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Kim KE, Comber JR, Pursel AJ, Hobby GC, McCormick CJ, Fisher MF, Marasa K, Perry B. Modular and divergent synthesis of 2, N3-disubstituted 4-quinazolinones facilitated by regioselective N-alkylation. Org Biomol Chem 2024; 22:4940-4949. [PMID: 38809109 DOI: 10.1039/d4ob00564c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The synthesis of a biologically relevant 2-amino-N3-alkylamido 4-quinazolinone has been accomplished in four steps from commercially available materials using design principles from both modular and divergent synthesis. N3-Alkylation of 2-chloro-4(3H)-quinazolinone using methyl bromoacetate, followed by C2-amination produced a suitable scaffold for introducing molecular diversity. Optimization of alkylation conditions afforded full regioselectivity, enabling exclusive access to the N-alkylated isomer. Subsequent C2-amination using piperidine, pyrrolidine, or diethylamine, followed by amide bond formation using variously substituted phenethylamines, generated fifteen unique 4-quinazolinones bearing C2-amino and N3-alkylamido substituents. These efforts highlight the reciprocal influence of C2 and N3 substitution on functionalization at either position, establish an effective synthetic pathway toward 2,N3-disubstituted 4-quinazolinones, and enable preliminary bioactivity studies while providing an experiential learning opportunity for undergraduate student researchers.
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Affiliation(s)
- Kelly E Kim
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Jason R Comber
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Alexander J Pursel
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Grant C Hobby
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Carter J McCormick
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Matthew F Fisher
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Kyle Marasa
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, WA 98402, USA.
| | - Benjamin Perry
- Drugs for Neglected Diseases initiative, Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
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2
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Chen Y, Xu Y, Dai J, Ni W, Ding Q, Wu X, Fang J, Wu Y. Research trends in chemogenetics for neuroscience in recent 14 years: A bibliometric study in CiteSpace. Medicine (Baltimore) 2023; 102:e35291. [PMID: 37800804 PMCID: PMC10552966 DOI: 10.1097/md.0000000000035291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Chemogenetics has been widely adopted in Neuroscience. Neuroscience has become a hot research topic for scientists. Therefore, the purpose of this study is to explore the current status and trends in the global application of chemogenetics in neuroscience over the last 14 years via CiteSpace. METHODS Publications related to chemogenetics in neuroscience were retrieved from the Science Citation Index-Extended Web of Science from 2008 to 2021. We used CiteSpace to analyze publications, citations, cited journals, countries, institutions, authors, cited authors, cited references, and keywords. RESULTS A total of 947 records were retrieved from 2008 to 2021 on February 21, 2022. The number and rate of publications and citations increased significantly. Journal of Neuroscience was the most cited journal, and BRAIN RES BULL ranked first in the centrality of cited journals. The United States of America (USA) had the highest number of publications among the countries. Takashi Minamoto was the most prolific author and Armbruster BN ranked the first among authors cited. The first article in the frequency ranking of the references cited was published by Roth BL. The keyword of "nucleus accumben (NAc)" had the highest frequency. The top 3 keywords with the strongest citation bursts include "transgenic mice," "cancer," and "blood-brain barrier." CONCLUSION The period 2008 to 2021 has seen a marked increase in research on chemogenetics in neuroscience. The application of chemogenetics is indispensable for research in the field of neuroscience. This bibliometrics study provides the current situation and trend in chemogenetic methods in neuroscience in recent 14 years, which may help researchers to identify the hot topics and frontiers for future studies in this field.
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Affiliation(s)
- Yuerong Chen
- Key Laboratory of Acupuncture and Neurology of Zhejiang Province, The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yunyun Xu
- Key Laboratory of Acupuncture and Neurology of Zhejiang Province, The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiale Dai
- Key Laboratory of Acupuncture and Neurology of Zhejiang Province, The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenqin Ni
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qike Ding
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xinyuan Wu
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianqiao Fang
- Key Laboratory of Acupuncture and Neurology of Zhejiang Province, The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuanyuan Wu
- Key Laboratory of Acupuncture and Neurology of Zhejiang Province, The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- The Third School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
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3
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Tan HY, Liang FM, Zhang WJ, Zhang Y, Cui JH, Dai YY, Qiu XM, Wang WH, Zhou Y, Chen DP, Li CP. Novel 2-Amino-1,4-Naphthoquinone Derivatives Induce A549 Cell Death through Autophagy. Molecules 2023; 28:molecules28083289. [PMID: 37110525 PMCID: PMC10143525 DOI: 10.3390/molecules28083289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
A series of 1,4-naphthoquinone derivatives containing were synthesized as anti-cancer agents and the crystal structure of compound 5a was confirmed by X-ray diffraction. In addition, the inhibitory activities against four cancer cell lines (HepG2, A549, K562, and PC-3) were tested, respectively, and compound 5i showed significant cytotoxicity on the A549 cell line with the IC50 of 6.15 μM. Surprisingly, in the following preliminary biological experiments, we found that compound 5i induced autophagy by promoting the recycling of EGFR and signal transduction in the A549 cell, resulting in the activation of the EGFR signal pathway. The potential binding pattern between compound 5i and EGFR tyrosine kinase (PDB ID: 1M17) was also identified by molecular docking. Our research paves the way for further studies and the development of novel and powerful anti-cancer drugs.
