahia M. Abdelrahim
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
| | - Muhammet Tanc
- Università degli Studi di Firenze
- Polo Scientifico, Laboratorio di Chimica Bioinorganica
- 50019 Sesto Fiorentino (Florence), Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Claudiu T. Supuran
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Mihail Barboiu
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
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27
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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28
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Joshi G, Anslyn EV. Dynamic thiol exchange with β-sulfido-α,β-unsaturated carbonyl compounds and dithianes. Org Lett 2012; 14:4714-7. [PMID: 22934665 PMCID: PMC3472802 DOI: 10.1021/ol301781u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A reversible covalent bond exchange of thiols, β-sulfido-α,β-unsaturated carbonyls, and dithianes has been studied in DMSO and D(2)O/DMSO mixtures. The equilibrium between thiols and β-sulfido-α,β-unsaturated carbonyls is obtained within a few hours, while the equilibration starting with the β-dithiane carbonyls and thiols requires a few days. This time scale makes the system ideal for utilization in dynamic combinatorial chemistry.
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Affiliation(s)
- Gururaj Joshi
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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29
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Huck J, Philp D. Replication Processes-From Autocatalysis to Systems Chemistry. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Raindlová V, Pohl R, Hocek M. Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination. Chemistry 2012; 18:4080-7. [PMID: 22337599 DOI: 10.1002/chem.201103270] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 11/06/2022]
Abstract
5-(5-Formylthienyl)-, 5-(4-formylphenyl)- and 5-(2-fluoro-5-formylphenyl)cytosine 2'-deoxyribonucleoside mono- (dC(R)MP) and triphosphates (dC(R)TP) were prepared by aqueous Suzuki-Miyaura cross-coupling of 5-iodocytosine nucleotides with the corresponding formylarylboronic acids. The dC(R)TPs were excellent substrates for DNA polymerases and were incorporated into DNA by primer extension or PCR. Reductive aminations of the model dC(R)MPs with lysine or lysine-containing tripeptide were studied and optimized. In aqueous phosphate buffer (pH 6.7) the yields of the reductive aminations with tripeptide III were up to 25 %. Bioconjugation of an aldehyde-containing DNA with a lysine-containing tripeptide was achieved through reductive amination in yields of up to 90 % in aqueous phosphate buffer.
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Affiliation(s)
- Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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31
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Hanessian S, Maianti JP, Ly VL, Deschênes-Simard B. Structural and kinetic study of self-assembling macrocyclic dimer natural product aminoglycoside66-40C and unnatural variants. Chem Sci 2012. [DOI: 10.1039/c1sc00538c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies. J Mol Model 2011; 18:2553-66. [DOI: 10.1007/s00894-011-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/12/2011] [Indexed: 11/25/2022]
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33
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Folmer-Andersen JF, Lehn JM. Thermoresponsive dynamers: thermally induced, reversible chain elongation of amphiphilic poly(acylhydrazones). J Am Chem Soc 2011; 133:10966-73. [PMID: 21639138 DOI: 10.1021/ja2035909] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A nanostructured poly(acylhydrazone), which is reversibly formed in acidic aqueous solution from di(aldehyde) and di(acylhydrazine) monomers with appended hexaglyme groups, was found to display lower critical solution (LCS) behavior. Remarkably, under acidic conditions in which polymerization is reversible, large and reversible molecular weight (M(w)) increases were observed in response to elevated temperatures, both below and above the LCS temperature. No variation in M(w) was evident under neutral and alkaline conditions, in which the acylhydrazone condensation is essentially irreversible. Results of turbidometry studies, size-exclusion chromatography-multiangle laser light scattering (SEC-MALLS), and transmission electron microscopy (TEM) suggest that heating the polymer below the LCS temperature leads to polymer growth with preservation of the characteristic nanostructured morphology, whereas the onset of the microphase separated state causes a fundamental change in morphology, in which the polymer chains aggregate into larger bundles and fibers. van't Hoff analysis of a small molecule model system indicates that the acylhydrazone condensation is enthalpy driven (ΔH(eq) = -8.2 ± 0.2 kcal·mol(-1) and ΔS(eq) = -11.1 ± 0.4 = cal·mol(-1)·K(-1)), which suggests that the observed polymer growth with temperature is not a consequence of the intrinsic thermodynamics of the intermonomer linkage but is likely the result of the thermoresponsive characteristics conferred by the multiple hexaglyme groups. The system described displays double control of the dynamer state by two orthogonal agents, heat and protons (pH). It also represents a prototype for dynamic materials displaying multiple control adaptive behavior.
