1
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Zhao R, Zhu J, Jiang X, Bai R. Click chemistry-aided drug discovery: A retrospective and prospective outlook. Eur J Med Chem 2024; 264:116037. [PMID: 38101038 DOI: 10.1016/j.ejmech.2023.116037] [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: 10/22/2023] [Revised: 11/20/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Click chemistry has emerged as a valuable tool for rapid compound synthesis, presenting notable advantages and convenience in the exploration of potential drug candidates. In particular, in situ click chemistry capitalizes on enzymes as reaction templates, leveraging their favorable conformation to selectively link individual building blocks and generate novel hits. This review comprehensively outlines and introduces the extensive use of click chemistry in compound library construction, and hit and lead discovery, supported by specific research examples. Additionally, it discusses the limitations and precautions associated with the application of click chemistry in drug discovery. Our intention for this review is to contribute to the development of a modular synthetic approach for the rapid identification of drug candidates.
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Affiliation(s)
- Rui Zhao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, PR China; Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Junlong Zhu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, PR China; Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Xiaoying Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, PR China; Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, PR China
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, PR China; Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, PR China.
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2
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Han H, Choi YJ, Hong H, Kim CY, Byun MK, Cho JH, Lee JH, Park JW, Doherty TA, Park HJ. Effects of chitinase-1 inhibitor in obesity-induced and -aggravated asthma in a murine model. Life Sci 2023; 334:122163. [PMID: 37890698 DOI: 10.1016/j.lfs.2023.122163] [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: 07/01/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
AIMS Despite recent investigations on the role of chitinase in asthma, its role in obesity-induced asthma has not been evaluated. Therefore, we investigated the roles of chitin, chitinase-1, and a chitinase-1 inhibitor (compound X, CPX) in a murine model. MAIN METHODS We assigned C57BL/6 mice to the ovalbumin (OVA) model or obesity model group. In the OVA model, mice received intraperitoneal OVA twice within a 2-week interval and intranasal OVA for 3 consecutive days. Additionally, chitin was intranasally administered for 3 consecutive days, and CPX was intraperitoneally injected three times over 5 days. In the obesity model, a high-fat diet (HFD) was maintained for 13 weeks, and CPX was intraperitoneally injected eight times over 4 weeks. KEY FINDINGS In the OVA model, chitin aggravated OVA-induced airway hyper-responsiveness (AHR), increased bronchoalveolar lavage fluid (BALF) cell proliferation, increased fibrosis, and increased the levels of various inflammatory cytokines (including chitinase-1, TGF-β, TNF-α, IL-1 β, IL-6, IL-4, and IL-13). CPX treatment significantly ameliorated these effects. In the obesity model, HFD significantly increased AHR, BALF cell proliferation, fibrosis, and the levels of various inflammatory cytokines. Particularly, compared to the control group, the mRNA expression of chitinase, chitinase-like molecules, and other molecules associated with inflammation and the immune system was significantly upregulated in the HFD and HFD/OVA groups. Immunofluorescence analysis also showed increased chitinase-1 expression in these groups. CPX significantly ameliorated all these effects in this model. SIGNIFICANCE This study showed that CPX can be an effective therapeutic agent in asthma, especially, obesity-induced and -aggravated asthma to protect against the progression to airway remodeling and fibrosis.
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Affiliation(s)
- Heejae Han
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Yong Jun Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Hyerim Hong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Chi Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Min Kwang Byun
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jae Hwa Cho
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jae-Hyun Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Institute of Allergy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung-Won Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Institute of Allergy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Taylor A Doherty
- Section of Allergy and Immunology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hye Jung Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea; Section of Allergy and Immunology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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3
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Kassu M, Parvatkar PT, Milanes J, Monaghan NP, Kim C, Dowgiallo M, Zhao Y, Asakawa AH, Huang L, Wagner A, Miller B, Carter K, Barrett KF, Tillery LM, Barrett LK, Phan IQ, Subramanian S, Myler PJ, Van Voorhis WC, Leahy JW, Rice CA, Kyle DE, Morris J, Manetsch R. Shotgun Kinetic Target-Guided Synthesis Approach Enables the Discovery of Small-Molecule Inhibitors against Pathogenic Free-Living Amoeba Glucokinases. ACS Infect Dis 2023; 9:2190-2201. [PMID: 37820055 PMCID: PMC10644346 DOI: 10.1021/acsinfecdis.3c00284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/13/2023]
Abstract
Pathogenic free-living amoebae (pFLA) can cause life-threatening central nervous system (CNS) infections and warrant the investigation of new chemical agents to combat the rise of infection from these pathogens. Naegleria fowleri glucokinase (NfGlck), a key metabolic enzyme involved in generating glucose-6-phosphate, was previously identified as a potential target due to its limited sequence similarity with human Glck (HsGlck). Herein, we used our previously demonstrated multifragment kinetic target-guided synthesis (KTGS) screening strategy to identify inhibitors against pFLA glucokinases. Unlike the majority of previous KTGS reports, our current study implements a "shotgun" approach, where fragments were not biased by predetermined binding potentials. The study resulted in the identification of 12 inhibitors against 3 pFLA glucokinase enzymes─NfGlck, Balamuthia mandrillaris Glck (BmGlck), and Acanthamoeba castellanii Glck (AcGlck). This work demonstrates the utility of KTGS to identify small-molecule binders for biological targets where resolved X-ray crystal structures are not readily accessible.