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Affiliation(s)
- Hua-Yuan Tan
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Feng-Ming Liang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Wen-Jing Zhang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Yi Zhang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Jun-Hao Cui
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Yu-Yu Dai
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Xue-Mei Qiu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Wen-Hang Wang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Yue Zhou
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang 550025, China
| | - Dan-Ping Chen
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang 550025, China
| | - Cheng-Peng Li
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang 550025, China
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4
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Lim D, Zhou Q, Cox KJ, Law BK, Lee M, Kokkonda P, Sreekanth V, Pergu R, Chaudhary SK, Gangopadhyay SA, Maji B, Lai S, Amako Y, Thompson DB, Subramanian HKK, Mesleh MF, Dančík V, Clemons PA, Wagner BK, Woo CM, Church GM, Choudhary A. A general approach to identify cell-permeable and synthetic anti-CRISPR small molecules. Nat Cell Biol 2022; 24:1766-1775. [PMID: 36396978 PMCID: PMC9891305 DOI: 10.1038/s41556-022-01005-8] [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: 09/16/2021] [Accepted: 09/02/2022] [Indexed: 11/18/2022]
Abstract
The need to control the activity and fidelity of CRISPR-associated nucleases has resulted in a demand for inhibitory anti-CRISPR molecules. The small-molecule inhibitor discovery platforms available at present are not generalizable to multiple nuclease classes, only target the initial step in the catalytic activity and require high concentrations of nuclease, resulting in inhibitors with suboptimal attributes, including poor potency. Here we report a high-throughput discovery pipeline consisting of a fluorescence resonance energy transfer-based assay that is generalizable to contemporary and emerging nucleases, operates at low nuclease concentrations and targets all catalytic steps. We applied this pipeline to identify BRD7586, a cell-permeable small-molecule inhibitor of SpCas9 that is twofold more potent than other inhibitors identified to date. Furthermore, unlike the reported inhibitors, BRD7586 enhanced SpCas9 specificity and its activity was independent of the genomic loci, DNA-repair pathway or mode of nuclease delivery. Overall, these studies describe a general pipeline to identify inhibitors of contemporary and emerging CRISPR-associated nucleases.
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Affiliation(s)
- Donghyun Lim
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul, South Korea
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Benjamin K Law
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Miseon Lee
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Soumyashree A Gangopadhyay
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Sophia Lai
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David B Thompson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California-Riverside, Riverside, CA, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA.
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Dryopteris juxtapostia Root and Shoot: Determination of Phytochemicals; Antioxidant, Anti-Inflammatory, and Hepatoprotective Effects; and Toxicity Assessment. Antioxidants (Basel) 2022; 11:antiox11091670. [PMID: 36139744 PMCID: PMC9495791 DOI: 10.3390/antiox11091670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
An estimated 450 species of Dryopteris in the Dryoperidaceae family grow in Japan, North and South Korea, China, Pakistan, and Kashmir. This genus has been reported to have biological capabilities; however, research has been conducted on Dryopteris juxtapostia. Therefore, with the present study, we aimed to exploring the biological potential of D. juxtapostia root and shoot extracts. We extracted dichloromethane and methanol separately from the roots and shoots of D. juxtapostia. Antioxidant activity was determined using DPPH, FRAP, and H2O2 assays, and anti-inflammatory activities were evaluated using both in vitro (antiurease activity) and in vivo (carrageenan- and formaldehyde-induced paw edema) studies. Toxicity was evaluated by adopting a brine shrimp lethality assay followed by determination of cytotoxic activity using an MTT assay. Hepatoprotective effects of active crude extracts were examined in rats. Activity-bearing compounds were tentatively identified using LC-ESI-MS/MS analysis. Results suggested that D. juxtapostia root dichloromethane extract exhibited better antioxidant (DPPH, IC50 of 42.0 µg/mL; FRAP, 46.2 mmol/g; H2O2, 71% inhibition), anti-inflammatory (urease inhibition, 56.7% at 50 µg/mL; carrageenan-induced edema inhibition, 61.7% at 200 µg/mL; formaldehyde-induced edema inhibition, 67.3% at 200 µg/mL), brine shrimp % mortality (100% at 1000 µg/mL), and cytotoxic (HeLa cancer, IC50 of 17.1 µg/mL; prostate cancer (PC3), IC50 of 45.2 µg/mL) effects than D. juxtapostia root methanol extract. D. juxtapostia shoot dichloromethane and methanol