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Schmitz B, Frieg B, Homeyer N, Jessen G, Gohlke H. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin. Arch Pharm (Weinheim) 2024; 357:e2300612. [PMID: 38319801 DOI: 10.1002/ardp.202300612] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.
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Affiliation(s)
- Birte Schmitz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gisela Jessen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
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2
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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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3
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Zheng L, Shi F, Peng C, Xu M, Fan F, Li Y, Zhang L, Du J, Wang Z, Lin Z, Sun Y, Deng C, Duan X, Wei L, Zhao C, Fang L, Zhang P, Ma S, Lai L, Yang M. Application scenario-oriented molecule generation platform developed for drug discovery. Methods 2024; 222:112-121. [PMID: 38215898 DOI: 10.1016/j.ymeth.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/22/2023] [Accepted: 12/23/2023] [Indexed: 01/14/2024] Open
Abstract
Design of molecules for candidate compound selection is one of the central challenges in drug discovery due to the complexity of chemical space and requirement of multi-parameter optimization. Here we present an application scenario-oriented platform (ID4Idea) for molecule generation in different scenarios of drug discovery. This platform utilizes both library or rule based and generative based algorithms (VAE, RNN, GAN, etc.), in combination with various AI learning types (pre-training, transfer learning, reinforcement learning, active learning, etc.) and input representations (1D SMILES, 2D graph, 3D shape, binding site, pharmacophore, etc.), to enable customized solutions for a given molecular design scenario. Besides the usual generation followed screening protocol, goal-directed molecule generation can also be conducted towards predefined goals, enhancing the efficiency of hit identification, lead finding, and lead optimization. We demonstrate the effectiveness of ID4Idea platform through case studies, showcasing customized solutions for different design tasks using various input information, such as binding pockets, pharmacophores, and compound representations. In addition, remaining challenges are discussed to unlock the full potential of AI models in drug discovery and pave the way for the development of novel therapeutics.
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Affiliation(s)
- Lianjun Zheng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Fangjun Shi
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Min Xu
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Fangda Fan
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Yuanpeng Li
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Lin Zhang
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Jiewen Du
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Zonghu Wang
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Yina Sun
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Chenglong Deng
- Jingtai Zhiyao Technology (Shanghai) Co., Ltd. (XtalPi), No. 207 Huanqiao Road, Pudong New Area, Shanghai 201315, China
| | - Xinli Duan
- XtalPi Innovation Center, XtalPi Inc., Beijing, China
| | - Lin Wei
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | | | - Lei Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Peiyu Zhang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Songling Ma
- XtalPi Innovation Center, XtalPi Inc., Beijing, China.
| | - Lipeng Lai
- XtalPi Innovation Center, XtalPi Inc., Beijing, China.
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China.
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4
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Hafeez S, Zafar Paracha R, Adnan F. Designing of fragment based inhibitors with improved activity against E. coli AmpC β-lactamase compared to the conventional antibiotics. Saudi J Biol Sci 2024; 31:103884. [PMID: 38125736 PMCID: PMC10730856 DOI: 10.1016/j.sjbs.2023.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
One of the most common primary resistance mechanism of multi-drug resistant (MDR) Gram negative pathogenic bacteria to combat β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems is the generation of β- lactamases. The uropathogenic E. coli is mostly getting multi-drug resistance due to the synthesis of AmpC β-lactamases and therefore new antibiotics and inhibitors are needed to treat the evolving infections. The current study was designed for targetting AmpC β-lactamase of E. coli using molecular docking based virtual screening, linking fragments for designing novel compounds and binding mode analysis using molecular dynamic simulation with target protein. The FCH group all-purpose fragment library consisting of 9388 fragments has been screened against AmpC β-lactamase protein of E. coli and the antibiotics and anti-infectives used in treatment of Urinary tract Infections (UTIs) were also screened with AmpC β-lactamase protein. Among the 9388 fragments, 339 fragment candidates were selected and linked with cefepime antibiotic having maximum binding affinity for AmpC target protein. Computational analysis of interactions as well as molecular dynamics (MD) simulations were also conducted for identifying the most promising ligand-pocket complexes from docking investigations to comprehend their thermodynamic properties and verify the docking outcomes as well. Overall, the linked complexes (LCs) showed good binding interactions with AmpC β-lactamase. Interestingly, our fragment-based LCs remained relatively stable in comparison with cefepime antibiotic. Moreover, S12 fragment linked complex remained the most stable during 50 ns with remarkable number of interactions indicating it as promising candidate in novel lead discovery against MDR E. coli infections.
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Affiliation(s)
- Sidrah Hafeez
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Sciences (SINES), National University of Science and Technology (NUST), Islamabad 44000, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
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5
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Tan Y, Dai L, Huang W, Guo Y, Zheng S, Lei J, Chen H, Yang Y. DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. J Chem Inf Model 2022; 62:5907-5917. [PMID: 36404642 DOI: 10.1021/acs.jcim.2c00982] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fragment-based drug discovery is a widely used strategy for drug design in both academic and pharmaceutical industries. Although fragments can be linked to generate candidate compounds by the latest deep generative models, generating linkers with specified attributes remains underdeveloped. In this study, we presented a novel framework, DRlinker, to control fragment linking toward compounds with given attributes through reinforcement learning. The method has been shown to be effective for many tasks from controlling the linker length and log P, optimizing predicted bioactivity of compounds, to various multiobjective tasks. Specifically, our model successfully generated 91.0% and 93.9% of compounds complying with the desired linker length and log P and improved the 7.5 pChEMBL value in bioactivity optimization. Finally, a quasi-scaffold-hopping study revealed that DRlinker could generate nearly 30% molecules with high 3D similarity but low 2D similarity to the lead inhibitor, demonstrating the benefits and applicability of DRlinker in actual fragment-based drug design.
