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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024. [PMID: 38411278 DOI: 10.1039/d3np00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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2
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Wagh SB, Maslivetc VA, La Clair JJ, Kornienko A. Lessons in Organic Fluorescent Probe Discovery. Chembiochem 2021; 22:3109-3139. [PMID: 34062039 PMCID: PMC8595615 DOI: 10.1002/cbic.202100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/22/2021] [Indexed: 02/03/2023]
Abstract
Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - Vladimir A Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - James J La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1062, USA
| | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
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Doraghi F, Kianmehr E, Foroumadi A. Metal-free regioselective C5-cyanoalkylation of the 8-aminoquinolineamides/sulfonamides via oxidative cross-dehydrogenative coupling with alkylnitriles. Org Chem Front 2021. [DOI: 10.1039/d1qo00570g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A practical, versatile and Metal-free regioselective C5-cyanoalkylation of the 8-aminoquinolineamides/sulfonamides with acetonitrile has been described.
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Affiliation(s)
- Fatemeh Doraghi
- School of Chemistry, College of Science, University of Tehran, Tehran 1417614411, Iran
| | - Ebrahim Kianmehr
- School of Chemistry, College of Science, University of Tehran, Tehran 1417614411, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
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4
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Affiliation(s)
- Bhuttu Khan
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Himangsu Sekhar Dutta
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Dipankar Koley
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
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Beuzer P, La Clair JJ, Cang H. Color-Coded Super-Resolution Small-Molecule Imaging. Chembiochem 2016; 17:999-1003. [PMID: 26994590 PMCID: PMC5291120 DOI: 10.1002/cbic.201600013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 12/15/2022]
Abstract
Although the development of super-resolution microscopy dates back to 1994, its applications have been primarily focused on visualizing cellular structures and targets, including proteins, DNA and sugars. We now report on a system that allows both monitoring of the localization of exogenous small molecules in live cells at low resolution and subsequent super-resolution imaging by using stochastic optical reconstruction microscopy (STORM) on fixed cells. This represents a powerful new tool to understand the dynamics of subcellular trafficking associated with the mode and mechanism of action of exogenous small molecules.
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Affiliation(s)
- Paolo Beuzer
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James J La Clair
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1052, USA.
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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Park KY, Song HJ, Heo JN. Proline-Catalyzed Cyclization Reaction for the Synthesis of Naphthostyrils: Application to the Total Synthesis of Prioline. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Álvarez-Micó X, Rocha DD, Guimarães LA, Ambrose A, Chapman E, Costa-Lotufo LV, La Clair JJ, Fenical W. The Hybrid Pyrroloisoindolone-Dehydropyrrolizine Alkaloid (-)-Chlorizidine A Targets Proteins within the Glycolytic Pathway. Chembiochem 2015; 16:2002-6. [PMID: 26267855 DOI: 10.1002/cbic.201500229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/25/2023]
Abstract
The cytotoxic activity of (-)-chlorizidine A, a marine alkaloid containing a unique fusion between a pyrroloisoindolone and dehydropyrrolizine, was explored by using a combination of cellular and molecular methods. Our studies began by applying preliminary SAR evidence gathered from semisynthetic bioactivity evaluations to prepare an active immunoaffinity fluorescent (IAF) probe. This probe was then used to identify two cytosolic proteins, GAPDH and hENO1, as the targets of (-)-chlorizidine A.
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Affiliation(s)
- Xavier Álvarez-Micó
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0204, USA
| | - Danilo D Rocha
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil
| | - Larissa A Guimarães
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil
| | - Andrew Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, P.O. Box 210207, Tucson, AZ, 85721, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, P.O. Box 210207, Tucson, AZ, 85721, USA
| | - Leticia V Costa-Lotufo
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, 60.430-270, Brazil.,Departamento de Farmacologia, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0358, USA.
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0204, USA.
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Liu Y, Zhang JL, Song RJ, Qian PC, Li JH. Cascade Nitration/Cyclization of 1,7-Enynes withtBuONO and H2O: One-Pot Self-Assembly of Pyrrolo[4,3,2-de]quinolinones. Angew Chem Int Ed Engl 2014; 53:9017-20. [DOI: 10.1002/anie.201404192] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 01/12/2023]
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Liu Y, Zhang JL, Song RJ, Qian PC, Li JH. Cascade Nitration/Cyclization of 1,7-Enynes withtBuONO and H2O: One-Pot Self-Assembly of Pyrrolo[4,3,2-de]quinolinones. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404192] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Cheng YB, Jensen PR, Fenical W. Cytotoxic and Antimicrobial Napyradiomycins from Two Marine-Derived, MAR 4 Streptomyces Strains. European J Org Chem 2013; 2013. [PMID: 24376369 DOI: 10.1002/ejoc.201300349] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cancer cell cytotoxicity-guided fractionation of the acetone extracts of two cultured marine-derived Streptomyces strains belonging to the MAR4 group yielded six new napyradiomycins, compounds A-F (1-6), together with three known compounds, napyradiomycins B2-B4 (7-9). Napyradiomycins 1-4 are new members of the napyradiomycin "C type" meroterpenoids that possess a linear monoterpene moiety bridging between C-7 and C-10a. Compound 4 has an additional tetrahydropyran ring fused to the phenol moiety. Compounds 5-9 are related to the napyradiomycin "B type" meroterpenoids. The structures of all new compounds were assigned by interpretation of 1D and 2D NMR, MS and other spectroscopic data. The relative configurations were assigned based upon interpretation of ROESY 2D NMR experiments. The cytotoxicity of 1-9 against the human colon carcinoma cell line HCT-116, and their antibacterial activities against Methicillin-resistant Staphylococcus aureus (MRSA) are presented.
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Affiliation(s)
- Yuan-Bin Cheng
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0204 USA, , Homepage: http://sio.ucsd.edu/Profile/wfenical
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0204 USA, , Homepage: http://sio.ucsd.edu/Profile/wfenical
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0204 USA, , Homepage: http://sio.ucsd.edu/Profile/wfenical
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Moldovan RP, Zöllinger M, Jones PG, Kelter G, Fiebig HH, Lindel T. Synthesis and Cytotoxicity of Ring C-Functionalized Derivatives of the Marine Natural Product (-)-Dibromophakellstatin. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101175] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Vera B, Rodríguez AD, La Clair JJ. Aplysqualenol A binds to the light chain of dynein type 1 (DYNLL1). Angew Chem Int Ed Engl 2011; 50:8134-8. [PMID: 21744448 DOI: 10.1002/anie.201102546] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 01/29/2023]
Abstract
A bidirectional affinity system has been developed for the identification of cancer-related natural products and their biological targets. Aplysqualenol A is thus selectively identified as a ligand of the dynein light chain. The use of forward and reverse affinity methods suggests that both small-molecule isolation and target identification can be conducted using conventional molecular biological methods.
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Affiliation(s)
- Brunilda Vera
- Department of Chemistry, University of Puerto Rico, UPR Station, San Juan, 00931-3346, USA
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Zurwerra D, Wullschleger CW, Altmann KH. Wertvolles aus der Tiefe des Meeres: die Entdeckung und Totalsynthese der Ammosamide. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zurwerra D, Wullschleger CW, Altmann KH. Treasures from the Sea: Discovery and Total Synthesis of Ammosamides. Angew Chem Int Ed Engl 2010; 49:6936-8. [DOI: 10.1002/anie.201002788] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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