extracts exhibited non-influential activity in all biological assays and were not selected for hepatoprotective study. D. juxtapostia root methanol extract showed improvement in hepatic cell structure and low cellular infiltration but, in contrast the dichloromethane extract, did not show any significant improvement in hepatocyte morphology, cellular infiltration, or necrosis of hepatocytes in comparison to the positive control, i.e., paracetamol. LC-ESI-MS/MS analysis showed the presence of albaspidin PP, 3-methylbutyryl-phloroglucinol, flavaspidic acid AB and BB, filixic acid ABA and ABB, tris-desaspidin BBB, tris-paraaspidin BBB, tetra-flavaspidic BBBB, tetra-albaspidin BBBB, and kaempferol-3-O-glucoside in the dichloromethane extract, whereas kaempferol, catechin, epicatechin, quinic acid, liquitrigenin, and quercetin 7-O-galactoside in were detected in the methanol extract, along with all the compounds detected in the dichloromethane extract. Hence, D. juxtapostia is safe, alongside other species of this genus, although detailed safety assessment of each isolated compound is obligatory during drug discovery.
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6
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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7
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Choi Y, Lee S, Kim H, Park SB. Design and Synthesis of Conformationally Diverse Pyrimidine-Embedded Medium/Macro- and Bridged Cycles via Skeletal Transformation. Front Chem 2022; 10:841250. [PMID: 35444999 PMCID: PMC9014854 DOI: 10.3389/fchem.2022.841250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
The rigidity and flexibility of small molecules are complementary in 3-dimensional ligand-protein interaction. Therefore, the chemical library with conformational diversity would be a valuable resource for investigating the influence of skeletal flexibility on the biological system. In this regard, we designed and synthesized ten conformationally diverse pyrimidine-embedded medium/macro- and bridged cyclic scaffolds covering 7- to 14-member rings via an efficient skeletal transformation strategy. Their high conformational and shape diversity was confirmed by chemoinformatic analysis.
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Affiliation(s)
- Yoona Choi
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Subin Lee
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Heejun Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
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8
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Recent Advances in Divergent Synthetic Strategies for Indole-Based Natural Product Libraries. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072171. [PMID: 35408569 PMCID: PMC9000743 DOI: 10.3390/molecules27072171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/26/2023]
Abstract
Considering the potential bioactivities of natural product and natural product-like compounds with highly complex and diverse structures, the screening of collections and small-molecule libraries for high-throughput screening (HTS) and high-content screening (HCS) has emerged as a powerful tool in the development of novel therapeutic agents. Herein, we review the recent advances in divergent synthetic approaches such as complexity-to-diversity (Ctd) and biomimetic strategies for the generation of structurally complex and diverse indole-based natural product and natural product-like small-molecule libraries.
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9
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Lv S. Research fronts of Chemical Biology. PURE APPL CHEM 2021. [DOI: 10.1515/pac-2020-1004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Over the past decades, researchers have witnessed substantially increasing and ever-growing interests and efforts in Chemical Biology studies, thanks to the development of genome and epi-genome sequencing (revealing potential drug targets), synthetic chemistry (producing new medicines), bioorthogonal chemistry (chemistry in living systems) and high-throughput screening technologies (in vitro cell systems, protein binding assays and phenotypic assays). This report presents literature search results for current research in Chemical Biology, to explore basic principles, summarize recent advances, identify key challenges, and provide suggestions for future research (with a focus on Chemical Biology in the context of human health and diseases). Chemical Biology research can positively contribute to delivering a better understanding of the molecular and cellular mechanisms that accompany pathology underlying diseases, as well as developing improved methods for diagnosis, drug discovery, and therapeutic delivery. While much progress has been made, as shown in this report, there are still further needs and opportunities. For instance, pressing challenges still exist in selecting appropriate targets in biological systems and adopting more rational design strategies for the development of innovative and sustainable diagnostic technologies and medical treatments. Therefore, more than ever, researchers from different disciplines need to collaborate to address the challenges in Chemical Biology.
