1
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Hu S, Jiang C, Jin Q. Discovery of pyrido[3,2-d]pyrimidin-6(5H)-one derivatives as checkpoint kinase 1 (CHK1) inhibitors with potent antitumor efficacy. Eur J Med Chem 2024; 269:116351. [PMID: 38547734 DOI: 10.1016/j.ejmech.2024.116351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Checkpoint kinase 1 (CHK1) plays a crucial role in the DNA damage response pathway, making it an attractive target for cancer therapy. Herein, we present the synthesis, optimization, and evaluation of selective CHK1 inhibitors with a pyrido[3,2-d]pyrimidin-6(5H)-one scaffold. Among them, compound 11 showed single-digit nanomolar potency against CHK1 (IC50: 0.55 nM) with good kinase selectivity. Notably, 11 showed anti-proliferative effect in MV-4-11 cells singly (IC50 = 202 nM) and a synergistic effect in combination with gemcitabine in HT-29 cells (IC50 = 63.53 nM). Furthermore, the combination of 11 and gemcitabine exhibited synergistic effect in the HT-29 xenograft mouse model. Overall, this work provides a strong foundation for the development of selective CHK1 inhibitors and the therapeutic strategy for cancer.
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Affiliation(s)
- Shihe Hu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu, China; SkyRun Pharma Co., Ltd., No. 9 Weidi Road, Nanjing, 210046, China
| | - Cuihua Jiang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu, China
| | - Qiaomei Jin
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu, China.
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2
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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3
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. Angew Chem Int Ed Engl 2022; 61:e202211510. [PMID: 36112310 PMCID: PMC9827864 DOI: 10.1002/anie.202211510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 01/12/2023]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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4
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Li Z, Wu Y, Zhen S, Su K, Zhang L, Yang F, McDonough MA, Schofield CJ, Zhang X. In Situ Inhibitor Synthesis and Screening by Fluorescence Polarization: An Efficient Approach for Accelerating Drug Discovery. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202211510. [PMID: 38505687 PMCID: PMC10947266 DOI: 10.1002/ange.202211510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Target-directed dynamic combinatorial chemistry has emerged as a useful tool for hit identification, but has not been widely used, in part due to challenges associated with analyses involving complex mixtures. We describe an operationally simple alternative: in situ inhibitor synthesis and screening (ISISS), which links high-throughput bioorthogonal synthesis with screening for target binding by fluorescence. We exemplify the ISISS method by showing how coupling screening for target binding by fluorescence polarization with the reaction of acyl-hydrazides and aldehydes led to the efficient discovery of a potent and novel acylhydrazone-based inhibitor of human prolyl hydroxylase 2 (PHD2), a target for anemia treatment, with equivalent in vivo potency to an approved medicine.
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Affiliation(s)
- Zhihong Li
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Yue Wu
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Shuai Zhen
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Kaijun Su
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Linjian Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Fulai Yang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
| | - Michael A. McDonough
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Xiaojin Zhang
- State Key Laboratory of Natural MedicinesJiangsu Key Laboratory of Drug Design and Optimization, and Department of ChemistryChina Pharmaceutical UniversityNanjing211198China
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5
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Geng H, Zhong QZ, Li J, Lin Z, Cui J, Caruso F, Hao J. Metal Ion-Directed Functional Metal-Phenolic Materials. Chem Rev 2022; 122:11432-11473. [PMID: 35537069 DOI: 10.1021/acs.chemrev.1c01042] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal ions are ubiquitous in nature and play significant roles in assembling functional materials in fields spanning chemistry, biology, and materials science. Metal-phenolic materials are assembled from phenolic components in the presence of metal ions through the formation of metal-organic complexes. Alkali, alkali-earth, transition, and noble metal ions as well as metalloids interacting with phenolic building blocks have been widely exploited to generate diverse hybrid materials. Despite extensive studies on the synthesis of metal-phenolic materials, a comprehensive summary of how metal ions guide the assembly of phenolic compounds is lacking. A fundamental understanding of the roles of metal ions in metal-phenolic materials engineering will facilitate the assembly of materials with specific and functional properties. In this review, we focus on the diversity and function of metal ions in metal-phenolic material engineering and emerging applications. Specifically, we discuss the range of underlying interactions, including (i) cation-π, (ii) coordination, (iii) redox, and (iv) dynamic covalent interactions, and highlight the wide range of material properties resulting from these interactions. Applications (e.g., biological, catalytic, and environmental) and perspectives of metal-phenolic materials are also highlighted.
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Affiliation(s)
- Huimin Geng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Qi-Zhi Zhong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China.,Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jianhua Li
- Department of Biomaterials, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhixing Lin
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jiwei Cui
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Frank Caruso
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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6
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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7
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Jian J, Hammink R, McKenzie CJ, Bickelhaupt FM, Poater J, Mecinović J. Probing the Lewis Acidity of Boronic Acids through Interactions with Arene Substituents. Chemistry 2022; 28:e202104044. [PMID: 34958482 PMCID: PMC9306523 DOI: 10.1002/chem.202104044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/23/2022]
Abstract
Boronic acids are Lewis acids that exist in equilibrium with boronate forms in aqueous solution. Here we experimentally and computationally investigated the Lewis acidity of 2,6-diarylphenylboronic acids; specially designed phenylboronic acids that possess two flanking aromatic rings with tunable aromatic character. Hammett analysis of 2,6-diarylphenylboronic acids reveals that their Lewis acidity remains unchanged upon the introduction of EWG/EDG at the distant para position of the flanking aromatic rings. Structural and computational studies demonstrate that polar-π interactions and solvation effects contribute to the stabilization of boronic acids and boronate forms by aromatic rings. Our physical-organic chemistry work highlights that boronic acids and boronates can be stabilized by aromatic systems, leading to an important molecular knowledge for rational design and development of boronic acid-based catalysts and inhibitors of biomedically important proteins.