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Affiliation(s)
- Youhai Tan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou510006, China
| | - Lingxue Dai
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou510006, China
| | - Weifeng Huang
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou510006, China
| | - Yinfeng Guo
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou510006, China
| | - Shuangjia Zheng
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou510006, China.,Galixir Technologies, Beijing100083, China
| | - Jinping Lei
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou510006, China
| | - Hongming Chen
- Guangzhou Laboratory, No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou510005, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou510006, China
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6
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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7
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Zagiel B, Peker T, Marquant R, Cazals G, Webb G, Miclet E, Bich C, Sachon E, Moumné R. Dynamic Amino Acid Side‐Chains Grafting on Folded Peptide Backbone**. Chemistry 2022; 28:e202200454. [DOI: 10.1002/chem.202200454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Benjamin Zagiel
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Taleen Peker
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Rodrigue Marquant
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Guillaume Cazals
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Gabrielle Webb
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Emeric Miclet
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM Institut des Biomolécules Max Mousseron (IBMM) Université de Montpellier 34293 Montpellier France
| | - Emmanuelle Sachon
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
- MS3 U platform UFR 926 UFR 927 Sorbonne Université 4 place Jussieu 75005 Paris France
| | - Roba Moumné
- Sorbonne Université École normale supérieure PSL University CNRS Laboratoire des biomolécules, LBM 75005 Paris France
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8
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Gay M, Diaz-Lobo M, Gusi-Vives M, Arauz-Garofalo G, Vilanova M, Giralt E, Vilaseca M, Guardiola S. Proteomic tools for the quantitative analysis of artificial peptide libraries: detection and characterization of target-amplified PD-1 inhibitors. Chembiochem 2022; 23:e202200152. [PMID: 35362647 DOI: 10.1002/cbic.202200152] [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: 03/16/2022] [Revised: 03/31/2022] [Indexed: 11/07/2022]
Abstract
We report a quantitative proteomics data analysis pipeline which, coupled to protein-directed dynamic combinatorial chemistry (DDC) experiments, enables the rapid discovery and direct characterization of protein-protein interaction (PPI) modulators. A low-affinity PD-1 binder was incubated with a library of >100 D-peptides under thiol-exchange favoring conditions, in the presence of the target protein PD-1, and we determined the S-linked dimeric species that resulted amplified in the protein samples versus the controls. We chemically synthesized the target dimer candidates and validated them by thermophoresis binding and protein-protein interaction assays. The results provide a proof-of-concept for using this strategy in the high-throughput search of improved drug-like peptide binders that block therapeutically relevant protein-protein interactions.
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Affiliation(s)
- Marina Gay
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mireia Diaz-Lobo
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mar Gusi-Vives
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, SPAIN
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Mar Vilanova
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, mas, SPAIN
| | - Ernest Giralt
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, SPAIN
| | - Marta Vilaseca
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Mass Spectrometry Core Facility, SPAIN
| | - Salvador Guardiola
- Institute for Research in Biomedicine: Institut de Recerca Biomedica, Pharmacology, Baldiri Reixac, 4, 08028, Barcelona, SPAIN
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9
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Electrophilically activated nitroalkanes in the synthesis of substituted 1,3,4-oxadiazoles from amino acid derivatives. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Li Z, Zhang L, Zhou Y, Zha D, Hai Y, You L. Dynamic Covalent Reactions Controlled by Ring‐Chain Tautomerism of 2‐Formylbenzoic Acid. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ziyi Li
- College of Chemistry and Material Science Fujian Normal University Fuzhou Fujian 350007 China
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Ling Zhang
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yuntao Zhou
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Daijun Zha
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lei You
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou Fujian 350108 China
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11
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Zhao S, Wu Y, Hu L. Identification and synthesis of selective cholesterol esterase inhibitor using dynamic combinatorial chemistry. Bioorg Chem 2021; 119:105520. [PMID: 34864280 DOI: 10.1016/j.bioorg.2021.105520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022]
Abstract
In this study, the concept of dynamic combinatorial chemistry (DCC) was applied to explore novel cholesterol esterase (CEase) inhibitors. In the presence of enzyme, two substrates (A1H3 and A2H3) were amplified from the dynamic combinatorial library (DCL), which was generated through reversible acylhydrazone formation reaction. In the in vitro biological evaluation, compound A1H3 exhibited not only potent (IC50 in nanomolar range) but also selective inhibition (>120 folds of selectivity for CEase over AChE). Furthermore, the binding pattern and possible binding mechanism were investigated in the kinetic experiment and molecular docking study, respectively.
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Affiliation(s)
- Shuang Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China
| | - Yao Wu
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, Zhenjiang, 301 Xuefu Rd., Zhenjiang, China.