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Affiliation(s)
- Shanshan Lv
- State Key Laboratory of Organic-Inorganic Composite Materials , Beijing University of Chemical Technology , Beijing , , China
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10
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Kim KE, Kim AN, McCormick CJ, Stoltz BM. Late-Stage Diversification: A Motivating Force in Organic Synthesis. J Am Chem Soc 2021; 143:16890-16901. [PMID: 34614361 PMCID: PMC9285880 DOI: 10.1021/jacs.1c08920] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interest in therapeutic discovery typically drives the preparation of natural product analogs, but these undertakings contribute significant advances for synthetic chemistry as well. The need for a highly efficient and scalable synthetic route to a complex molecular scaffold for diversification frequently inspires new methodological development or unique application of existing methods on structurally intricate systems. Additionally, synthetic planning with an aim toward late-stage diversification can provide access to otherwise unavailable compounds or facilitate preparation of complex molecules with diverse patterns of substitution around a shared carbon framework. For these reasons among others, programs dedicated to the diversification of natural product frameworks and other complex molecular scaffolds have been increasing in popularity, a trend likely to continue given their fruitfulness and breadth of impact. In this Perspective, we discuss our experience using late-stage diversification as a guiding principle for the synthesis of natural product analogs and reflect on the impact such efforts have on the future of complex molecule synthesis.
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Affiliation(s)
- Kelly E Kim
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, Washington 98402, United States
| | - Alexia N Kim
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Carter J McCormick
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, Washington 98402, United States
| | - Brian M Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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11
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Camacho CM, Pizzio MG, Roces DL, Boggián DB, Mata EG, Bellizzi Y, Barrionuevo E, Blank VC, Roguin LP. Design, synthesis and cytotoxic evaluation of a library of oxadiazole-containing hybrids. RSC Adv 2021; 11:29741-29751. [PMID: 35479556 PMCID: PMC9040754 DOI: 10.1039/d1ra05602f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/20/2021] [Indexed: 11/30/2022] Open
Abstract
The development of hybrid compounds led to the discovery of new pharmacologically active agents for some of the most critical diseases, including cancer. Herein, we describe a new series of oxadiazole-containing structures designed by a molecular hybridization approach. Penicillin derivatives and amino acids were linked to amino acid and aromatic moieties through the formation of a 1,2,4-oxadiazole ring. Alternatively, condensation between amino acid-derived hydrazides and an activated penicillanic acid led to a series of 1,3,4-oxadiazole penicillin-containing hybrids and non-cyclized diacylhydrazides. From the cytotoxicity assays it is highlighted that two 1,2,4-oxadiazoles and one 1,3,4-oxadiazole connecting a penicillin and aliphatic amino acids displayed a high degree of cytotoxic selectivity, ranging between being three and four times more potent against tumor cells than normal cells. The results give a very interesting perspective suggesting that these hybrid compounds can offer a novel antitumor scaffold with promising cytotoxicity profiles. Synthesized hybrids of 1,2,4-oxadiazole and 1,3,4-oxadiazole connecting a penicillin and aliphatic amino acids displayed a high degree of cytotoxic selectivity.![]()
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Affiliation(s)
- Cristián M. Camacho
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Marianela G. Pizzio
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - David L. Roces
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Dora B. Boggián
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Ernesto G. Mata
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Yanina Bellizzi
- Instituto de Química y Fisicoquímica Biológicas (UBA – CONICET), Facultad de Farmacia y Bioquímica, UBA, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Elizabeth Barrionuevo
- Instituto de Química y Fisicoquímica Biológicas (UBA – CONICET), Facultad de Farmacia y Bioquímica, UBA, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Viviana C. Blank
- Instituto de Química y Fisicoquímica Biológicas (UBA – CONICET), Facultad de Farmacia y Bioquímica, UBA, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Leonor P. Roguin
- Instituto de Química y Fisicoquímica Biológicas (UBA – CONICET), Facultad de Farmacia y Bioquímica, UBA, Junín 956, C1113AAD Buenos Aires, Argentina
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12
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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13
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Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD. Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD. ACS Chem Biol 2020; 15:3112-3123. [PMID: 33196168 DOI: 10.1021/acschembio.0c00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), collectively named c9ALS/FTD, are triggered by hexanucleotide GGGGCC repeat expansions [r(G4C2)exp] within the C9orf72 gene. In these diseases, neuronal loss occurs through an interplay of deleterious phenotypes, including r(G4C2)exp RNA gain-of-function mechanisms. Herein, we identified a benzimidazole derivative, CB096, that specifically binds to a repeating 1 × 1 GG internal loop structure, 5'CGG/3'GGC, that is formed when r(G4C2)exp folds. Structure-activity relationship (SAR) studies and molecular dynamics (MD) simulations were used to define the molecular interactions formed between CB096 and r(G4C2)exp that results in the rescue of disease-associated pathways. Overall, this study reveals a unique structural feature within r(G4C2)exp that can be exploited for the development of lead medicines and chemical probes.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kye Won Wang