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Affiliation(s)
- Jie Jian
- Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkCampusvej, 555230OdenseDenmark
| | - Roel Hammink
- Division of ImmunotherapyOncode InstituteRadboud University Medical Center6525 GANijmegenThe Netherlands
- Department of Tumor ImmunologyRadboud Institute for Molecular Life SciencesRadboud University Medical CenterGeert Grooteplein 266525 GANijmegenThe Netherlands
| | - Christine J. McKenzie
- Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkCampusvej, 555230OdenseDenmark
| | - F. Matthias Bickelhaupt
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
- Department of Theoretical ChemistryAmsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Jordi Poater
- ICREAPasseig Lluís Companys 2308010BarcelonaSpain
- Departament de Química Inorgànica i Orgànica & IQTCUBUniversitat de BarcelonaMartí i Franquès 1-1108028BarcelonaSpain
| | - Jasmin Mecinović
- Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkCampusvej, 555230OdenseDenmark
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8
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Perry GS, Das M, Woon ECY. Inhibition of AlkB Nucleic Acid Demethylases: Promising New Epigenetic Targets. J Med Chem 2021; 64:16974-17003. [PMID: 34792334 DOI: 10.1021/acs.jmedchem.1c01694] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The AlkB family of nucleic acid demethylases is currently of intense chemical, biological, and medical interest because of its critical roles in several key cellular processes, including epigenetic gene regulation, RNA metabolism, and DNA repair. Emerging evidence suggests that dysregulation of AlkB demethylases may underlie the pathogenesis of several human diseases, particularly obesity, diabetes, and cancer. Hence there is strong interest in developing selective inhibitors for these enzymes to facilitate their mechanistic and functional studies and to validate their therapeutic potential. Herein we review the remarkable advances made over the past 20 years in AlkB demethylase inhibition research. We discuss the rational design of reported inhibitors, their mode-of-binding, selectivity, cellular activity, and therapeutic opportunities. We further discuss unexplored structural elements of the AlkB subfamilies and propose potential strategies to enable subfamily selectivity. It is hoped that this perspective will inspire novel inhibitor design and advance drug discovery research in this field.
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Affiliation(s)
- Gemma S Perry
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mohua Das
- Lab of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Esther C Y Woon
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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9
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Song S, Gao P, Sun L, Kang D, Kongsted J, Poongavanam V, Zhan P, Liu X. Recent developments in the medicinal chemistry of single boron atom-containing compounds. Acta Pharm Sin B 2021; 11:3035-3059. [PMID: 34729302 PMCID: PMC8546671 DOI: 10.1016/j.apsb.2021.01.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Various boron-containing drugs have been approved for clinical use over the past two decades, and more are currently in clinical trials. The increasing interest in boron-containing compounds is due to their unique binding properties to biological targets; for example, boron substitution can be used to modulate biological activity, pharmacokinetic properties, and drug resistance. In this perspective, we aim to comprehensively review the current status of boron compounds in drug discovery, focusing especially on progress from 2015 to December 2020. We classify these compounds into groups showing anticancer, antibacterial, antiviral, antiparasitic and other activities, and discuss the biological targets associated with each activity, as well as potential future developments.