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Affiliation(s)
- Mintesinot Kassu
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Prakash T. Parvatkar
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Jillian Milanes
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Neil P. Monaghan
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Chungsik Kim
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Matthew Dowgiallo
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Yingzhao Zhao
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Ami H. Asakawa
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Lili Huang
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Alicia Wagner
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Brandon Miller
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Karissa Carter
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kayleigh F. Barrett
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Logan M. Tillery
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Lynn K. Barrett
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - Isabelle Q. Phan
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Sandhya Subramanian
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Peter J. Myler
- Center for Global Infectious Diseases Research, Seattle Children’s Research Center, Seattle, Washington 98109, United States
| | - Wesley C. Van Voorhis
- Center
for Emerging and Re-emerging Infectious Diseases (CERID), Division
of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98109, United States
| | - James W. Leahy
- Department of Chemistry, University
of
South Florida, Tampa, Florida 33620, United States
| | - Christopher A. Rice
- Department
of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Institute for Drug Discovery (PIDD), Purdue
University, West Lafayette, Indiana 47907, United States
- Purdue Institute
of Inflammation, Immunology and Infectious Disease (PI4D), Purdue University, West Lafayette, Indiana 47907, United States
- Department
of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Dennis E. Kyle
- Department
of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - James Morris
- Eukaryotic
Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Roman Manetsch
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett
Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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4
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Liu P, Jiang Y, Jiao L, Luo Y, Wang X, Yang T. Strategies for the Discovery of Oxazolidinone Antibacterial Agents: Development and Future Perspectives. J Med Chem 2023; 66:13860-13873. [PMID: 37807849 DOI: 10.1021/acs.jmedchem.3c01040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Oxazolidinones represent a significant class of synthetic bacterial protein synthesis inhibitors that are primarily effective against Gram-positive bacteria. The commercial success of linezolid, the first FDA-approved oxazolidinone antibiotic, has motivated researchers to develop more potent oxazolidinones by employing various drug development strategies to fight against antimicrobial resistance, some of which have shown promising results. Thus, this Perspective aims to discuss the strategies employed in constructing oxazolidinone-based antibacterial agents and summarize recent advances in discovering oxazolidinone antibiotics to provide valuable insights for potentially developing next-generation oxazolidinone antibacterial agents or other pharmaceuticals.
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Affiliation(s)
- Pingxian Liu
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunhan Jiang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Jiao
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaodong Wang
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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5
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Zhan F, Zhu J, Xie S, Xu J, Xu S. Advances of bioorthogonal coupling reactions in drug development. Eur J Med Chem 2023; 253:115338. [PMID: 37037138 DOI: 10.1016/j.ejmech.2023.115338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Currently, bioorthogonal coupling reactions have garnered considerable interest due to their high substrate selectivity and less restrictive reaction conditions. During recent decades, bioorthogonal coupling reactions have emerged as powerful tools in drug development. This review describes the current applications of bioorthogonal coupling reactions in compound library building mediated by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and in situ click chemistry or conjunction with other techniques; druggability optimization with 1,2,3-triazole groups; and intracellular self-assembly platforms with ring tension reactions, which are presented from the viewpoint of drug development. There is a reasonable prospect that bioorthogonal coupling reactions will accelerate the screening of lead compounds, the designing strategies of small molecules and expand the variety of designed compounds, which will be a new trend in drug development in the future.
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6
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Nacheva K, Kulkarni SS, Kassu M, Flanigan D, Monastyrskyi A, Iyamu ID, Doi K, Barber M, Namelikonda N, Tipton JD, Parvatkar P, Wang HG, Manetsch R. Going beyond Binary: Rapid Identification of Protein-Protein Interaction Modulators Using a Multifragment Kinetic Target-Guided Synthesis Approach. J Med Chem 2023; 66:5196-5207. [PMID: 37000900 PMCID: PMC10620989 DOI: 10.1021/acs.jmedchem.3c00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Indexed: 04/03/2023]
Abstract
Kinetic target-guided synthesis (KTGS) is a powerful screening approach that enables identification of small molecule modulators for biomolecules. While many KTGS variants have emerged, a majority of the examples suffer from limited throughput and a poor signal/noise ratio, hampering reliable hit detection. Herein, we present our optimized multifragment KTGS screening strategy that tackles these limitations. This approach utilizes selected reaction monitoring liquid chromatography tandem mass spectrometry for hit detection, enabling the incubation of 190 fragment combinations per screening well. Consequentially, our fragment library was expanded from 81 possible combinations to 1710, representing the largest KTGS screening library assembled to date. The expanded library was screened against Mcl-1, leading to the discovery of 24 inhibitors. This work unveils the true potential of KTGS with respect to the rapid and reliable identification of hits, further highlighting its utility as a complement to the existing repertoire of screening methods used in drug discovery.