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Affiliation(s)
- J Frantz Folmer-Andersen
- Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 8 Allée Gaspard-Monge, BP 70028, 67083 Strasbourg, France
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34
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Upadhyay A, Chompoo J, Kishimoto W, Makise T, Tawata S. HIV-1 integrase and neuraminidase inhibitors from Alpinia zerumbet. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:2857-2862. [PMID: 21306110 DOI: 10.1021/jf104813k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
AIDS and influenza are viral pandemics and remain one of the leading causes of human deaths worldwide. The increasing resistance of these diseases to synthetic drugs demands the search for novel compounds from plant-based sources. In this regard, the leaves and rhizomes of Alpinia zerumbet, a traditionally important economic plant in Okinawa, were investigated for activity against HIV-1 integrase (IN) and neuraminidase (NA). The aqueous extracts of leaves and rhizomes had IN inhibitory activity with IC(50) values of 30 and 188 μg/mL, whereas against NA they showed 50% inhibition at concentrations of 43 and 57 μg/mL, respectively. 5,6-Dehydrokawain (DK), dihydro-5,6-dehydrokawain (DDK), and 8(17),12-labdadiene-15,16-dial (labdadiene) were isolated from the rhizomes and were tested for enzyme inhibitions. DK and DDK strongly inhibited IN with IC(50) of 4.4 and 3.6 μg/mL, respectively. Against NA, DK, DDK, and labdadiene exhibited mixed type of inhibition with respective IC(50) values of 25.5, 24.6, and 36.6 μM and K(i) values ranging from 0.3 to 2.8 μM. It was found that DDK is a slow and time-dependent reversible inhibitor of NA, probably with a methoxy group as its functionally active site. These results suggest that alpinia could be used as a source of bioactive compounds against IN and NA and that DK and DDK may have possibilities in the design of drugs against these viral diseases.
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Affiliation(s)
- Atul Upadhyay
- Department of Biochemistry and Applied Bioscience, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
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35
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Azéma L, Bathany K, Rayner B. 2'-O-Appended polyamines that increase triple-helix-forming oligonucleotide affinity are selected by dynamic combinatorial chemistry. Chembiochem 2011; 11:2513-6. [PMID: 21104718 DOI: 10.1002/cbic.201000538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Laurent Azéma
- U869, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France
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36
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Constitutional Dynamic Chemistry: Bridge from Supramolecular Chemistry to Adaptive Chemistry. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:1-32. [DOI: 10.1007/128_2011_256] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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37
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Barboiu M. Multistate and Phase Change Selection in Constitutional Multivalent Systems. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:33-53. [DOI: 10.1007/128_2011_196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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von Delius M, Geertsema EM, Leigh DA, Tang DTD. Design, Synthesis, and Operation of Small Molecules That Walk along Tracks. J Am Chem Soc 2010; 132:16134-45. [PMID: 20979418 DOI: 10.1021/ja106486b] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Max von Delius
- School of Chemistry, University of Edinburgh, The King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Edzard M. Geertsema
- School of Chemistry, University of Edinburgh, The King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Edinburgh, The King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Dan-Tam D. Tang
- School of Chemistry, University of Edinburgh, The King’s Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
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39
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Caraballo R, Sakulsombat M, Ramström O. Towards Dynamic Drug Design: Identification and Optimization of β-Galactosidase Inhibitors from a Dynamic Hemithioacetal System. Chembiochem 2010; 11:1600-6. [DOI: 10.1002/cbic.201000158] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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40
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Bhat VT, Caniard AM, Luksch T, Brenk R, Campopiano DJ, Greaney MF. Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry. Nat Chem 2010; 2:490-7. [PMID: 20489719 PMCID: PMC2913121 DOI: 10.1038/nchem.658] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 03/30/2010] [Indexed: 12/25/2022]
Abstract
Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site.