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, Florida 32224, United States
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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14
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Design and synthesis of nature-inspired chromenopyrroles as potential modulators of mitochondrial metabolism. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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An Z, Zhao Z, Zhao L, Yue Q, Li K, Zhao B, Miao J, Su L. The novel HOCl fluorescent probe CAN induced A549 apoptosis by inhibiting chlorination activity of MPO. Bioorg Med Chem Lett 2020; 30:127394. [PMID: 32717611 DOI: 10.1016/j.bmcl.2020.127394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022]
Abstract
Hypochlorous acid (HOCl) is an important signaling molecule for cell survival. However, it has been reported that excessive HOCl contributes to a variety of diseases such as cancers. And in cancer cells, the level of HOCl is much higher than that in normal cells. Here a coumarin-based fluorescent probe 7-Diethylamino-3-(2,3-dihydro-1H-perimidin-2-yl)-chromen-2-one (CAN) was successfully developed for HOCl detection. The probe could be oxidized by HOCl to induce significant change in its fluorescence profile, which made it feasible for ratiometric detecting HOCl. CAN (below 1 µM) did not affect cell viability and had good capacity in ratiometric detection of HOCl in RAW 264.7 cells. CAN induced A549 apoptosis and inhibited tumor growth in vitro and in vivo. And CAN could decrease the chlorination activity of myeloperoxidase (MPO) in A549. These findings suggested that CAN (below 1 µM) would develop into a HOCl probe. High activity of MPO and level of HOCl might be helpful for A549 survival. A549 could be induced apoptosis by reducing the HOCl level by CAN. It implies a new anticancer strategy by targeting HOCl.
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Affiliation(s)
- Zaiyong An
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Zhimin Zhao
- Institute of Developmental Biology, School of Life Science, Shandong University, Qingdao 266237, China
| | - Lin Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Qiulin Yue
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Kunlun Li
- Jinan Hangchen Biotechnology Co., Ltd., Jinan 250353, China
| | - Baoxiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Junying Miao
- Institute of Developmental Biology, School of Life Science, Shandong University, Qingdao 266237, China
| | - Le Su
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
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16
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Finding the mechanism of esterase D activation by a small molecule. Bioorg Med Chem Lett 2020; 30:127150. [DOI: 10.1016/j.bmcl.2020.127150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/20/2020] [Accepted: 03/27/2020] [Indexed: 11/24/2022]
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17
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Solinski AE, Scharnow AM, Fraboni AJ, Wuest WM. Synthetic Simplification of Carolacton Enables Chemical Genetic Studies in Streptococcus mutans. ACS Infect Dis 2019; 5:1480-1486. [PMID: 31243986 PMCID: PMC7169375 DOI: 10.1021/acsinfecdis.9b00213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the broader biological impact of carolacton, a macrolactone natural product, has been ongoing for the past decade. Multiple studies have shown connections to regulatory systems, acid tolerance mechanisms, biofilm formation, and recently folate dehydrogenase (FolD). Progress elucidating the cause of biofilm-specific activity in Streptococcus mutans has been limited due to low-throughput analyses of carolacton-treated cells. We disclose the discovery of a simplified carolacton-inspired analog that demonstrates inhibitory activity against S. mutans biofilm cells. This discovery permitted a proof of concept chemical genetic screen of S. mutans mutants identifying the carbon catabolite protein A signaling pathway as a putative target.
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Affiliation(s)
- Amy E. Solinski
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Amber M. Scharnow
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Americo J. Fraboni
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- Emory Antibiotic Resistance Center, Emory University School of Medicine, 201 Dowman Drive, Atlanta, Georgia 30322, United States
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18
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Iegre J, Brear P, Baker DJ, Tan YS, Atkinson EL, Sore HF, O' Donovan DH, Verma CS, Hyvönen M, Spring DR. Efficient development of stable and highly functionalised peptides targeting the CK2α/CK2β protein-protein interaction. Chem Sci 2019; 10:5056-5063. [PMID: 31183056 PMCID: PMC6530537 DOI: 10.1039/c9sc00798a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be applied to many PPI targets and has the potential to ease the study of PPIs by efficiently providing access to functionalised peptides.
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Affiliation(s)
- Jessica Iegre
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Paul Brear
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David J Baker
- Discovery Sciences , IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
| | - Eleanor L Atkinson
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | - Hannah F Sore
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
| | | | - Chandra S Verma
- Bioinformatics Institute , Agency for Science, Technology and Research (ASTAR) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - Marko Hyvönen
- Department of Biochemistry , University of Cambridge , Tennis Court Road , CB2 1GA , Cambridge , UK .
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW , Cambridge , UK .