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Affiliation(s)
- Katya Nacheva
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Sameer S. Kulkarni
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Mintesinot Kassu
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - David Flanigan
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Sciences, Hillsborough Community College, Tampa, Florida 33619, United States
| | - Andrii Monastyrskyi
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Iredia D. Iyamu
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kenichiro Doi
- Department
of Pediatrics, Division of Pediatric Hematology and Oncology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Megan Barber
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Niranjan Namelikonda
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Jeremiah D. Tipton
- Proteomics
and Mass Spectrometry Core Facility, University
of South Florida, Tampa, Florida 33620, United States
| | - Prakash Parvatkar
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Hong-Gang Wang
- Department
of Pediatrics, Division of Pediatric Hematology and Oncology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Roman Manetsch
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Center for
Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Barnett
Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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7
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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8
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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9
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Galvez-Llompart M, Zanni R, Galvez J, Garcia-Domenech R. Molecular Topology QSAR Strategy for Crop Protection: New Natural Fungicides with Chitin Inhibitory Activity. ACS OMEGA 2020; 5:16358-16365. [PMID: 32685798 PMCID: PMC7364431 DOI: 10.1021/acsomega.0c00177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/23/2020] [Indexed: 05/11/2023]
Abstract
Nowadays, crop protection is a major concern and how to proceed is a delicate point of contention. New products must be safe and ecofriendly in accordance with the actual legislation. In this context, we present a quantitative structure-activity relationship strategy based on molecular topology as a tool for generating natural products as potential fungicides following a mechanism of action based on the synthesis of chitin inhibition (chitinase inhibition). Two discriminant equations using statistical linear discriminant analysis were used to identify three potential candidates (1-methylxanthine, hematommic acid, and antheraxanthin). The equations showed accuracy and specificity levels above 80%, minimizing the risk of selecting false active compounds.
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Affiliation(s)
- Maria Galvez-Llompart
- Instituto
de Tecnologia Quimica, UPV-CSIC, Universidad
Politecnica de Valencia, Avenida de los Naranjos s/n, Valencia E-46022, Spain
- Molecular
Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Valencia 46010, Spain
| | - Riccardo Zanni
- Departamento
de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Bulevar Louis Pasteur 31, Malaga 29071, Spain
- Molecular
Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Valencia 46010, Spain
| | - Jorge Galvez
- Molecular
Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Valencia 46010, Spain
| | - Ramon Garcia-Domenech
- Molecular
Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, Valencia 46010, Spain
- . Phone: +34-963544291
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10
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Kitamura S, Zheng Q, Woehl JL, Solania A, Chen E, Dillon N, Hull MV, Kotaniguchi M, Cappiello JR, Kitamura S, Nizet V, Sharpless KB, Wolan DW. Sulfur(VI) Fluoride Exchange (SuFEx)-Enabled High-Throughput Medicinal Chemistry. J Am Chem Soc 2020; 142:10899-10904. [PMID: 32479075 DOI: 10.1021/jacs.9b13652] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Optimization of small-molecule probes or drugs is a synthetically lengthy, challenging, and resource-intensive process. Lack of automation and reliance on skilled medicinal chemists is cumbersome in both academic and industrial settings. Here, we demonstrate a high-throughput hit-to-lead process based on the biocompatible sulfur(VI) fluoride exchange (SuFEx) click chemistry. A high-throughput screening hit benzyl (cyanomethyl)carbamate (Ki = 8 μM) against a bacterial cysteine protease SpeB was modified with a SuFExable iminosulfur oxydifluoride [RN═S(O)F2] motif, rapidly diversified into 460 analogs in overnight reactions, and the products were directly screened to yield drug-like inhibitors with 480-fold higher potency (Ki = 18 nM). We showed that the improved molecule is active in a bacteria-host coculture. Since this SuFEx linkage reaction succeeds on picomole scale for direct screening, we anticipate our methodology can accelerate the development of robust biological probes and drug candidates.
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Affiliation(s)
| | | | | | | | | | | | | | - Miyako Kotaniguchi
- Laboratory of Advanced Food Process Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Nakaku, Sakai, Osaka 599-8570, Japan
| | | | - Shinichi Kitamura
- Laboratory of Advanced Food Process Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Nakaku, Sakai, Osaka 599-8570, Japan
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11
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Miyake Y, Itoh Y, Suzuma Y, Kodama H, Kurohara T, Yamashita Y, Narozny R, Hanatani Y, Uchida S, Suzuki T. Metalloprotein-Catalyzed Click Reaction for In Situ Generation of a Potent Inhibitor. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuka Miyake
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yoshinori Suzuma
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Hidehiko Kodama
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Takashi Kurohara
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yasunobu Yamashita
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Remy Narozny
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yutaro Hanatani
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Shusaku Uchida
- Graduate School of Medicine, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamo-hangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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12
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Bosc D, Camberlein V, Gealageas R, Castillo-Aguilera O, Deprez B, Deprez-Poulain R. Kinetic Target-Guided Synthesis: Reaching the Age of Maturity. J Med Chem 2019; 63:3817-3833. [PMID: 31820982 DOI: 10.1021/acs.jmedchem.9b01183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinetic target-guided synthesis (KTGS) is an original discovery strategy allowing a target to catalyze the irreversible synthesis of its own ligands from a pool of reagents. Although pioneered almost two decades ago, it only recently proved its usefulness in medicinal chemistry, as exemplified by the increasing number of protein targets used, the wider range of target and pocket types, and the diversity of therapeutic areas explored. In recent years, two new leads for in vivo studies were released. Amidations and multicomponent reactions expanded the armamentarium of reactions beyond triazole formation and two new examples of in cellulo KTGS were also disclosed. Herein, we analyze the origins and the chemical space of both KTGS ligands and warhead-bearing reagents. We review the KTGS timeline focusing on recent cases in order to give medicinal chemists the full scope of this strategy which has great potential for hit discovery and hit or lead optimization.