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Key Words
- ACTs, artemisinin combination therapies
- ADCs, Acinetobacter-derived cephalosporinases
- AML, acute myeloid leukemia
- AMT, aminopterin
- BLs, β-lactamases
- BNCT, boron neutron capture therapy
- BNNPs, boron nitride nanoparticles
- BNNTs, boron nitride nanotubes
- Boron-containing compounds
- CEs, carboxylesterases
- CIA, collagen-induced arthritis
- COVID-19, coronavirus disease 2019
- ClpP, casein protease P
- Covalent inhibitors
- GSH, glutathione
- HADC1, class I histone deacetylase
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HIV, human immunodeficiency virus
- LeuRS, leucyl-tRNA synthetase
- Linker components
- MBLs, metal β-lactamases
- MDR-TB, multidrug-resistant tuberculosis
- MERS, Middle East respiratory syndrome
- MIDA, N-methyliminodiacetic acid
- MM, multiple myeloma
- MTX, methotrexate
- Mcl-1, myeloid cell leukemia 1
- Mtb, Mycobacterium tuberculosis
- NA, neuraminidase
- NS5B, non-nucleoside polymerase
- OBORT, oxaborole tRNA capture
- OPs, organophosphate
- PBA, phenylboronic acid
- PDB, Protein Data Bank
- PPI, protein–protein interaction
- Prodrug
- QM, quinone methide
- RA, rheumatoid arthritis
- ROS, reactive oxygen species
- SARS-CoV-2, syndrome coronavirus 2
- SBLs, serine β-lactamases
- SERD, selective estrogen receptor downregulator
- SHA, salicyl hydroxamic acid
- SaClpP, Staphylococcus aureus caseinolytic protease P
- TB, tuberculosis
- TTR, transthyretin
- U4CR, Ugi 4-component reaction
- cUTI, complex urinary tract infection
- dCTPase, dCTPase pyrophosphatase
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Affiliation(s)
- Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
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10
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Lutz E, Moulin E, Tchakalova V, Benczédi D, Herrmann A, Giuseppone N. Design of Stimuli-Responsive Dynamic Covalent Delivery Systems for Volatile Compounds (Part 1): Controlled Hydrolysis of Micellar Amphiphilic Imines in Water. Chemistry 2021; 27:13457-13467. [PMID: 34270124 DOI: 10.1002/chem.202102049] [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: 06/10/2021] [Indexed: 12/29/2022]
Abstract
Despite their intrinsic hydrolysable character, imine bonds can become remarkably stable in water when self-assembled in amphiphilic micellar structures. In this work, we systematically studied some of these structures and the influence of various parameters that can be used to take control of their hydrolysis, including pH, concentration, the position of the imine function in the amphiphilic structure, relative lengths of the linked hydrophilic and hydrophobic moieties. Thermodynamic and kinetic data led us to the rational design of stable imines in water, partly based on the location of the imine function within the hydrophobic part of the amphiphile and on a predictable quantitative term that we define as the total hydrophilic-lipophilic balance (HLB). In addition, we show that such stable systems are also stimuli-responsive and therefore, of potential interest in trapping and releasing micellar components on demand.
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Affiliation(s)
- Eric Lutz
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Vera Tchakalova
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Daniel Benczédi
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Andreas Herrmann
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Nicolas Giuseppone
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
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11
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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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12
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Giardina SF, Werner DS, Pingle M, Feinberg PB, Foreman KW, Bergstrom DE, Arnold LD, Barany F. Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase. J Med Chem 2020; 63:3004-3027. [PMID: 32057241 DOI: 10.1021/acs.jmedchem.9b01689] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition. X-ray crystallography validated the dimeric mechanism of inhibition, and compounds demonstrated high selectivity against related proteases, good target engagement, and tryptase inhibition in HMC1 xenograft models. Screening 3872 possible combinations from 44 boronic acid and 88 diol derivatives revealed several combinations that produced nanomolar inhibition, and seven unique pairs produced greater than 100-fold improvement in potency over monomeric inhibition. These heterodimeric tryptase inhibitors demonstrate the power of target-driven combinatorial chemistry to deliver bivalent drugs in a small molecule form.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Douglas S Werner
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States.,Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Kenneth W Foreman
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Donald E Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafa-yette, Indiana 47907, United States
| | - Lee D Arnold
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
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13
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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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14
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Baraniak MK, Lalancette RA, Jäkle F. Electron‐Deficient Borinic Acid Polymers: Synthesis, Supramolecular Assembly, and Examination as Catalysts in Amide Bond Formation. Chemistry 2019; 25:13799-13810. [DOI: 10.1002/chem.201903196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/10/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Monika K. Baraniak
- Department of ChemistryRutgers University-Newark 73 Warren Street Newark NJ 07102 USA
| | - Roger A. Lalancette
- Department of ChemistryRutgers University-Newark 73 Warren Street Newark NJ 07102 USA
| | - Frieder Jäkle
- Department of ChemistryRutgers University-Newark 73 Warren Street Newark NJ 07102 USA
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15
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Krajnc A, Brem J, Hinchliffe P, Calvopiña K, Panduwawala TD, Lang PA, Kamps JJAG, Tyrrell JM, Widlake E, Saward BG, Walsh TR, Spencer J, Schofield CJ. Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-β-Lactamases. J Med Chem 2019; 62:8544-8556. [PMID: 31454231 PMCID: PMC6767355 DOI: 10.1021/acs.jmedchem.9b00911] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
bicyclic boronate VNRX-5133 (taniborbactam) is a new type of
β-lactamase inhibitor in clinical development. We report that
VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically
important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2.
VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not
observed. Crystallography reveals how VNRX-5133 binds to the class
D SBL OXA-10 and MBL NDM-1. The crystallographic results highlight
the ability of bicyclic boronates to inhibit SBLs and MBLs via binding
of a tetrahedral (sp3) boron species. The structures imply
conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1,
by crystallography, we observed an unanticipated VNRX-5133 binding
mode involving cyclization of its acylamino oxygen onto the boron
of the bicyclic core. Different side-chain binding modes for bicyclic
boronates for SBLs and MBLs imply scope for side-chain optimization.
The results further support the “high-energy-intermediate”
analogue approach for broad-spectrum β-lactamase inhibitor development
and highlight the ability of boron inhibitors to interchange between
different hybridization states/binding modes.