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12
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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13
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Cao Y, Yang J, Eichin D, Zhao F, Qi D, Kahari L, Jia C, Peurla M, Rosenholm JM, Zhao Z, Jalkanen S, Li J. Self‐Synthesizing Nanorods from Dynamic Combinatorial Libraries against Drug Resistant Cancer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yu Cao
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Jian Yang
- State Key Laboratory of Component-based Chinese Medicine Tianjin International Joint Academy of Biotechnology & Medicine Tianjin P. R. China
- Research and Development Center of Tianjin University of Traditional Chinese Medicine Tianjin International Joint Academy of Biotechnology & Medicine Tianjin P. R. China
| | - Dominik Eichin
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Fangzhe Zhao
- State Key Laboratory of Component-based Chinese Medicine Tianjin International Joint Academy of Biotechnology & Medicine Tianjin P. R. China
- Research and Development Center of Tianjin University of Traditional Chinese Medicine Tianjin International Joint Academy of Biotechnology & Medicine Tianjin P. R. China
| | - Dawei Qi
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Laura Kahari
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Chunman Jia
- Hainan Provincial Key Lab of Fine Chem Key laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education Hainan University Haikou 570228 P. R. China
| | - Markus Peurla
- Institute of Biomedicine and FICAN West Cancer Research Laboratories University of Turku Kiinamyllynkatu 10 20520 Turku Finland
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory Faculty of Science and Engineering Åbo Akademi University Tykistökatu 6 20520 Turku Finland
| | - Zhao Zhao
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
| | - Jianwei Li
- MediCity Research Laboratory University of Turku Tykistökatu 6 20520 Turku Finland
- Hainan Provincial Key Lab of Fine Chem Key laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education Hainan University Haikou 570228 P. R. China
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14
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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15
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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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16
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Cao Y, Yang J, Eichin D, Zhao F, Qi D, Kahari L, Jia C, Peurla M, Rosenholm JM, Zhao Z, Jalkanen S, Li J. Self-Synthesizing Nanorods from Dynamic Combinatorial Libraries against Drug Resistant Cancer. Angew Chem Int Ed Engl 2020; 60:3062-3070. [PMID: 33112477 DOI: 10.1002/anie.202010937] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/06/2020] [Indexed: 01/25/2023]
Abstract
Molecular self-assembly has been widely used to develop nanocarriers for drug delivery. However, most of them have unsatisfactory drug loading capacity (DLC) and the dilemma between stimuli-responsiveness and stability, stagnating their translational process. Herein, we overcame these drawbacks using dynamic combinatorial chemistry. A carrier molecule was spontaneously and quantitatively synthesized, aided by co-self-assembly with a template molecule and an anti-cancer drug doxorubicin (DOX) from a dynamic combinatorial library that was operated by disulfide exchange under thermodynamic control. The highly selective synthesis guaranteed a stable yet pH- and redox- responsive nanocarrier with a maximized DLC of 40.1 % and an enhanced drug potency to fight DOX resistance in vitro and in vivo. Our findings suggested that harnessing the interplay between synthesis and self-assembly in complex chemical systems could yield functional nanomaterials for advanced applications.
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Affiliation(s)
- Yu Cao
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Jian Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin, P. R. China.,Research and Development Center of Tianjin University of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin, P. R. China
| | - Dominik Eichin
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Fangzhe Zhao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin, P. R. China.,Research and Development Center of Tianjin University of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology & Medicine, Tianjin, P. R. China
| | - Dawei Qi
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Laura Kahari
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Chunman Jia
- Hainan Provincial Key Lab of Fine Chem, Key laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education, Hainan University, Haikou, 570228, P. R. China
| | - Markus Peurla
- Institute of Biomedicine and FICAN West Cancer Research Laboratories, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Jessica M Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Zhao Zhao
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland
| | - Jianwei Li
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, 20520, Turku, Finland.,Hainan Provincial Key Lab of Fine Chem, Key laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education, Hainan University, Haikou, 570228, P. R. China
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17
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Schaufelberger F, Seigel K, Ramström O. Hydrogen-Bond Catalysis of Imine Exchange in Dynamic Covalent Systems. Chemistry 2020; 26:15581-15588. [PMID: 32427370 DOI: 10.1002/chem.202001666] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 12/28/2022]
Abstract
The reversibility of imine bonds has been exploited to great effect in the field of dynamic covalent chemistry, with applications such as preparation of functional systems, dynamic materials, molecular machines, and covalent organic frameworks. However, acid catalysis is commonly needed for efficient equilibration of imine mixtures. Herein, it is demonstrated that hydrogen bond donors such as thioureas and squaramides can catalyze the equilibration of dynamic imine systems under unprecedentedly mild conditions. Catalysis occurs in a range of solvents and in the presence of many sensitive additives, showing moderate to good rate accelerations for both imine metathesis and transimination with amines, hydrazines, and hydroxylamines. Furthermore, the catalyst proved simple to immobilize, introducing both reusability and extended control of the equilibration process.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Karolina Seigel
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH-Royal Institute of Technology, Teknikringen 36, 10044, Stockholm, Sweden.,Department of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA, 01854, USA.,Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182, Kalmar, Sweden
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18
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Li H, Gao MQ, Chen Y, Wang YX, Zhu XL, Yang GF. Discovery of Pyrazine-Carboxamide-Diphenyl-Ethers as Novel Succinate Dehydrogenase Inhibitors via Fragment Recombination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14001-14008. [PMID: 33185088 DOI: 10.1021/acs.jafc.0c05646] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The discovery of novel succinate dehydrogenase inhibitors (SDHIs) has attracted great attention worldwide. Herein, a fragment recombination strategy was proposed to design new SDHIs by understanding the ligand-receptor interaction mechanism of SDHIs. Three fragments, pyrazine from pyraziflumid, diphenyl-ether from flubeneteram, and a prolonged amide linker from pydiflumetofen and fluopyram, were identified and recombined to produce a pyrazine-carboxamide-diphenyl-ether scaffold as a new SDHI. After substituent optimization, compound 6y was successfully identified with good inhibitory activity against porcine SDH, which was about 2-fold more potent than pyraziflumid. Furthermore, compound 6y exhibited 95% and 80% inhibitory rates against soybean gray mold and wheat powdery mildew at a dosage of 100 mg/L in vivo assay, respectively. The results of the present work showed that the pyrazine-carboxamide-diphenyl-ether scaffold could be used as a new starting point for the discovery of new SDHIs.