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Affiliation(s)
- Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Virgyl Camberlein
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ronan Gealageas
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Omar Castillo-Aguilera
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.,Institut Universitaire de France, F- 75005 Paris, France
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13
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Marine chitinolytic enzymes, a biotechnological treasure hidden in the ocean? Appl Microbiol Biotechnol 2018; 102:9937-9948. [PMID: 30276711 DOI: 10.1007/s00253-018-9385-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022]
Abstract
Chitinolytic enzymes are capable to catalyze the chitin hydrolysis. Due to their biomedical and biotechnological applications, nowadays chitinolytic enzymes have attracted worldwide attention. Chitinolytic enzymes have provided numerous useful materials in many different industries, such as food, pharmaceutical, cosmetic, or biomedical industry. Marine enzymes are commonly employed in industry because they display better operational properties than animal, plant, or bacterial homologs. In this mini-review, we want to describe marine chitinolytic enzymes as versatile enzymes in different biotechnological fields. In this regard, interesting comments about their biological role, reaction mechanism, production, functional characterization, immobilization, and biotechnological application are shown in this work.
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14
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Jin X, Daher SS, Lee M, Buttaro B, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions Using Resistant Bacteria as Reaction Vessels: in Cellulo Click Chemistry. ACS Med Chem Lett 2018; 9:907-911. [PMID: 30258539 DOI: 10.1021/acsmedchemlett.8b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/13/2018] [Indexed: 01/21/2023] Open
Abstract
In situ click chemistry has been a powerful method for fragment-based drug design since its discovery in 2002. Recently, we demonstrated that the bacterial ribosome can template the azide-alkyne cycloaddition reaction to expedite the discovery of novel antibiotics. We now report this process can be performed in an antibiotic-resistant bacterial cell. The corresponding triazole products formed in cellulo are potent antibiotics that inhibit bacterial growth; moreover, the potency of each cycloadduct can be visualized using the traditional MIC assay in a 96-well plate format. We characterized the in cellulo clicked products by independent chemical synthesis and LC-MS analysis, which showed that mass count percent increase was directly proportional to 1/MIC. In other words, potent compounds detected by MIC were formed in greater amounts. Control experiments unambiguously showed the ribosome was responsible for templating triazole formation. Significantly, our method (1) obviates the need to isolate bacterial ribosomes; (2) could be applied to different bacterial strains, which broadens the scope and facilitates the discovery of narrow-spectrum antibiotics; and (3) does not require the knowledge of mode-of-action and thus could uncover novel antibiotic targets. We believe this method could be expanded and implemented as a novel approach for antibiotic drug discovery.
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Affiliation(s)
- Xiao Jin
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Miseon Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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15
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Unver MY, Gierse RM, Ritchie H, Hirsch AKH. Druggability Assessment of Targets Used in Kinetic Target-Guided Synthesis. J Med Chem 2018; 61:9395-9409. [DOI: 10.1021/acs.jmedchem.8b00266] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Robin M. Gierse
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Harry Ritchie
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Helmholtz Institute for Pharmaceutical Research (HIPS) − Helmholtz Centre for Infection Research (HZI), Department for Drug Design and Optimization, Campus Building E 8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
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16
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Abstract
Cyclooxygenase-2 isozyme is a promising anti-inflammatory drug target, and overexpression of this enzyme is also associated with several cancers and neurodegenerative diseases. The amino-acid sequence and structural similarity between inducible cyclooxygenase-2 and housekeeping cyclooxygenase-1 isoforms present a significant challenge to design selective cyclooxygenase-2 inhibitors. Herein, we describe the use of the cyclooxygenase-2 active site as a reaction vessel for the in situ generation of its own highly specific inhibitors. Multi-component competitive-binding studies confirmed that the cyclooxygenase-2 isozyme can judiciously select most appropriate chemical building blocks from a pool of chemicals to build its own highly potent inhibitor. Herein, with the use of kinetic target-guided synthesis, also termed as in situ click chemistry, we describe the discovery of two highly potent and selective cyclooxygenase-2 isozyme inhibitors. The in vivo anti-inflammatory activity of these two novel small molecules is significantly higher than that of widely used selective cyclooxygenase-2 inhibitors.Traditional inflammation and pain relief drugs target both cyclooxygenase 1 and 2 (COX-1 and COX-2), causing severe side effects. Here, the authors use in situ click chemistry to develop COX-2 specific inhibitors with high in vivo anti-inflammatory activity.
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17
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In situ click chemistry generation of cyclooxygenase-2 inhibitors. Nat Commun 2017; 8:1. [PMID: 28232747 PMCID: PMC5431875 DOI: 10.1038/s41467-016-0009-6] [Citation(s) in RCA: 3217] [Impact Index Per Article: 459.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 11/14/2016] [Indexed: 12/18/2022] Open
Abstract
Cyclooxygenase-2 isozyme is a promising anti-inflammatory drug target, and overexpression of this enzyme is also associated with several cancers and neurodegenerative diseases. The amino-acid sequence and structural similarity between inducible cyclooxygenase-2 and housekeeping cyclooxygenase-1 isoforms present a significant challenge to design selective cyclooxygenase-2 inhibitors. Herein, we describe the use of the cyclooxygenase-2 active site as a reaction vessel for the in situ generation of its own highly specific inhibitors. Multi-component competitive-binding studies confirmed that the cyclooxygenase-2 isozyme can judiciously select most appropriate chemical building blocks from a pool of chemicals to build its own highly potent inhibitor. Herein, with the use of kinetic target-guided synthesis, also termed as in situ click chemistry, we describe the discovery of two highly potent and selective cyclooxygenase-2 isozyme inhibitors. The in vivo anti-inflammatory activity of these two novel small molecules is significantly higher than that of widely used selective cyclooxygenase-2 inhibitors. Traditional inflammation and pain relief drugs target both cyclooxygenase 1 and 2 (COX-1 and COX-2), causing severe side effects. Here, the authors use in situ click chemistry to develop COX-2 specific inhibitors with high in vivo anti-inflammatory activity.