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Affiliation(s)
- Alen Krajnc
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Karina Calvopiña
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tharindi D Panduwawala
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jos J A G Kamps
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Benjamin G Saward
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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16
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Tong L, Song P, Jiang K, Xu L, Jin T, Wang P, Hu X, Fang S, Gao A, Zhou Y, Liu T, Li J, Hu Y. Discovery of (R)-5-((5-(1-methyl-1H-pyrazol-4-yl)-4-(methylamino)pyrimidin-2-yl)amino)-3-(piperidin-3-yloxy)picolinonitrile, a novel CHK1 inhibitor for hematologic malignancies. Eur J Med Chem 2019; 173:44-62. [DOI: 10.1016/j.ejmech.2019.03.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 11/17/2022]
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17
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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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18
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Krajnc A, Lang PA, Panduwawala TD, Brem J, Schofield CJ. Will morphing boron-based inhibitors beat the β-lactamases? Curr Opin Chem Biol 2019; 50:101-110. [PMID: 31004962 PMCID: PMC6591701 DOI: 10.1016/j.cbpa.2019.03.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023]
Abstract
The β-lactams remain the most important antibacterials, but their use is increasingly compromised by resistance, importantly by β-lactamases. Although β-lactam and non-β-lactam inhibitors forming stable acyl-enzyme complexes with nucleophilic serine β-lactamases (SBLs) are widely used, these are increasingly susceptible to evolved SBLs and do not inhibit metallo-β-lactamases (MBLs). Boronic acids and boronate esters, especially cyclic ones, can potently inhibit both SBLs and MBLs. Vaborbactam, a monocyclic boronate, is approved for clinical use, but its β-lactamase coverage is limited. Bicyclic boronates rapidly react with SBLs and MBLs forming stable enzyme-inhibitor complexes that mimic the common anionic high-energy tetrahedral intermediates in SBL/MBL catalysis, as revealed by crystallography. The ability of boronic acids to 'morph' between sp2 and sp3 hybridisation states may help enable potent inhibition. There is limited structure-activity relationship information on the (bi)cyclic boronate inhibitors compared to β-lactams, hence scope for creativity towards new boron-based β-lactamase inhibitors/antibacterials.
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Affiliation(s)
- Alen Krajnc
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Pauline A Lang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tharindi D Panduwawala
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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19
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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20
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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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21
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3. Chem Asian J 2018; 13:2854-2867. [PMID: 29917331 DOI: 10.1002/asia.201800729] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/12/2018] [Indexed: 12/18/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC50 =2.6 μm) and ALKBH3 (8; IC50 =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/antagonists & inhibitors
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/chemistry
- AlkB Homolog 5, RNA Demethylase/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Catalysis
- Combinatorial Chemistry Techniques/methods
- Enzyme Inhibitors/chemistry
- Fluorometry/methods
- Humans
- Hydrazones/chemistry
- Kinetics
- Ligands
- Molecular Structure
- Oxidoreductases, O-Demethylating/antagonists & inhibitors
- Oxidoreductases, O-Demethylating/chemistry
- Oxidoreductases, O-Demethylating/genetics
- Peptides/chemistry
- Peptides/genetics
- Protein Denaturation
- Protein Engineering
- Protein Structure, Secondary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Transition Temperature
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Affiliation(s)
- Mohua Das
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jinghua Dong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Fransisca Prasetya
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yiming Xie
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Adeline Cheong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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22
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Cain R, Brem J, Zollman D, McDonough MA, Johnson RM, Spencer J, Makena A, Abboud MI, Cahill S, Lee SY, McHugh PJ, Schofield CJ, Fishwick CWG. In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-β-lactamase Inhibitors. J Med Chem 2018; 61:1255-1260. [PMID: 29271657 DOI: 10.1021/acs.jmedchem.7b01728] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Zinc ion-dependent β-lactamases (MBLs) catalyze the hydrolysis of almost all β-lactam antibiotics and resist the action of clinically available β-lactamase inhibitors. We report how application of in silico fragment-based molecular design employing thiol-mediated metal anchorage leads to potent MBL inhibitors. The new inhibitors manifest potent inhibition of clinically important B1 subfamily MBLs, including the widespread NDM-1, IMP-1, and VIM-2 enzymes; with lower potency, some of them also inhibit clinically relevant Class A and D serine-β-lactamases. The inhibitors show selectivity for bacterial MBL enzymes compared to that for human MBL fold nucleases. Cocrystallization of one inhibitor, which shows potentiation of Meropenem activity against MBL-expressing Enterobacteriaceae, with VIM-2 reveals an unexpected binding mode, involving interactions with residues from conserved active site bordering loops.
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Affiliation(s)
- Ricky Cain
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David Zollman
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rachel M Johnson
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Anne Makena
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Martine I Abboud
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Samuel Cahill
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sook Y Lee
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.,Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Colin W G Fishwick
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
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23
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Ekström AG, Wang JT, Bella J, Campopiano DJ. Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library. Org Biomol Chem 2018; 16:8144-8149. [DOI: 10.1039/c8ob01918e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.
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Affiliation(s)
| | | | - Juraj Bella
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
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24
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Worrell BT, Mavila S, Wang C, Kontour TM, Lim CH, McBride MK, Musgrave CB, Shoemaker R, Bowman CN. A user's guide to the thiol-thioester exchange in organic media: scope, limitations, and applications in material science. Polym Chem 2018. [DOI: 10.1039/c8py01031e] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The dynamic exchange of thiols and thioesters in organic media was explored, leading to room temperature plasticity in crosslinked polymers.