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Affiliation(s)
- Hua Li
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Meng-Qi Gao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yan Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yu-Xia Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, People's Republic of China
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19
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Mancini F, Unver MY, Elgaher WAM, Jumde VR, Alhayek A, Lukat P, Herrmann J, Witte MD, Köck M, Blankenfeldt W, Müller R, Hirsch AKH. Protein-Templated Hit Identification through an Ugi Four-Component Reaction*. Chemistry 2020; 26:14585-14593. [PMID: 32428268 PMCID: PMC7756422 DOI: 10.1002/chem.202002250] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Kinetic target-guided synthesis represents an efficient hit-identification strategy, in which the protein assembles its own inhibitors from a pool of complementary building blocks via an irreversible reaction. Herein, we pioneered an in situ Ugi reaction for the identification of novel inhibitors of a model enzyme and binders for an important drug target, namely, the aspartic protease endothiapepsin and the bacterial β-sliding clamp DnaN, respectively. Highly sensitive mass-spectrometry methods enabled monitoring of the protein-templated reaction of four complementary reaction partners, which occurred in a background-free manner for endothiapepsin or with a clear amplification of two binders in the presence of DnaN. The Ugi products we identified show low micromolar activity on endothiapepsin or moderate affinity for the β-sliding clamp. We succeeded in expanding the portfolio of chemical reactions and biological targets and demonstrated the efficiency and sensitivity of this approach, which can find application on any drug target.
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Affiliation(s)
- Federica Mancini
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - M. Yagiz Unver
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Walid A. M. Elgaher
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Varsha R. Jumde
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Alaa Alhayek
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Peer Lukat
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
| | - Jennifer Herrmann
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Martin D. Witte
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Matthias Köck
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigSpielmannstr. 738106BraunschweigGermany
| | - Rolf Müller
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
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20
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Canal-Martín A, Pérez-Fernández R. Protein-Directed Dynamic Combinatorial Chemistry: An Efficient Strategy in Drug Design. ACS OMEGA 2020; 5:26307-26315. [PMID: 33110958 PMCID: PMC7581073 DOI: 10.1021/acsomega.0c03800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/24/2020] [Indexed: 05/05/2023]
Abstract
Protein-directed dynamic combinatorial chemistry (P-D DCC) is considered a powerful strategy to identify ligands to pharmacologically relevant protein targets. The protein selects its affinity ligands in situ through a thermodynamic templated effect in which the library composition shifts to the formation of specific library members at the expense of other (nonbinding) species. The increase in concentration of the selected species is known as amplification and leads to the discovery of new hit compounds for protein targets. This Mini-Review contains an updated overview of the protein-directed DCC applications and the fundamental aspects to take into account when designing a P-D DCC experiment such as the most biocompatible reversible reactions and the methodology used to analyze the experiments.
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21
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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22
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Yang Y, Zheng S, Su S, Zhao C, Xu J, Chen H. SyntaLinker: automatic fragment linking with deep conditional transformer neural networks. Chem Sci 2020; 11:8312-8322. [PMID: 34123096 PMCID: PMC8163338 DOI: 10.1039/d0sc03126g] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Linking fragments to generate a focused compound library for a specific drug target is one of the challenges in fragment-based drug design (FBDD). Hereby, we propose a new program named SyntaLinker, which is based on a syntactic pattern recognition approach using deep conditional transformer neural networks. This state-of-the-art transformer can link molecular fragments automatically by learning from the knowledge of structures in medicinal chemistry databases (e.g. ChEMBL database). Conventionally, linking molecular fragments was viewed as connecting substructures that were predefined by empirical rules. In SyntaLinker, however, the rules of linking fragments can be learned implicitly from known chemical structures by recognizing syntactic patterns embedded in SMILES notations. With deep conditional transformer neural networks, SyntaLinker can generate molecular structures based on a given pair of fragments and additional restrictions. Case studies have demonstrated the advantages and usefulness of SyntaLinker in FBDD.