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18
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Wang Y, Zhu J, Zhang L. Discovery of Cell-Permeable O-GlcNAc Transferase Inhibitors via Tethering in Situ Click Chemistry. J Med Chem 2016; 60:263-272. [DOI: 10.1021/acs.jmedchem.6b01237] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yue Wang
- School
of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Jingjing Zhu
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Lianwen Zhang
- College
of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and
Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, China
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19
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Biotin Protein Ligase Is a Target for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5030026. [PMID: 27463729 PMCID: PMC5039522 DOI: 10.3390/antibiotics5030026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
There is a desperate need for novel antibiotic classes to combat the rise of drug resistant pathogenic bacteria, such as Staphylococcus aureus. Inhibitors of the essential metabolic enzyme biotin protein ligase (BPL) represent a promising drug target for new antibacterials. Structural and biochemical studies on the BPL from S. aureus have paved the way for the design and development of new antibacterial chemotherapeutics. BPL employs an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5′-AMP from substrates biotin and ATP. Here we review the structure and catalytic mechanism of the target enzyme, along with an overview of chemical analogues of biotin and biotinyl-5′-AMP as BPL inhibitors reported to date. Of particular promise are studies to replace the labile phosphoroanhydride linker present in biotinyl-5′-AMP with alternative bioisosteres. A novel in situ click approach using a mutant of S. aureus BPL as a template for the synthesis of triazole-based inhibitors is also presented. These approaches can be widely applied to BPLs from other bacteria, as well as other closely related metabolic enzymes and antibacterial drug targets.
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20
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Glassford I, Teijaro CN, Daher SS, Weil A, Small MC, Redhu SK, Colussi DJ, Jacobson MA, Childers WE, Buttaro B, Nicholson AW, MacKerell AD, Cooperman BS, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry. J Am Chem Soc 2016; 138:3136-44. [PMID: 26878192 PMCID: PMC4785600 DOI: 10.1021/jacs.5b13008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over half of all antibiotics target the bacterial ribosome-nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semisynthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a 16-component reaction (i.e., azide 2 and 15 alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd values. Computational analysis using the site-identification by ligand competitive saturation (SILCS) approach indicated that the relative affinity of the ligands was associated with the alteration of macrolactone+desosamine-ribosome interactions caused by the different alkynes. Protein synthesis inhibition experiments confirmed the mechanism of action. Evaluation of the minimal inhibitory concentrations (MIC) quantified the potency of the in situ click products and demonstrated the efficacy of this method in the triaging and prioritization of potent antibiotics that target the bacterial ribosome. Cell viability assays in human fibroblasts confirmed 2 and four analogues with therapeutic indices for bactericidal activity over in vitro mammalian cytotoxicity as essentially identical to solithromycin (1).
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Affiliation(s)
- Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | | | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Amy Weil
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Meagan C. Small
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122
| | - Dennis J. Colussi
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Marlene A. Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Wayne E. Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140
| | | | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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21
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Kinetic target-guided synthesis in drug discovery and chemical biology: a comprehensive facts and figures survey. Future Med Chem 2016; 8:381-404. [DOI: 10.4155/fmc-2015-0007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
For the last 15 years, kinetic target-guided syntheses, including in situ click chemistry, have been used as alternative methods to find ligands to therapeutically relevant proteins. In this review, a comprehensive survey of biological targets used in kinetic target-guided synthesis covers historical and recent examples. The chemical reactions employed and practical aspects, including controls, library sizes and product detection, are presented. A particular focus is on the reagents and warhead selection and design with a critical overview of the challenges encountered. As protein supply remains a key success factor, it appears that increased efforts should be taken toward miniaturization in order to expand the scope of this strategy and qualify it as a fully fledged drug discovery tool.
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22
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Toguchi S, Hirose T, Yorita K, Fukui K, Sharpless KB, Ōmura S, Sunazuka T. In Situ Click Chemistry for the Identification of a Potent D-Amino Acid Oxidase Inhibitor. Chem Pharm Bull (Tokyo) 2016; 64:695-703. [DOI: 10.1248/cpb.c15-00867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shohei Toguchi
- Graduate School of Infection Control Sciences, Kitasato University
| | - Tomoyasu Hirose
- Graduate School of Infection Control Sciences, Kitasato University
- The Kitasato Institute for Life Sciences, Kitasato University
| | | | | | | | - Satoshi Ōmura
- The Kitasato Institute for Life Sciences, Kitasato University
| | - Toshiaki Sunazuka
- Graduate School of Infection Control Sciences, Kitasato University
- The Kitasato Institute for Life Sciences, Kitasato University
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23
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Hirose T, Sunazuka T, Ōmura S. Rapid Identification via <i>In Situ</i> Click Chemistry of a Novel Chitinase Inhibitor. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.1090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomoyasu Hirose
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Toshiaki Sunazuka
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University
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24
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Hu MH, Chen X, Chen SB, Ou TM, Yao M, Gu LQ, Huang ZS, Tan JH. A new application of click chemistry in situ: development of fluorescent probe for specific G-quadruplex topology. Sci Rep 2015; 5:17202. [PMID: 26603780 PMCID: PMC4658637 DOI: 10.1038/srep17202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 11/28/2022] Open
Abstract
Target-guided synthesis is an approach to drug discovery that allows the target to self-assemble its own binding agents. So far, target-guided synthesis and especially in situ click chemistry have attracted extensive attention and have led to the identification of highly potent inhibitors for proteins. In this study, we expand the application of in situ click chemistry and present a procedure using this approach to identify selective fluorescent probes for a specific topology of G-quadruplex nucleic acids, the parallel G-quadruplexes. On this basis, compound 15 assembled by triarylimidazole scaffold and carboxyl side chain was a positive hit, demonstrating highly potential in the sensitive and selective detection of parallel G-quadruplexes. Such selective fluorescence response can be rationalized in terms of different binding affinities between 15 and G-quadruplexes. Our work accordingly represents a new development towards the application of in situ click chemistry to develop selective fluorescent probes and may also shed light on the search for probes for a specific G-quadruplex topology.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Meicun Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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25
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Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice. Nat Commun 2015; 6:8250. [PMID: 26394692 PMCID: PMC4580987 DOI: 10.1038/ncomms9250] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer's disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes. Inhibiting insulin-degrading enzyme (IDE) has been proposed as a potential therapeutic strategy for the treatment of patients with diabetes. Here, the authors develop a novel IDE inhibitor but find that, surprisingly, IDE inhibition has negative effects on glucose tolerance in mice.