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Affiliation(s)
- Venugopal T. Bhat
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Anne M. Caniard
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Torsten Luksch
- College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Ruth Brenk
- College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Dominic J. Campopiano
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Michael F. Greaney
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
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41
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Ludlow RF, Otto S. The Impact of the Size of Dynamic Combinatorial Libraries on the Detectability of Molecular Recognition Induced Amplification. J Am Chem Soc 2010; 132:5984-6. [DOI: 10.1021/ja1013689] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- R. Frederick Ludlow
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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42
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Besenius P, Cormack PAG, Ludlow RF, Otto S, Sherrington DC. Affinity chromatography in dynamic combinatorial libraries: one-pot amplification and isolation of a strongly binding receptor. Org Biomol Chem 2010; 8:2414-8. [PMID: 20448900 DOI: 10.1039/c000333f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the one-pot amplification and isolation of a nanomolar receptor in a multibuilding block aqueous dynamic combinatorial library using a polymer-bound template. By appropriate choice of a poly(N,N-dimethylacrylamide)-based support, nonselective ion-exchange type behaviour between the oppositely charged cationic guest and polyanionic hosts was overcome, such that the selective molecular recognition arising in aqueous solution reactions is manifest also in the analogous templated solid phase DCL syntheses. The ability of a polymer bound template to identify and isolate a synthetic receptor via dynamic combinatorial chemistry was not compromised by the large size of the library, consisting of well over 140 theoretical members, demonstrating the practical advantages of a polymer-supported DCL methodology.
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Affiliation(s)
- Pol Besenius
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK G1 1XL
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43
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Prediction of Mutation Positions in H5N1 Neuraminidases From Influenza A Virus by Means of Neural Network. Ann Biomed Eng 2010; 38:984-92. [DOI: 10.1007/s10439-010-9907-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Scott DE, Dawes GJ, Ando M, Abell C, Ciulli A. A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry. Chembiochem 2009; 10:2772-9. [PMID: 19827080 PMCID: PMC4458376 DOI: 10.1002/cbic.200900537] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Indexed: 11/06/2022]
Abstract
A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.
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Affiliation(s)
- Duncan E. Scott
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Gwen J. Dawes
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Michiyo Ando
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Chris Abell
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Alessio Ciulli
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
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45
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Nasr G, Petit E, Supuran CT, Winum JY, Barboiu M. Carbonic anhydrase II-induced selection of inhibitors from a dynamic combinatorial library of Schiff’s bases. Bioorg Med Chem Lett 2009; 19:6014-7. [PMID: 19796939 DOI: 10.1016/j.bmcl.2009.09.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/14/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
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46
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Hierarchical functional gradients of pH-responsive self-assembled monolayers using dynamic covalent chemistry on surfaces. Nat Chem 2009; 1:649-56. [DOI: 10.1038/nchem.400] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 09/08/2009] [Indexed: 11/08/2022]
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47
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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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48
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Nasr G, Petit E, Vullo D, Winum JY, Supuran CT, Barboiu M. Carbonic Anhydrase-Encoded Dynamic Constitutional Libraries: Toward the Discovery of Isozyme-Specific Inhibitors. J Med Chem 2009; 52:4853-9. [PMID: 19580287 DOI: 10.1021/jm900449v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gihane Nasr
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
| | - Eddy Petit
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
| | - Daniela Vullo
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS-UM1-UM2, Bâtiment de Recherche Max Mousseron, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l’Ecole Normale, 34296 Montpellier Cedex, France
| | - Claudiu T. Supuran
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy
| | - Mihail Barboiu
- Adaptative Supramolecular Nanosystems Group, Institut Européen des Membranes, ENSCM/UMII/UMR-CNRS 5635, Place Eugène Bataillon, CC 047, 34095 Montpellier, Cedex 5, France
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49
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Magano J. Synthetic Approaches to the Neuraminidase Inhibitors Zanamivir (Relenza) and Oseltamivir Phosphate (Tamiflu) for the Treatment of Influenza. Chem Rev 2009; 109:4398-438. [DOI: 10.1021/cr800449m] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Javier Magano
- Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340
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50
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Orita M, Ohno K, Niimi T. Two ‘Golden Ratio’ indices in fragment-based drug discovery. Drug Discov Today 2009; 14:321-8. [DOI: 10.1016/j.drudis.2008.10.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 10/07/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
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