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Affiliation(s)
- Brady T. Worrell
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Sudheendran Mavila
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Chen Wang
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Taylor M. Kontour
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Chern-Hooi Lim
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Matthew K. McBride
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Charles B. Musgrave
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Richard Shoemaker
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
| | - Christopher N. Bowman
- Department of Chemical and Biological Engineering
- University of Colorado – Boulder
- Boulder
- USA
- Material Science and Engineering Program
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25
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Zhang Y, Xie S, Yan M, Ramström O. Dynamic Covalent Chemistry of Aldehyde Enamines: Bi III - and Sc III -Catalysis of Amine-Enamine Exchange. Chemistry 2017; 23:11908-11912. [PMID: 28722305 PMCID: PMC5656824 DOI: 10.1002/chem.201702363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 01/09/2023]
Abstract
The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry.
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Affiliation(s)
- Yang Zhang
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Sheng Xie
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Mingdi Yan
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
- Department of ChemistryUniversity of Massachusetts Lowell1 University Ave.LowellMA01854USA
| | - Olof Ramström
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
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26
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Huang CM, Zhu Y, Jin DQ, Kelly RT, Fang Q. Direct Surface and Droplet Microsampling for Electrospray Ionization Mass Spectrometry Analysis with an Integrated Dual-Probe Microfluidic Chip. Anal Chem 2017; 89:9009-9016. [PMID: 28780855 DOI: 10.1021/acs.analchem.7b01679] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ambient mass spectrometry (MS) has revolutionized the way of MS analysis and broadened its application in various fields. This paper describes the use of microfluidic techniques to simplify the setup and improve the functions of ambient MS by integrating the sampling probe, electrospray emitter probe, and online mixer on a single glass microchip. Two types of sampling probes, including a parallel-channel probe and a U-shaped channel probe, were designed for dry-spot and liquid-phase droplet samples, respectively. We demonstrated that the microfabrication techniques not only enhanced the capability of ambient MS methods in analysis of dry-spot samples on various surfaces, but also enabled new applications in the analysis of nanoliter-scale chemical reactions in an array of droplets. The versatility of the microchip-based ambient MS method was demonstrated in multiple different applications including evaluation of residual pesticide on fruit surfaces, sensitive analysis of low-ionizable analytes using postsampling derivatization, and high-throughput screening of Ugi-type multicomponent reactions.
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Affiliation(s)
- Cong-Min Huang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Di-Qiong Jin
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Innovation Center for Cell Signaling Network, Zhejiang University , Hangzhou, 310058, China
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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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28
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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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29
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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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30
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Wu K, Cheng R, Zhang J, Meng F, Deng C, Zhong Z. Micellar nanoformulation of lipophilized bortezomib: high drug loading, improved tolerability and targeted treatment of triple negative breast cancer. J Mater Chem B 2017. [DOI: 10.1039/c7tb01297g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lipophilization of bortezomib with pinanediol enables efficacious drug loading and targeted tumor chemotherapy with reduction-sensitive self-crosslinked micellar systems.
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Affiliation(s)
- Kaiqi Wu
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Ru Cheng
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Jian Zhang
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Fenghua Meng
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Chao Deng
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Zhiyuan Zhong
- Biomedical Polymers Laboratory
- and Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
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31
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van der Vlag R, Hirsch A. Analytical Methods in Protein-Templated Dynamic Combinatorial Chemistry. COMPREHENSIVE SUPRAMOLECULAR CHEMISTRY II 2017. [PMCID: PMC7150222 DOI: 10.1016/b978-0-12-409547-2.12559-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Reverte M, Barvik I, Vasseur JJ, Smietana M. RNA-directed off/on switch of RNase H activity using boronic ester formation. Org Biomol Chem 2017; 15:8204-8210. [DOI: 10.1039/c7ob02145c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new concept to modulate RNase H activity is presented based on the boronic acid/boronate switch.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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33
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Li GB, Abboud MI, Brem J, Someya H, Lohans CT, Yang SY, Spencer J, Wareham DW, McDonough MA, Schofield CJ. NMR-filtered virtual screening leads to non-metal chelating metallo-β-lactamase inhibitors. Chem Sci 2016; 8:928-937. [PMID: 28451231 PMCID: PMC5369532 DOI: 10.1039/c6sc04524c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based virtual screening approach combined with NMR filtering led to the identification of inhibitors of the clinically relevant Verona Integron-encoded MBL (VIM)-2. Crystallographic analyses reveal a new mode of MBL inhibition involving binding adjacent to the active site zinc ions, but which does not involve metal chelation. The results will aid efforts to develop new types of clinically useful inhibitors targeting MBLs/MBL-fold metallo-enzymes involved in antibacterial and anticancer drug resistance.