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26
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Sugawara A, Maita N, Gouda H, Yamamoto T, Hirose T, Kimura S, Saito Y, Nakano H, Kasai T, Nakano H, Shiomi K, Hirono S, Watanabe T, Taniguchi H, O̅mura S, Sunazuka T. Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase. J Med Chem 2015; 58:4984-97. [DOI: 10.1021/acs.jmedchem.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Akihiro Sugawara
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuo Maita
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Hiroaki Gouda
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tsuyoshi Yamamoto
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Saori Kimura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoshifumi Saito
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hayato Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takako Kasai
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hirofumi Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuro Shiomi
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuichi Hirono
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takeshi Watanabe
- Department
of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hisaaki Taniguchi
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Satoshi O̅mura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
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27
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Oueis E, Sabot C, Renard PY. New insights into the kinetic target-guided synthesis of protein ligands. Chem Commun (Camb) 2015; 51:12158-69. [DOI: 10.1039/c5cc04183j] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review describes the recent applications of the kinetic target guided synthesis and highlights the new advances of this strategy.
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Affiliation(s)
- Emilia Oueis
- Biomedical Sciences Research Council
- University of St. Andrews
- St. Andrews KY16 9ST
- UK
| | - Cyrille Sabot
- Normandie University
- COBRA
- UMR 6014 & FR 3038; Univ Rouen; INSA Rouen; CNRS
- Cedex
- France
| | - Pierre-Yves Renard
- Normandie University
- COBRA
- UMR 6014 & FR 3038; Univ Rouen; INSA Rouen; CNRS
- Cedex
- France
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28
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Murar CE, Thuaud F, Bode JW. KAHA Ligations That Form Aspartyl Aldehyde Residues as Synthetic Handles for Protein Modification and Purification. J Am Chem Soc 2014; 136:18140-8. [DOI: 10.1021/ja511231f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Claudia E. Murar
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
| | - Frédéric Thuaud
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Jeffrey W. Bode
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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29
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Hirose T. [Study on the discovery of novel chitinase inhibitors based on natural products]. YAKUGAKU ZASSHI 2014; 132:1001-10. [PMID: 23023416 DOI: 10.1248/yakushi.132.1001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chitin, the second most abundant polysaccharide in nature, is a constituent of fungal cell walls, the exoskeletons of crustaceans and insects and the microfilarial sheaths of parasitic nematodes. Chitin has, so far, not been found in mammals. Accumulation of chitin by organisms is modulated by chitin synthase-mediated biosynthesis and by chitinase-mediated hydrolytic degradation. Thus, chitinases are expected to be specific targets for antifungal, insecticidal and antiparasitic agents. Paradoxically, while chitin does not exist in mammals, human chitinase family members, such as acidic mammalian chitinase, have recently been described, and offer significant potential for the treatment of asthma and other related diseases in humans. This review covers the development of two chitinase inhibitors of natural origin, Argifin and Argadin, isolated from the cultured broth of microorganisms in our laboratory. In particular, the practical total synthesis of these natural products and discovery methods that generate only highly-active compounds using a kinetic target (chitinase)-guided synthesis approach (termed in situ click chemistry) are described.
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Affiliation(s)
- Tomoyasu Hirose
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan.
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30
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Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor. Proc Natl Acad Sci U S A 2013; 110:15892-7. [PMID: 24043811 DOI: 10.1073/pnas.1315049110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation.
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31
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Kazancioglu EA, Kazancioglu MZ, Fistikci M, Secen H, Altundas R. Photooxygenation of Azidoalkyl Furans: Catalyst-Free Triazole and New Endoperoxide Rearrangement. Org Lett 2013; 15:4790-3. [DOI: 10.1021/ol402163u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | - Meryem Fistikci
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
| | - Hasan Secen
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
| | - Ramazan Altundas
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
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32
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Millward SW, Agnew HD, Lai B, Lee SS, Lim J, Nag A, Pitram S, Rohde R, Heath JR. In situ click chemistry: from small molecule discovery to synthetic antibodies. Integr Biol (Camb) 2013; 5:87-95. [PMID: 22836343 DOI: 10.1039/c2ib20110k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Advances in the fields of proteomics, molecular imaging, and therapeutics are closely linked to the availability of affinity reagents that selectively recognize their biological targets. Here we present a review of Iterative Peptide In Situ Click Chemistry (IPISC), a novel screening technology for designing peptide multiligands with high affinity and specificity. This technology builds upon in situ click chemistry, a kinetic target-guided synthesis approach where the protein target catalyzes the conjugation of two small molecules, typically through the azide-alkyne Huisgen cycloaddition. Integrating this methodology with solid phase peptide libraries enables the assembly of linear and branched peptide multiligands we refer to as Protein Catalyzed Capture Agents (PCC Agents). The resulting structures can be thought of as analogous to the antigen recognition site of antibodies and serve as antibody replacements in biochemical and cell-based applications. In this review, we discuss the recent progress in ligand design through IPISC and related approaches, focusing on the improvements in affinity and specificity as multiligands are assembled by target-catalyzed peptide conjugation. We compare the IPISC process to small molecule in situ click chemistry with particular emphasis on the advantages and technical challenges of constructing antibody-like PCC Agents.