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Affiliation(s)
- Yuyao Yang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Shuangjia Zheng
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Shimin Su
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Chao Zhao
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Hongming Chen
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
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23
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Troelsen NS, Clausen MH. Library Design Strategies To Accelerate Fragment‐Based Drug Discovery. Chemistry 2020; 26:11391-11403. [DOI: 10.1002/chem.202000584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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24
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25
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Jiao T, Wu G, Zhang Y, Shen L, Lei Y, Wang C, Fahrenbach AC, Li H. Self‐Assembly in Water with N‐Substituted Imines. Angew Chem Int Ed Engl 2020; 59:18350-18367. [DOI: 10.1002/anie.201910739] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Tianyu Jiao
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Guangcheng Wu
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Yang Zhang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Libo Shen
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Ye Lei
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Cai‐Yun Wang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | | | - Hao Li
- Department of Chemistry Zhejiang University Hangzhou 310027 China
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26
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Xu J, Zhang S, Zhao S, Hu L. Identification and synthesis of an efficient multivalent E. coli heat labile toxin inhibitor __ A dynamic combinatorial chemistry approach. Bioorg Med Chem 2020; 28:115436. [DOI: 10.1016/j.bmc.2020.115436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022]
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27
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Jia C, Qi D, Zhang Y, Rissanen K, Li J. Strategies for Exploring Functions from Dynamic Combinatorial Libraries. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chunman Jia
- Hainan Provincial Key Lab of Fine ChemKey laboratory of Advanced Materials of Tropical Island Resources of Ministry of EducationHainan University Haikou 570228 China
| | - Dawei Qi
- MediCity Research LaboratoryUniversity of Turku Tykistökatu 6 20520 Turku Finland
| | - Yucang Zhang
- Hainan Provincial Key Lab of Fine ChemKey laboratory of Advanced Materials of Tropical Island Resources of Ministry of EducationHainan University Haikou 570228 China
| | - Kari Rissanen
- Department of ChemistryUniversity of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
| | - Jianwei Li
- Hainan Provincial Key Lab of Fine ChemKey laboratory of Advanced Materials of Tropical Island Resources of Ministry of EducationHainan University Haikou 570228 China
- MediCity Research LaboratoryUniversity of Turku Tykistökatu 6 20520 Turku Finland
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28
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Chen W, Tian X, He W, Li J, Feng Y, Pan G. Emerging functional materials based on chemically designed molecular recognition. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s42833-019-0007-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThe specific interactions responsible for molecular recognition play a crucial role in the fundamental functions of biological systems. Mimicking these interactions remains one of the overriding challenges for advances in both fundamental research in biochemistry and applications in material science. However, current molecular recognition systems based on host–guest supramolecular chemistry rely on familiar platforms (e.g., cyclodextrins, crown ethers, cucurbiturils, calixarenes, etc.) for orienting functionality. These platforms limit the opportunity for diversification of function, especially considering the vast demands in modern material science. Rational design of novel receptor-like systems for both biological and chemical recognition is important for the development of diverse functional materials. In this review, we focus on recent progress in chemically designed molecular recognition and their applications in material science. After a brief introduction to representative strategies, we describe selected advances in these emerging fields. The developed functional materials with dynamic properties including molecular assembly, enzyme-like and bio-recognition abilities are highlighted. We have also selected materials with dynamic properties in contract to traditional supramolecular host–guest systems. Finally, the current limitations and some future trends of these systems are discussed.
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29
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Olgac A, Yalcin I, Aki-Yalcin E. The 12 th AFMC International Medicinal Chemistry Symposium (AIMECS 2019) in Istanbul, Turkey. ChemMedChem 2020; 15:162-167. [PMID: 31724830 DOI: 10.1002/cmdc.201900623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 11/05/2022]
Abstract
AFMC-AIMECS meetings are internationally organized biannually by the Asian Federation for Medicinal Chemistry (AFMC) and are focused on recent studies in drug discovery and development both in academia and industry. Member organizations of the AFMC are the Pharmaceutical Society of Japan, the Chinese Pharmaceutical Association, the Royal Australian Chemical Institute, the Pharmaceutical Society of Korea, the Korean Chemical Society, the Chemical Society Located in Taipei, the Indonesian Society of Medicinal Chemistry, the Medicinal Chemistry Section of the Israel Chemical Society, and the Computer-Aided Drug Design & Development Society in Turkey. Each time, the symposium is organized within these member countries. The AIMECS 2019 symposium was held in Turkey this year, as Prof. Dr. Esin Aki-Yalcin is the current president of the AFMC (2018-2020); the next AIMECS meeting will be organized in 2021 in Tokyo, Japan. In this report, we discuss key topics at the 12th AFMC International Medicinal Chemistry Symposium - New Avenues for Design and Development of Translational Medicine (AIMECS 2019) held in Istanbul, September 8-11, 2019.
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Affiliation(s)
- Abdurrahman Olgac
- Department of Pharmaceutical Chemistry, Gazi University Faculty of Pharmacy, Emniyet Mah. Tac Sk. No.3, 06330, Yenimahalle, Ankara, Turkey.,Laboratory of Molecular Modeling, Evias Pharmaceutical R&D Ltd., Gazi Teknopark G1-101, 06830, Golbasi, Ankara, Turkey
| | - Ismail Yalcin
- Department of Pharmaceutical Chemistry, Ankara University Faculty of Pharmacy, Emniyet Mah. Degol Cd. No.4, 06560, Yenimahalle, Ankara, Turkey
| | - Esin Aki-Yalcin
- Department of Pharmaceutical Chemistry, Ankara University Faculty of Pharmacy, Emniyet Mah. Degol Cd. No.4, 06560, Yenimahalle, Ankara, Turkey
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30
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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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31
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Xu J, Zhao S, Zhang S, Pei J, Li Y, Zhang Y, He X, Hu L. Development of a multivalent acetylcholinesterase inhibitor via dynamic combinatorial chemistry. Int J Biol Macromol 2019; 150:1184-1191. [PMID: 31758986 DOI: 10.1016/j.ijbiomac.2019.10.127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 01/13/2023]
Abstract
In this study, we report the generation of a polymer based dynamic combinatorial library (DCL) using aldehyde-functionalized linear poly(glycidol) and hydrazide derivatives as initial building blocks. In combination with tetrameric acetylcholinesterase (AChE), a certain type of amplified acylhydrazone side chain is identified and further used for the synthesis of a multivalent AChE inhibitor. The cytotoxicity and inhibition properties of the multivalent inhibitor are evaluated, and the results indicate superior bioactivity compared to the commercial reference Edrophonium chloride.
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Affiliation(s)
- Jintao Xu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Shuang Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Shixin Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Jialu Pei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Yanhong Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Yongxin Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Xiangyang He
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China
| | - Lei Hu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China.