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Affiliation(s)
- Guo-Bo Li
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , West China School of Pharmacy , Sichuan University , Chengdu , 610041 , China
| | - Martine I Abboud
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Jürgen Brem
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Hidenori Someya
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Medicinal Chemistry Research Laboratories , New Drug Research Division , Otsuka Pharmaceutical Co., Ltd. , 463-10 Kagasuno, Kawauchi-cho , Tokushima 771-0192 , Japan
| | - Christopher T Lohans
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy , West China Hospital , West China Medical School , Sichuan University , Sichuan 610041 , China
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol BS8 1TD , UK
| | - David W Wareham
- Antimicrobial Research Group , Barts & The London School of Medicine and Dentistry , Queen Mary University of London , London , E1 2AT , UK
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
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34
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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35
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Mondal M, Radeva N, Fanlo-Virgós H, Otto S, Klebe G, Hirsch AKH. Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2016; 55:9422-6. [PMID: 27400756 PMCID: PMC5113778 DOI: 10.1002/anie.201603074] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/05/2016] [Indexed: 12/31/2022]
Abstract
Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
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36
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Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery. Molecules 2016; 21:molecules21070910. [PMID: 27438816 PMCID: PMC6273345 DOI: 10.3390/molecules21070910] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023] Open
Abstract
Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.
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37
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Mondal M, Radeva N, Fanlo‐Virgós H, Otto S, Klebe G, Hirsch AKH. Fragmentverknüpfung und ‐optimierung von Hemmstoffen der Aspartylprotease Endothiapepsin: Fragmentbasiertes Wirkstoffdesign beschleunigt durch dynamische kombinatorische Chemie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Milon Mondal
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Hugo Fanlo‐Virgós
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
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38
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Yang Z, Fang Z, He W, Wang Z, Gan H, Tian Q, Guo K. Identification of inhibitors for vascular endothelial growth factor receptor by using dynamic combinatorial chemistry. Bioorg Med Chem Lett 2016; 26:1671-4. [PMID: 26920800 DOI: 10.1016/j.bmcl.2016.02.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/01/2016] [Accepted: 02/20/2016] [Indexed: 01/26/2023]
Abstract
The novel analysis method consisting of size-exclusion chromatography (SEC) and HRMS analysis was firstly applied in the discovery of potential inhibitors towards cancer drug targets. With vascular endothelial growth factor receptor (VEGFR-2) as a target, dynamic combinatorial libraries (DCLs) were prepared by reacting aldehydes with amines. Four sensitive binders targeted VEGFR-2 were directly isolated from the library. Antitumor activity test in vitro and inhibition experiments toward angiogenesis were also carried out.
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Affiliation(s)
- Zhao Yang
- School of Pharmaceutical Engineering, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211816, China
| | - Zheng Fang
- School of Pharmaceutical Science, Nanjing Technology University, No. 30 Puzhu South Road, Nanjing 211816, China
| | - Wei He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, No. 30 Puzhu South Road, Nanjing 211816, China
| | - Zhixiang Wang
- School of Pharmaceutical Engineering, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211816, China
| | - Haifeng Gan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, No. 30 Puzhu South Road, Nanjing 211816, China
| | - Qitao Tian
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, No. 30 Puzhu South Road, Nanjing 211816, China
| | - Kai Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Technology University, No. 30 Puzhu South Road, Nanjing 211816, China
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39
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Pharmacological targeting of the HIF hydroxylases--A new field in medicine development. Mol Aspects Med 2016; 47-48:54-75. [PMID: 26791432 DOI: 10.1016/j.mam.2016.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022]
Abstract
In human cells oxygen levels are 'sensed' by a set of ferrous iron and 2-oxoglutarate dependent dioxygenases. These enzymes regulate a broad range of cellular and systemic responses to hypoxia by catalysing the post-translational hydroxylation of specific residues in the alpha subunits of hypoxia inducible factor (HIF) transcriptional complexes. The HIF hydroxylases are now the subject of pharmaceutical targeting by small molecule inhibitors that aim to activate or augment the endogenous HIF transcriptional response for the treatment of anaemia and other hypoxic human diseases. Here we consider the rationale for this therapeutic strategy from the biochemical, biological and medical perspectives. We outline structural and mechanistic considerations that are relevant to the design of HIF hydroxylase inhibitors, including likely determinants of specificity, and review published reports on their activity in pre-clinical models and clinical trials.
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40
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Tong KL, Yee CC, Tse YC, Au-Yeung HY. Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template? Inorg Chem Front 2016. [DOI: 10.1039/c5qi00227c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.
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Affiliation(s)
- King-Lung Tong
- Department of Chemistry
- The University of Hong Kong
- PR China
| | - Chi-Chung Yee
- Department of Chemistry
- The University of Hong Kong
- PR China
| | | | - Ho Yu Au-Yeung
- Department of Chemistry
- The University of Hong Kong
- PR China
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41
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Lei Y, Hu T, Wu X, Wu Y, Bao Q, Zhang L, Xia H, Sun H, You Q, Zhang X. Affinity-Based Fluorescence Polarization Assay for High-Throughput Screening of Prolyl Hydroxylase 2 Inhibitors. ACS Med Chem Lett 2015; 6:1236-40. [PMID: 26713111 DOI: 10.1021/acsmedchemlett.5b00394] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/09/2015] [Indexed: 12/30/2022] Open
Abstract
Prolyl hydroxylase domain 2 (PHD2) enzyme, a Fe(II) and 2-oxoglutarate (2-OG) dependent oxygenase, mediates key physiological responses to hypoxia by modulating the levels of hypoxia inducible factor 1-α (HIF1α). PHD2 has been shown to have the therapeutic potentials for conditions including anemia and ischemic disease. Currently, many activity-based assays have been developed for identifying PHD2 inhibitors. Here we report an affinity-based fluorescence polarization method using FITC-labeled HIF1α (556-574) peptide as a probe for quantitative and site-specific screening of small molecule PHD2 inhibitors.