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19
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Li N, Qu G, Xue J, Li X, Zhao X, Yan Y, Gao D, Zhang L, Wang P, Zhang M, Zhao B, Miao J, Lin Z. Discovery of a new autophagy inducer for A549 lung cancer cells. Bioorg Med Chem 2019; 27:2845-2856. [PMID: 31103402 DOI: 10.1016/j.bmc.2019.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/28/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022]
Abstract
Biological activities of a series of fluorescent compounds against human lung cancer cell line A549 were investigated. The results showed that (E)-1,3,3-trimethyl-2-(4-(piperidin-1-yl)styryl)-3H-indol-1-ium iodide (8) and (E)-2-(5,5-dimethyl-3-(4-(piperazin-1-yl)styryl)cyclohex-2-en-1-ylidene) malononitrile (11) could inhibit the growth of A549 cancer cells in a dose and time-dependent manner. Furthermore, compound 8 could trigger autophagy and apoptosis, but not obviously induce necrosis under the stimulatory condition. Therefore, 8 can be used as autophagy activator to investigate the regulatory mechanism of autophagy and may offer a new candidate for the treatment of lung cancer.
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Affiliation(s)
- Na Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - GuoJing Qu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - JingNa Xue
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Xiao Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Xuan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - YeHao Yan
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - DongFang Gao
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Lu Zhang
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Peng Wang
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Ming Zhang
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - BaoXiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - JunYing Miao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - ZhaoMin Lin
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan 250033, PR China.
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20
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Punchi Hewage AND, Yao H, Nammalwar B, Gnanasekaran KK, Lovell S, Bunce RA, Eshelman K, Phaniraj SM, Lee MM, Peterson BR, Battaile KP, Reitz AB, Rivera M. Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J Am Chem Soc 2019; 141:8171-8184. [PMID: 31038945 PMCID: PMC6535718 DOI: 10.1021/jacs.9b00394] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The iron storage
protein bacterioferritin (BfrB) is central to
bacterial iron homeostasis. The mobilization of iron from BfrB, which
requires binding by a cognate ferredoxin (Bfd), is essential to the
regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small
molecule inhibitors of the BfrB–Bfd protein–protein
interaction. The process was initiated by screening a fragment library
and followed by obtaining the structure of a fragment hit bound to
BfrB. The structural insights were used to develop a series of 4-(benzylamino)-
and 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively
bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent
growth phenotype. Further investigation determined that the analogs
elicit a pyoverdin hyperproduction phenotype that is consistent with
blockade of the BfrB–Bfd interaction and ensuing irreversible
accumulation of iron in BfrB, with concomitant depletion of iron in
the cytosol. The irreversible accumulation of iron in BfrB prompted
by the 4-substituted isoindoline analogs was confirmed by visualization
of BfrB-iron in P. aeruginosa cell lysates separated
on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial
fluoroquinolone and our isoindoline analogs results in significantly
lower cell survival relative to treatment with either antibiotic or
analog alone. Collectively, these findings furnish proof of concept
for the usefulness of small molecule probes designed to dysregulate
bacterial iron homeostasis by targeting a protein–protein interaction
pivotal for iron storage in the bacterial cell.
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Affiliation(s)
- Achala N D Punchi Hewage
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Huili Yao
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
| | - Baskar Nammalwar
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | | | - Scott Lovell
- Protein Structure Laboratory , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Richard A Bunce
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Kate Eshelman
- Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Sahishna M Phaniraj
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Molly M Lee
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Blake R Peterson
- Department of Medicinal Chemistry , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Kevin P Battaile
- IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc. , 3805 Old Easton Road , Doylestown , Pennsylvania 18902 , United States
| | - Mario Rivera
- Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States
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21
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Rugen MD, Vernet MMJL, Hantouti L, Soenens A, Andriotis VME, Rejzek M, Brett P, van den Berg RJBHN, Aerts JMFG, Overkleeft HS, Field RA. A chemical genetic screen reveals that iminosugar inhibitors of plant glucosylceramide synthase inhibit root growth in Arabidopsis and cereals. Sci Rep 2018; 8:16421. [PMID: 30401902 PMCID: PMC6219604 DOI: 10.1038/s41598-018-34749-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/19/2018] [Indexed: 01/11/2023] Open
Abstract
Iminosugars are carbohydrate mimics that are useful as molecular probes to dissect metabolism in plants. To analyse the effects of iminosugar derivatives on germination and seedling growth, we screened a library of 390 N-substituted iminosugar analogues against Arabidopsis and the small cereal Eragrostis tef (Tef). The most potent compound identified in both systems, N-5-(adamantane-1-yl-ethoxy)pentyl- L-ido-deoxynojirimycin (L-ido-AEP-DNJ), inhibited root growth in agar plate assays by 92% and 96% in Arabidopsis and Tef respectively, at 10 µM concentration. Phenocopying the effect of L-ido-AEP-DNJ with the commercial inhibitor (PDMP) implicated glucosylceramide synthase as the target responsible for root growth inhibition. L-ido-AEP-DNJ was twenty-fold more potent than PDMP. Liquid chromatography-mass spectrometry (LC-MS) analysis of ceramide:glucosylceramide ratios in inhibitor-treated Arabidopsis seedlings showed a decrease in the relative quantity of the latter, confirming that glucosylceramide synthesis is perturbed in inhibitor-treated plants. Bioinformatic analysis of glucosylceramide synthase indicates gene conservation across higher plants. Previous T-DNA insertional inactivation of glucosylceramide synthase in Arabidopsis caused seedling lethality, indicating a role in growth and development. The compounds identified herein represent chemical alternatives that can overcome issues caused by genetic intervention. These inhibitors offer the potential to dissect the roles of glucosylceramides in polyploid crop species.