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32
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Gu CX, Zhang BL, Bai WW, Liu J, Zhou W, Ling ZQ, Lu Y, Xu L, Wan YJ. Characterization of the endothiapepsin-like protein in the entomopathogenic fungus Beauveria bassiana and its virulence effect on the silkworm, Bombyx mori. J Invertebr Pathol 2019; 169:107277. [PMID: 31715184 DOI: 10.1016/j.jip.2019.107277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022]
Abstract
Endothiapepsin is an aspartic proteinase that was first isolated from the plant pathogenic fungus Endothia parasitica. In previous studies, we reported on three endothiapepsin-like proteins in the entomopathogenic fungus Beauveria bassiana; the genes were up-regulated in B. bassiana hyper-virulent strain GXsk1011 at early stage infection in the silkworm. However, whether these proteins play a role in pathogenicity or not remains unknown. In this study, we cloned one protein, BbepnL-1 gene (BBA-07766), that has 98% homology with B. bassiana strain Bb2860, and expressed it in the yeast Pichia pastoris to investigate its function. The endothiapepsin-like protein is a secreted proteinase of molecular weight approximately 40 kDa. It has an N-glycosylation site and a mutation in the C-terminal conserved domain- a Thr was mutated to Gly in B. bassiana GXsk1011 and is different than the endothiapepsin of Endothia parasitica. The recombinant endothiapepsin-like protein showed enzyme activity and degraded the protein components of the silkworm cuticle. To further investigate the activity of the endothiapepsin-like protein, we knocked out the gene BbepnL-1 and showed that the loss of BbepnL-1 reduced the virulence in the silkworm. These results demonstrated that the endothiapepsin-like protein of B. bassiana is a virulence factor.
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Affiliation(s)
- Cai-Xia Gu
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Bao-Ling Zhang
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Wen-Wen Bai
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Jing Liu
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Wei Zhou
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Zi-Qi Ling
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Yan Lu
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Liang Xu
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China
| | - Yong-Ji Wan
- Laboratory of Invertebrate Pathology and Applied Microbiology, College of Biotechnology, Southwest University, Chongqing 400716, China.
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Abstract
Predicting the strength of stacking interactions involving heterocycles is vital for several fields, including structure-based drug design. While quantum chemical computations can provide accurate stacking interaction energies, these come at a steep computational cost. To address this challenge, we recently developed quantitative predictive models of stacking interactions between druglike heterocycles and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.1021/jacs.9b00936 ). These models depend on heterocycle descriptors derived from electrostatic potentials (ESPs) computed using density functional theory and provide accurate stacking interactions without the need for expensive computations on stacked dimers. Herein, we show that these ESP-based descriptors can be reliably evaluated directly from the atom connectivity of the heterocycle, providing a means of predicting both the descriptors and the potential for a given heterocycle to engage in stacking interactions without resorting to any quantum chemical computations. This enables the rapid conversion of simple molecular representations (e.g., SMILES) directly into accurate stacking interaction energies using a freely available online tool, thereby providing a way to rank the stacking abilities of large sets of heterocycles.
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Affiliation(s)
- Andrea N Bootsma
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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34
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Hartman AM, Gierse RM, Hirsch AKH. Protein-Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol. European J Org Chem 2019; 2019:3581-3590. [PMID: 31680778 PMCID: PMC6813629 DOI: 10.1002/ejoc.201900327] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 01/08/2023]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify bioactive compounds. This efficient technique allows the target to select its own binders and circumvents the need for synthesis and biochemical evaluation of all individual derivatives. An ever-increasing number of publications report the use of DCC on biologically relevant target proteins. This minireview complements previous reviews by focusing on the experimental protocol and giving detailed examples of essential steps and factors that need to be considered, such as protein stability, buffer composition and cosolvents.
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Affiliation(s)
- Alwin M. Hartman
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Robin M. Gierse
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryHelmholtz Centre for Infection Research (HZI)University of GroningenNijenborgh 79747AG GroningenThe Netherlands
- Department of PharmacyMedicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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35
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Yoneyama K, Suzuki R, Kuramochi Y, Satake A. A Candidate for Multitopic Probes for Ligand Discovery in Dynamic Combinatorial Chemistry. Molecules 2019; 24:E2166. [PMID: 31181809 PMCID: PMC6600254 DOI: 10.3390/molecules24112166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022] Open
Abstract
Multifunctionalized materials are expected to be versatile probes to find specific interactions between a ligand and a target biomaterial. Thus, efficient methods to prepare possible combinations of the functionalities is desired. The concept of dynamic combinatorial chemistry (DCC) is ideal for the generation of any possible combination, as well as screening for target biomaterials. Here, we propose a new molecular design of multitopic probes for ligand discovery in DCC. We synthesized a new Gable Porphyrin, GP1, having prop-2-yne groups as a scaffold to introduce various functional groups. GP1 is a bis(imidazolylporphyrinatozinc) compound connected through a 1,3-phenylene moiety, and it gives macrocycles spontaneously and quantitatively by strong imidazole-to-zinc complementary coordination. Some different types of functional groups were introduced into GP1 in high yields. Formation of heterogeneous macrocycles composed of GP1 derivatives having different types of substituents was accomplished under equilibrium conditions. These results promise that enormous numbers of macrocycles having various functional groups can be provided when the kinds of GP components increase. These features are desirable for DCC, and the present system using GP1 is a potential candidate to provide a dynamic combinatorial library of multitopic probes to discover specific interactions between a ligand and a biomaterial.