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Affiliation(s)
- Steven W Millward
- Department of Experimental Diagnostic Imaging, University of Texas MD Anderson Cancer Center, Experimental Diagnostic Imaging, Unit 603, P.O. Box 301402, Houston, TX 77230-1402, USA.
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33
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Wakasugi M, Gouda H, Hirose T, Sugawara A, Yamamoto T, Shiomi K, Sunazuka T, Ōmura S, Hirono S. Human acidic mammalian chitinase as a novel target for anti-asthma drug design using in silico screening. Bioorg Med Chem 2013; 21:3214-20. [PMID: 23623259 DOI: 10.1016/j.bmc.2013.03.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 11/29/2022]
Abstract
Human acidic mammalian chitinase (hAMCase) was recently shown to be involved in the development of asthma, suggesting a possible application for hAMCase inhibitors as novel therapeutic agents for asthma. We therefore initiated drug discovery research into hAMCase using a combination of in silico methodologies and a hAMCase assay system. We first selected 23 candidate hAMCase inhibitors from a database of four million compounds using a multistep screening system combining Tripos Topomer Search technology, a docking calculation and two-dimensional molecular similarity analysis. We then measured hAMCase inhibitory activity of the selected compounds and identified seven compounds with IC50 values ≤100 μM. A model describing the binding modes of these hit compounds to hAMCase was constructed, and we discuss the structure-activity relationships of the compounds we identified, suggested by the model and the actual inhibitory activities of the compounds.
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Affiliation(s)
- Masaki Wakasugi
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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34
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Oakdale JS, Fokin VV, Umezaki S, Fukuyama T. Preparation of 1,5-Disubstituted 1,2,3-Triazoles via Ruthenium-catalyzed Azide Alkyne Cycloaddition. ACTA ACUST UNITED AC 2013; 90:96-104. [PMID: 25253916 DOI: 10.15227/orgsyn.090.0096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Tieu W, Soares da Costa TP, Yap MY, Keeling KL, Wilce MCJ, Wallace JC, Booker GW, Polyak SW, Abell AD. Optimising in situ click chemistry: the screening and identification of biotin protein ligase inhibitors. Chem Sci 2013. [DOI: 10.1039/c3sc51127h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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36
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Tanaka K, Shirotsuki S, Iwata T, Kageyama C, Tahara T, Nozaki S, Siwu ERO, Tamura S, Douke S, Murakami N, Onoe H, Watanabe Y, Fukase K. Template-assisted and self-activating clicked peptide as a synthetic mimic of the SH2 domain. ACS Chem Biol 2012; 7:637-45. [PMID: 22239652 DOI: 10.1021/cb2003175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new synthetic strategy for obtaining artificial receptors that selectively regulate and/or control specific protein/protein interactions was developed based on the template-assisted and the self-activating click reaction applied to a combinatorial library. Synthetic mimics of the Grb2-SH2 domain, examined as a model case, selectively bound to a target signaling protein to induce cytotoxicity and inhibit tumor growth in vivo.
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Affiliation(s)
- Katsunori Tanaka
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Sanae Shirotsuki
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Takayuki Iwata
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Chika Kageyama
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Tsuyoshi Tahara
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Satoshi Nozaki
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Eric R. O. Siwu
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Satoru Tamura
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Shunsuke Douke
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Nobutoshi Murakami
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Hirotaka Onoe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Koichi Fukase
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
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37
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Biros S, Hof F. Supramolecular Approaches to Medicinal Chemistry. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Solution-phase total synthesis of the hydrophilic natural product argifin using 3,4,5-tris(octadecyloxy)benzyl tag. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.05.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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39
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40
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Kulkarni SS, Hu X, Doi K, Wang HG, Manetsch R. Screening of protein-protein interaction modulators via sulfo-click kinetic target-guided synthesis. ACS Chem Biol 2011; 6:724-32. [PMID: 21506574 DOI: 10.1021/cb200085q] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Kinetic target-guided synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting from a randomly designed library consisting of 9 thio acids and 9 sulfonyl azides leading to 81 potential acylsulfonamides, the target protein, Bcl-X(L), selectively assembled four PPIMs, acylsulfonamides SZ4TA2, SZ7TA2, SZ9TA1, and SZ9TA5, which have been shown to modulate Bcl-X(L)/BH3 interactions. To further investigate the Bcl-X(L) templation effect, control experiments were carried out using two mutants of Bcl-X(L). In one mutant, phenylalanine Phe131 and aspartic acid Asp133, which are critical for the BH3 domain binding, were substituted by alanines, while arginine Arg139, a residue identified to play a crucial role in the binding of ABT-737, a BH3 mimetic, was replaced by an alanine in the other mutant. Incubation of these mutants with the reactive fragments and subsequent LC/MS-SIM analysis confirmed that these building block combinations yield the corresponding acylsulfonamides at the BH3 binding site, the actual "hot spot" of Bcl-X(L). These results validate kinetic TGS using the sulfo-click reaction as a valuable tool for the straightforward identification of high-quality PPIMs.