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Affiliation(s)
- Yonghua Lei
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Tianhan Hu
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xingsen Wu
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yue Wu
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Qichao Bao
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lianshan Zhang
- National Engineering and Research Center for Target Drugs, Lianyungang 222000, China
| | - Hua Xia
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaojin Zhang
- Jiangsu
Key Laboratory of Drug Design and Optimization, and State Key Laboratory
of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department
of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing 210009, China
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42
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Recent Advances in Developing Inhibitors for Hypoxia-Inducible Factor Prolyl Hydroxylases and Their Therapeutic Implications. Molecules 2015; 20:20551-68. [PMID: 26610437 PMCID: PMC6332328 DOI: 10.3390/molecules201119717] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/13/2022] Open
Abstract
Hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs) are members of the 2-oxoglutarate dependent non-heme iron dioxygenases. Due to their physiological roles in regulation of HIF-1α stability, many efforts have been focused on searching for selective PHD inhibitors to control HIF-1α levels for therapeutic applications. In this review, we first describe the structure of PHD2 as a molecular basis for structure-based drug design (SBDD) and various experimental methods developed for measuring PHD activity. We further discuss the current status of the development of PHD inhibitors enabled by combining SBDD approaches with high-throughput screening. Finally, we highlight the clinical implications of small molecule PHD inhibitors.
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Kakei Y, Yamazaki C, Suzuki M, Nakamura A, Sato A, Ishida Y, Kikuchi R, Higashi S, Kokudo Y, Ishii T, Soeno K, Shimada Y. Small-molecule auxin inhibitors that target YUCCA are powerful tools for studying auxin function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:827-37. [PMID: 26402640 DOI: 10.1111/tpj.13032] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 09/07/2015] [Accepted: 09/11/2015] [Indexed: 05/12/2023]
Abstract
Auxin is essential for plant growth and development, this makes it difficult to study the biological function of auxin using auxin-deficient mutants. Chemical genetics have the potential to overcome this difficulty by temporally reducing the auxin function using inhibitors. Recently, the indole-3-pyruvate (IPyA) pathway was suggested to be a major biosynthesis pathway in Arabidopsis thaliana L. for indole-3-acetic acid (IAA), the most common member of the auxin family. In this pathway, YUCCA, a flavin-containing monooxygenase (YUC), catalyzes the last step of conversion from IPyA to IAA. In this study, we screened effective inhibitors, 4-biphenylboronic acid (BBo) and 4-phenoxyphenylboronic acid (PPBo), which target YUC. These compounds inhibited the activity of recombinant YUC in vitro, reduced endogenous IAA content, and inhibited primary root elongation and lateral root formation in wild-type Arabidopsis seedlings. Co-treatment with IAA reduced the inhibitory effects. Kinetic studies of BBo and PPBo showed that they are competitive inhibitors of the substrate IPyA. Inhibition constants (Ki ) of BBo and PPBo were 67 and 56 nm, respectively. In addition, PPBo did not interfere with the auxin response of auxin-marker genes when it was co-treated with IAA, suggesting that PPBo is not an inhibitor of auxin sensing or signaling. We propose that these compounds are a class of auxin biosynthesis inhibitors that target YUC. These small molecules are powerful tools for the chemical genetic analysis of auxin function.
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Affiliation(s)
- Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Chiaki Yamazaki
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Masashi Suzuki
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Ayako Nakamura
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Akiko Sato
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Yosuke Ishida
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Rie Kikuchi
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
| | - Shouichi Higashi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yumiko Kokudo
- National Agriculture and Food Research Organization (NARO), Western Region Agricultural Research Center (WARC), Senyu, Zentsuji, Kagawa, 765-8508, Japan
| | - Takahiro Ishii
- National Agriculture and Food Research Organization (NARO), Western Region Agricultural Research Center (WARC), Senyu, Zentsuji, Kagawa, 765-8508, Japan
| | - Kazuo Soeno
- National Agriculture and Food Research Organization (NARO), Western Region Agricultural Research Center (WARC), Senyu, Zentsuji, Kagawa, 765-8508, Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813, Japan
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44
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Li G, Zheng W, Chen Z, Zhou Y, Liu Y, Yang J, Huang Y, Li X. Design, preparation, and selection of DNA-encoded dynamic libraries. Chem Sci 2015; 6:7097-7104. [PMID: 28757982 PMCID: PMC5510007 DOI: 10.1039/c5sc02467f] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/09/2015] [Indexed: 01/10/2023] Open
Abstract
We report a method for the preparation and selection of DNA-encoded dynamic libraries (DEDLs). The library is composed of two sets of DNA-linked small molecules that are under dynamic exchange through DNA hybridization. Addition of the protein target shifted the equilibrium, favouring the assembly of high affinity bivalent binders. Notably, we introduced a novel locking mechanism to stop the dynamic exchange and "freeze" the equilibrium, thereby enabling downstream hit isolation and decoding by PCR amplification and DNA sequencing. Our DEDL approach has circumvented the limitation of library size and realized the analysis and selection of large dynamic libraries. In addition, this method also eliminates the requirement for modified and immobilized target proteins.