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Affiliation(s)
- Keiko Yoneyama
- Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Rina Suzuki
- Graduate School of Chemical Sciences and Technology, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Yusuke Kuramochi
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Akiharu Satake
- Department of Chemistry, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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36
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Beatty MA, Pye AT, Shaurya A, Kim B, Selinger AJ, Hof F. Using reversible non-covalent and covalent bonds to create assemblies and equilibrating molecular networks that survive 5 molar urea. Org Biomol Chem 2019; 17:2081-2086. [PMID: 30698579 DOI: 10.1039/c8ob02909a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The limits of self-assembly and host-guest chemistry in water solutions containing competitive solutes are largely unexplored. We report here a new family of self-assembling systems that are stitched together at two levels by reversible hydrazone bonds and by non-covalent self-assembly in strongly denaturing conditions. Three different hydrazides of various charge and hydrophobicity are combined with an aldehyde-containing calixarene, and each system spontaneously forms AB hydrazones that subsequently self-assemble into four-component (AB)2 structures in water. The assemblies display varying responses to added NaCl and/or urea. The most robust assembly survives completely intact in solution up to 5 M urea. We also combine the aldehyde calixarene with two different hydrazides in the same tube to create complex, competitive dynamic libraries. We report experiments in which the composition of the dynamic equilibrating library is under the control of self-assembly, allowing the systems to choose the components that form the most stable assemblies under a variety of competitive solutions conditions. These dynamic networks of equilibrating molecules maintain remarkably similar equilibrium positions under widely varying concentrations of urea and NaCl.
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Affiliation(s)
- Meagan A Beatty
- Department of Chemistry, University of Victoria, Victoria, BC V8W 3V6 Canada.
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37
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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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38
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García P, Alonso VL, Serra E, Escalante AM, Furlan RLE. Discovery of a Biologically Active Bromodomain Inhibitor by Target-Directed Dynamic Combinatorial Chemistry. ACS Med Chem Lett 2018; 9:1002-1006. [PMID: 30344907 DOI: 10.1021/acsmedchemlett.8b00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Target-directed dynamic combinatorial chemistry (DCC) has emerged as a strategy for the identification of inhibitors of relevant therapeutic targets. In this contribution, we use this strategy for the identification of a high-affinity binder of a parasite target, the Trypanosoma cruzi bromodomain-containing protein TcBDF3. This protein is essential for viability of T. cruzi, the protozoan parasite that causes Chagas disease. A small dynamic library of acylhydrazones was prepared from aldehydes and acylhydrazides at neutral pH in the presence of aniline. The most amplified library member shows (a) high affinity for the template, (b) interesting antiparasitic activity against different parasite forms, and (c) low toxicity against Vero cells. In addition, parasites are rescued from the compound toxicity by TcBDF3 overexpression, suggesting that the toxicity of this compound is due to the TcBDF3 inhibition, i.e., the binding event that initially drives the molecular amplification is reproduced in the parasite, leading to selective toxicity.
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Affiliation(s)
- Paula García
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Victoria L. Alonso
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Esteban Serra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Andrea M. Escalante
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ricardo L. E. Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, S2002LRK Rosario, Argentina
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39
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Cougnon FBL, Caprice K, Pupier M, Bauzá A, Frontera A. A Strategy to Synthesize Molecular Knots and Links Using the Hydrophobic Effect. J Am Chem Soc 2018; 140:12442-12450. [DOI: 10.1021/jacs.8b05220] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fabien B. L. Cougnon
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Kenji Caprice
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Marion Pupier
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Antonio Bauzá
- Department de Química, Universitat de les Illes Balears, Carretera de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department de Química, Universitat de les Illes Balears, Carretera de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
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40
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Bootsma AN, Wheeler SE. Stacking Interactions of Heterocyclic Drug Fragments with Protein Amide Backbones. ChemMedChem 2018; 13:835-841. [PMID: 29451739 DOI: 10.1002/cmdc.201700721] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/18/2018] [Indexed: 12/25/2022]
Abstract
Stacking interactions can be important enthalpic contributors to drug binding. Among the less well-studied stacking interactions are those occurring between an arene and the π-face of an amide group. Given the ubiquity of heterocycles in drugs, combined with the abundance of amides in the protein backbone, optimizing these noncovalent interactions can provide a potential route to enhanced drug binding. Previously, Diederich et al. (ChemMedChem 2013, 8, 397-404) studied stacked dimers of a model amide with a set of 18 heterocycles, showing that computed interaction energies correlate with the dipole moments of the heterocycles and providing guidelines for the optimization of these interactions. We considered stacked dimers of the same model amide with a larger set of 28 heterocycles common in pharmaceuticals, by using more robust ab initio methods. While the overall trends in these new data corroborate many of the results of Diederich et al., these data provide a more refined view of the nature of amide stacking interactions. We present a robust scoring function for amide stacking interaction energies based on the molecular dipole moment and strength of the electric field above the arene.
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Affiliation(s)
- Andrea N Bootsma
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.,Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
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Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies. Int J Mol Sci 2018; 19:ijms19010111. [PMID: 29301250 PMCID: PMC5796060 DOI: 10.3390/ijms19010111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022] Open
Abstract
Protein kinase is a novel therapeutic target for human diseases. The off-target and side effects of ATP-competitive inhibitors preclude them from the clinically relevant drugs. The compounds targeting the druggable allosteric sites outside the highly conversed ATP binding pocket have been identified as promising alternatives to overcome current barriers of ATP-competitive inhibitors. By simultaneously interacting with the αD region (new allosteric site) and sub-ATP binding pocket, the attractive compound CAM4066 was named as allosteric inhibitor of CK2α. It has been demonstrated that the rigid linker and non-ionizable substituted fragment resulted in significant decreased inhibitory activities of compounds. The molecular dynamics simulations and energy analysis revealed that the appropriate coupling between the linker and pharmacophore fragments were essential for binding of CAM4066 with CK2α. The lower flexible linker of compound 21 lost the capability of coupling fragments A and B to αD region and positive area, respectively, whereas the methyl benzoate of fragment B induced the re-orientated Pre-CAM4066 with the inappropriate polar interactions. Most importantly, the match between the optimized linker and pharmacophore fragments is the challenging work of fragment-linking based drug design. These results provide rational clues to further structural modification and development of highly potent allosteric inhibitors of CK2.