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Affiliation(s)
- Sameer S. Kulkarni
- Department of Chemistry, University of South Florida, CHE 205, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Xiangdong Hu
- Department of Chemistry, University of South Florida, CHE 205, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Kenichiro Doi
- Department of Pharmacology and Penn State Hershey Cancer Institute, Penn State College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, United States
| | - Hong-Gang Wang
- Department of Pharmacology and Penn State Hershey Cancer Institute, Penn State College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, United States
| | - Roman Manetsch
- Department of Chemistry, University of South Florida, CHE 205, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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41
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Uhlig N, Li CJ. Alkynes as an eco-compatible “on-call” functionality orthogonal to biological conditions in water. Chem Sci 2011. [DOI: 10.1039/c1sc00164g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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42
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Gouda H, Sunazuka T, Hirose T, Iguchi K, Yamaotsu N, Sugawara A, Noguchi Y, Saito Y, Yamamoto T, Watanabe T, Shiomi K, Ōmura S, Hirono S. NMR spectroscopy and computational analysis of interaction between Serratia marcescens chitinase B and a dipeptide derived from natural-product cyclopentapeptide chitinase inhibitor argifin. Bioorg Med Chem 2010; 18:5835-44. [DOI: 10.1016/j.bmc.2010.06.093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 06/25/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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43
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Ikeda K, Ikawa K, Aoki S, Morikawa N, Takahashi S, Tsukamoto T. LC Determination of Total Cefotiam Concentration in Human Serum: Application of Ultrafiltration to a High Protein-Binding Drug. Chromatographia 2010. [DOI: 10.1365/s10337-010-1613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Affiliation(s)
- Timothy J. Ward
- Millsaps College, 1701 N. State Street, Box 150306, Jackson, Mississippi 39210
| | - Karen D. Ward
- Millsaps College, 1701 N. State Street, Box 150306, Jackson, Mississippi 39210
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45
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Mamidyala SK, Finn MG. In situ click chemistry: probing the binding landscapes of biological molecules. Chem Soc Rev 2010; 39:1252-61. [PMID: 20309485 DOI: 10.1039/b901969n] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Combinatorial approaches to the discovery of new functional molecules are well established among chemists and biologists, inspired in large measure by the modular composition of many systems and molecules in Nature. Many approaches rely on the synthesis and testing of individual members of a candidate combinatorial library, but attention has also been paid to techniques that allow the target to self-assemble its own binding agents. These fragment-based methods, grouped under the general heading of target-guided synthesis (TGS), show great promise in lead discovery applications. In this tutorial review, we review the use of the 1,3-dipolar cycloaddition reaction of organic azides and alkynes in a kinetically-controlled TGS approach, termed in situ click chemistry. The azide-alkyne reaction has several distinct advantages, most notably high chemoselectivity, very low background ligation rates, facile synthetic accessibility, and the stability and properties of the 1,2,3-triazole products. Examples of the discovery of potent inhibitors of acetylcholinesterases, carbonic anhydrase, HIV-protease, and chitinase are described, as are methods for the templated assembly of agents that bind DNA and proteins.
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Affiliation(s)
- Sreeman K Mamidyala
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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46
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Hirose T, Sunazuka T, Ōmura S. Recent development of two chitinase inhibitors, Argifin and Argadin, produced by soil microorganisms. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:85-102. [PMID: 20154467 PMCID: PMC3417560 DOI: 10.2183/pjab.86.85] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Chitin, the second most abundant polysaccharide in nature, occurs in fungi, some algae and many invertebrates, including insects. Thus, chitin synthesis and degradation could represent specific targets for fungicides and insecticides. Chitinases hydrolyze chitin into oligomers of N-acetyl-D-glucosamine at key points in the life cycles of organisms, consequently, chitinase inhibitors have become subject of increasing interest. This review covers the development of two chitinase inhibitors of natural origin, Argifin and Argadin, isolated from the cultured broth of microorganisms in our laboratory. In particular, the practical total synthesis of these natural products, the synthesis of lead compounds via computer-aided rational molecular design, and discovery methods that generate only highly-active compounds using a kinetic target(chitinase)-guided synthesis approach (termed in situ click chemistry) are described.
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Affiliation(s)
- Tomoyasu Hirose
- The Kitasato Institute, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Toshiaki Sunazuka
- The Kitasato Institute, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
- Correspondence should be addressed: T. Sunazuka and S. Ōmura, The Kitasato Institute and Kitasato Institute for Life Science and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan (e-mail: and )
| | - Satoshi Ōmura
- The Kitasato Institute, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
- Correspondence should be addressed: T. Sunazuka and S. Ōmura, The Kitasato Institute and Kitasato Institute for Life Science and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan (e-mail: and )
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47
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La Clair JJ. Natural product mode of action (MOA) studies: a link between natural and synthetic worlds. Nat Prod Rep 2010; 27:969-95. [DOI: 10.1039/b909989c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Hirose T, Sunazuka T, Sugawara A, Noguchi Y, Tanaka T, Iguchi K, Yamamoto T, Gouda H, Shiomi K, Ōmura S. Solid-phase total synthesis of the chitinase inhibitor Argadin using a supported acetal resin. J Antibiot (Tokyo) 2009; 62:495-500. [DOI: 10.1038/ja.2009.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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