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Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences (BNLMS) , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Zitian Chen
- Biodynamic Optical Imaging Centre (BIOPIC) and College of Engineering , Peking University , Beijing , China 100871
| | - Yu Zhou
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Yu Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences (BNLMS) , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Junrui Yang
- Biodynamic Optical Imaging Centre (BIOPIC) and College of Engineering , Peking University , Beijing , China 100871
| | - Yanyi Huang
- Biodynamic Optical Imaging Centre (BIOPIC) and College of Engineering , Peking University , Beijing , China 100871
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences (BNLMS) , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 . .,Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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45
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Schaufelberger F, Ramström O. Dynamic covalent organocatalysts discovered from catalytic systems through rapid deconvolution screening. Chemistry 2015; 21:12735-40. [PMID: 26174068 PMCID: PMC4557047 DOI: 10.1002/chem.201502088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 11/11/2022]
Abstract
The first example of a bifunctional organocatalyst assembled through dynamic covalent chemistry (DCC) is described. The catalyst is based on reversible imine chemistry and can catalyze the Morita-Baylis-Hillman (MBH) reaction of enones with aldehydes or N-tosyl imines. Furthermore, these dynamic catalysts were shown to be optimizable through a systemic screening approach, in which large mixtures of catalyst structures were generated, and the optimal catalyst could be directly identified by using dynamic deconvolution. This strategy allowed one-pot synthesis and in situ evaluation of several potential catalysts without the need to separate, characterize, and purify each individual structure. The systems were furthermore shown to catalyze and re-equilibrate their own formation through a previously unknown thiourea-catalyzed transimination process.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
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46
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Nowak P, Colomb-Delsuc M, Otto S, Li J. Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library. J Am Chem Soc 2015; 137:10965-9. [PMID: 26192814 DOI: 10.1021/jacs.5b04380] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.
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Affiliation(s)
- Piotr Nowak
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jianwei Li
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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47
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Schaufelberger F, Hu L, Ramström O. trans-Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions. Chemistry 2015; 21:9776-83. [PMID: 26044061 PMCID: PMC4517097 DOI: 10.1002/chem.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Indexed: 11/08/2022]
Abstract
The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3-proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two-dimensional dynamic systems with a high degree of complexity evolution. The transamination-transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate-limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity-generating element.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
| | - Lei Hu
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
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48
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Reversible linkage of two distinct small molecule inhibitors of Myc generates a dimeric inhibitor with improved potency that is active in myc over-expressing cancer cell lines. PLoS One 2015; 10:e0121793. [PMID: 25875098 PMCID: PMC4398458 DOI: 10.1371/journal.pone.0121793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
We describe the successful application of a novel approach for generating dimeric Myc inhibitors by modifying and reversibly linking two previously described small molecules. We synthesized two directed libraries of monomers, each comprised of a ligand, a connector, and a bioorthogonal linker element, to identify the optimal dimer configuration required to inhibit Myc. We identified combinations of monomers, termed self-assembling dimeric inhibitors, which displayed synergistic inhibition of Myc-dependent cell growth. We confirmed that these dimeric inhibitors directly bind to Myc blocking its interaction with Max and affect transcription of MYC dependent genes. Control combinations that are unable to form a dimer do not show any synergistic effects in these assays. Collectively, these data validate our new approach to generate more potent and selective inhibitors of Myc by self-assembly from smaller, lower affinity components. This approach provides an opportunity for developing novel therapeutics against Myc and other challenging protein:protein interaction (PPI) target classes.
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49
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Atcher J, Moure A, Bujons J, Alfonso I. Salt-Induced Adaptation of a Dynamic Combinatorial Library of Pseudopeptidic Macrocycles: Unraveling the Electrostatic Effects in Mixed Aqueous Media. Chemistry 2015; 21:6869-78. [DOI: 10.1002/chem.201406155] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Joan Atcher
- Department of Biological Chemistry and Molecular Modeling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona (Spain)
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50
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Reddy ER, Trivedi R, Sarma AVS, Sridhar B, Anantaraju HS, Sriram D, Yogeeswari P, Nagesh N. Sugar-boronate ester scaffold tethered pyridyl-imine palladium(ii) complexes: synthesis and their in vitro anticancer evaluation. Dalton Trans 2015; 44:17600-16. [DOI: 10.1039/c5dt03266k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The anticancer activity of sugar-boronate ester containing palladium(ii) complexes is reported.
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Affiliation(s)
- Eda Rami Reddy
- Inorganic and Physical Chemistry Division
- CSIR-IICT
- Hyderabad-500007
- India
| | - Rajiv Trivedi
- Inorganic and Physical Chemistry Division
- CSIR-IICT
- Hyderabad-500007
- India
| | | | | | | | - Dharmarajan Sriram
- Department of Pharmacy
- Birla Institute of Technology & Science – Pilani
- Hyderabad 500 078
- India
| | - Perumal Yogeeswari
- Department of Pharmacy
- Birla Institute of Technology & Science – Pilani
- Hyderabad 500 078
- India
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad-500 007
- India
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