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Cvrtila I, Fanlo-Virgós H, Schaeffer G, Monreal Santiago G, Otto S. Redox Control over Acyl Hydrazone Photoswitches. J Am Chem Soc 2017; 139:12459-12465. [PMID: 28749147 PMCID: PMC5599877 DOI: 10.1021/jacs.7b03724] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/28/2022]
Abstract
Photoisomerization provides a clean and efficient way of reversibly altering physical properties of chemical systems and injecting energy into them. These effects have been applied in development of systems such as photoresponsive materials, molecular motors, and photoactivated drugs. Typically, switching from more to less stable isomer(s) is performed by irradiation with UV or visible light, while the reverse process proceeds thermally or by irradiation using another wavelength. In this work we developed a method of rapid and tunable Z→E isomerization of C═N bond in acyl hydrazones, using aromatic thiols as nucleophilic catalysts. As thiols can be oxidized into catalytically inactive disulfides, the isomerization rates can be controlled via the oxidation state of the catalyst, which, together with the UV irradiation, provides orthogonal means to control the E/Z state of the system. As a proof of this concept, we have applied this method to control the diversity of acyl hydrazone based dynamic combinatorial libraries.
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Affiliation(s)
- Ivica Cvrtila
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- 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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Frei P, Pang L, Silbermann M, Eriş D, Mühlethaler T, Schwardt O, Ernst B. Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target. Chemistry 2017; 23:11570-11577. [PMID: 28654733 DOI: 10.1002/chem.201701601] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 12/28/2022]
Abstract
Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established.
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Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Lijuan Pang
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Marleen Silbermann
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Deniz Eriş
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Tobias Mühlethaler
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Oliver Schwardt
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:7464-7485. [PMID: 32313319 PMCID: PMC7159557 DOI: 10.1002/ange.201610372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/28/2022]
Abstract
AbstractProteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery. Angew Chem Int Ed Engl 2017; 56:7358-7378. [PMID: 28117936 PMCID: PMC7159684 DOI: 10.1002/anie.201610372] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
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Innovationspreis in Medizinisch/Pharmazeutischer Chemie: A. K. H. Hirsch / Southern Chemist Award: G. Christou / Karl Heinz Beckurts‐Preis: K. Johnsson / ACS Akron Section Award: P. J. Hergenrother. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Innovation Prize in Medicinal/Pharmaceutical Chemistry: A. K. H. Hirsch / Southern Chemist Award: G. Christou / Karl Heinz Beckurts Prize: K. Johnsson / ACS Akron Section Award: P. J. Hergenrother. Angew Chem Int Ed Engl 2017; 56:3421. [DOI: 10.1002/anie.201701852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Giroud M, Ivkovic J, Martignoni M, Fleuti M, Trapp N, Haap W, Kuglstatter A, Benz J, Kuhn B, Schirmeister T, Diederich F. Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the S3 Pocket. ChemMedChem 2017; 12:257-270. [DOI: 10.1002/cmdc.201600563] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/19/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jakov Ivkovic
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Mara Martignoni
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marianne Fleuti
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wolfgang Haap
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Jörg Benz
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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50
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Fu J, Fu H, Dieu M, Halloum I, Kremer L, Xia Y, Pan W, Vincent SP. Identification of inhibitors targeting Mycobacterium tuberculosis cell wall biosynthesis via dynamic combinatorial chemistry. Chem Commun (Camb) 2017; 53:10632-10635. [DOI: 10.1039/c7cc05251k] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this study, we report a dynamic combinatorial approach along with highly efficient in situ screening to identify inhibitors of UDP-galactopyranose mutase (UGM), an essential enzyme involved in mycobacterial cell wall biosynthesis.
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Affiliation(s)
- Jian Fu
- Département de Chimie
- Laboratoire de Chimie Bio-Organique
- University of Namur (FUNDP)
- Namur B-5000
- Belgium
| | - Huixiao Fu
- Département de Chimie
- Laboratoire de Chimie Bio-Organique
- University of Namur (FUNDP)
- Namur B-5000
- Belgium
| | - Marc Dieu
- MaSUN
- Mass Spectrometry Facility
- University of Namur
- 5000 Namur
- Belgium
| | - Iman Halloum
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques
- CNRS UMR 5235
- Université de Montpellier
- France
| | - Laurent Kremer
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques
- CNRS UMR 5235
- Université de Montpellier
- France
| | - Yufen Xia
- State Key Laboratory of Functions and Applications of Medicinal Plants
- Guizhou Medical University
- Guiyang 550014
- China
| | - Weidong Pan
- State Key Laboratory of Functions and Applications of Medicinal Plants
- Guizhou Medical University
- Guiyang 550014
- China
| | - Stéphane P. Vincent
- Département de Chimie
- Laboratoire de Chimie Bio-Organique
- University of Namur (FUNDP)
- Namur B-5000
- Belgium
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