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Affiliation(s)
- Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mathieu M J L Vernet
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Laila Hantouti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Amalia Soenens
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
| | - Vasilios M E Andriotis
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard J B H N van den Berg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Hermen S Overkleeft
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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22
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Choi Y, Kim H, Park SB. A divergent synthetic pathway for pyrimidine-embedded medium-sized azacycles through an N-quaternizing strategy. Chem Sci 2018; 10:569-575. [PMID: 30746098 PMCID: PMC6335630 DOI: 10.1039/c8sc04061c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
A new divergent synthetic pathway for skeletally distinct pyrimidine-containing medium-sized azacycles was developed. Diversity-generating reactions via selective bond cleavages or migrations from N-quaternized intermediates were designed, and 14 discrete core skeletons were synthesized in an efficient manner. The skeletal diversity of the resulting molecular frameworks was confirmed by chemoinformatic analysis.
Medium-sized heterocycles have recently received significant attention because of their potential roles as modulators of protein–protein interactions, but their molecular diversity and synthetic availability are still inadequate to meet the demand. To address these issues, we developed a new divergent synthetic pathway for skeletally distinct pyrimidine-containing medium-sized azacycles. We introduced N-quaternized pyrimidine-containing polyheterocycles as novel key intermediates for diversity-generating reactions via selective bond cleavages or migrations and prepared 14 discrete core skeletons in an efficient manner. The skeletal diversity of the resulting molecular frameworks was confirmed by chemoinformatic analysis.
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Affiliation(s)
- Yoona Choi
- CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , 1 Gwanak-ro, Gwanak-gu , Seoul 08826 , Korea .
| | - Heejun Kim
- CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , 1 Gwanak-ro, Gwanak-gu , Seoul 08826 , Korea .
| | - Seung Bum Park
- CRI Center for Chemical Proteomics , Department of Chemistry , Seoul National University , 1 Gwanak-ro, Gwanak-gu , Seoul 08826 , Korea .
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23
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Styles MJ, Blackwell HE. Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium. Beilstein J Org Chem 2018; 14:2651-2664. [PMID: 30410627 PMCID: PMC6204753 DOI: 10.3762/bjoc.14.243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/26/2018] [Indexed: 12/19/2022] Open
Abstract
Quorum sensing (QS) allows many common bacterial pathogens to coordinate group behaviors such as virulence factor production, host colonization, and biofilm formation at high population densities. This cell–cell signaling process is regulated by N-acyl L-homoserine lactone (AHL) signals, or autoinducers, and LuxR-type receptors in Gram-negative bacteria. SdiA is an orphan LuxR-type receptor found in Escherichia, Salmonella, Klebsiella, and Enterobacter genera that responds to AHL signals produced by other species and regulates genes involved in several aspects of host colonization. The inhibition of QS using non-native small molecules that target LuxR-type receptors offers a non-biocidal approach for studying, and potentially controlling, virulence in these bacteria. To date, few studies have characterized the features of AHLs and other small molecules capable of SdiA agonism, and no SdiA antagonists have been reported. Herein, we report the screening of a set of AHL analogs to both uncover agonists and antagonists of SdiA and to start to delineate structure–activity relationships (SARs) for SdiA:AHL interactions. Using a cell-based reporter of SdiA in Salmonella enterica serovar Typhimurium, several non-natural SdiA agonists and the first set of SdiA antagonists were identified and characterized. These compounds represent new chemical probes for exploring the mechanisms by which SdiA functions during infection and its role in interspecies interactions. Moreover, as SdiA is highly stable when produced in vitro, these compounds could advance fundamental studies of LuxR-type receptor:ligand interactions that engender both agonism and antagonism.
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Affiliation(s)
- Matthew J Styles
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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Morin MD, Wang Y, Jones BT, Mifune Y, Su L, Shi H, Moresco EMY, Zhang H, Beutler B, Boger DL. Diprovocims: A New and Exceptionally Potent Class of Toll-like Receptor Agonists. J Am Chem Soc 2018; 140:14440-14454. [PMID: 30272974 DOI: 10.1021/jacs.8b09223] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A screen conducted with nearly 100000 compounds and a surrogate functional assay for stimulation of an immune response that measured the release of TNF-α from treated human THP-1 myeloid cells differentiated along the macrophage line led to the discovery of the diprovocims. Unique to these efforts and of special interest, the screening leads for this new class of activators of an immune response came from a compound library designed to promote cell-surface receptor dimerization. Subsequent comprehensive structure-activity relationship studies improved the potency 800-fold over that of the screening leads, providing diprovocim-1 and diprovocim-2. The diprovocims act by inducing cell-surface toll-like receptor (TLR)-2 dimerization and activation with TLR1 (TLR1/TLR2 agonist), bear no structural similarity to any known natural or synthetic TLR agonist, and are easy to prepare and synthetically modify, and selected members are active in both human and murine systems. The most potent diprovocim (3, diprovocim-1) elicits full agonist activity at extraordinarily low concentrations (EC50 = 110 pM) in human THP-1 cells, being more potent than the naturally derived TLR1/TLR2 agonist Pam3CSK4 or any other known small molecule TLR agonist.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Ying Wang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Yuto Mifune
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Lijing Su
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hexin Shi
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hong Zhang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
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25
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Robke L, Rodrigues T, Schröder P, Foley DJ, Bernardes GJ, Laraia L, Waldmann H. Discovery of 2,4-dimethoxypyridines as novel autophagy inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Méndez L, Poeylaut-Palena AA, Mata EG. Molecular Diversity by Olefin Cross-Metathesis on Solid Support. Generation of Libraries of Biologically Promising β-Lactam Derivatives. Molecules 2018; 23:E1193. [PMID: 29772720 PMCID: PMC6100001 DOI: 10.3390/molecules23051193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 11/16/2022] Open
Abstract
The application of the reagent-based diversification strategy for generation of libraries of biologically promising β-lactam derivatives is described. Key features are the versatility of the linker used and the cross-metathesis functionalization at the cleavage step. From an immobilized primary library, diversity was expanded by applying different cleavage conditions, leading to a series of cholesterol absorption inhibitor analogues together with interesting hybrid compounds through incorporation of a chalcone moiety.
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Affiliation(s)
- Luciana Méndez
- Instituto de Química Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha 531, Rosario S2002LRK, Argentina.
| | - Andrés A Poeylaut-Palena
- Instituto de Química Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha 531, Rosario S2002LRK, Argentina.
| | - Ernesto G Mata
- Instituto de Química Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-CONICET, Suipacha 531, Rosario S2002LRK, Argentina.
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27
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Pawar TJ, Jiang H, Vázquez MA, Villegas Gómez C, Cruz Cruz D. Aminocatalytic Privileged Diversity-Oriented Synthesis (ApDOS): An Efficient Strategy to Populate Relevant Chemical Spaces. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tushar J. Pawar
- Departamento de Química; División de Ciencias Naturales y Exactas; Universidad de Guanajuato; Noria Alta S/N 36050 Guanajuato Gto. México
| | - Hao Jiang
- Departamento de Química; División de Ciencias Naturales y Exactas; Universidad de Guanajuato; Noria Alta S/N 36050 Guanajuato Gto. México
| | - Miguel A. Vázquez
- Departamento de Química; División de Ciencias Naturales y Exactas; Universidad de Guanajuato; Noria Alta S/N 36050 Guanajuato Gto. México
| | - Clarisa Villegas Gómez
- Departamento de Química; División de Ciencias Naturales y Exactas; Universidad de Guanajuato; Noria Alta S/N 36050 Guanajuato Gto. México
| | - David Cruz Cruz
- Departamento de Química; División de Ciencias Naturales y Exactas; Universidad de Guanajuato; Noria Alta S/N 36050 Guanajuato Gto. México
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28
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Gregor R, David S, Meijler MM. Chemical strategies to unravel bacterial-eukaryotic signaling. Chem Soc Rev 2018; 47:1761-1772. [PMID: 29260158 DOI: 10.1039/c7cs00606c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The common language of bacteria and higher life forms is a lexicon of small molecules that the research community is only beginning to decipher. While many new signaling molecules have been discovered in recent years, the identification of their targets is mostly lagging. This review will focus on the latest chemical-probe based research aimed at understanding how bacteria interact chemically with mammals and plants. In general, chemical biology strategies remain under-utilized in this complex field of research, with a few key exceptions, and we hope that this review encourages others to implement these techniques in their research. Specifically, we highlight the chemical biology techniques used in recent studies, especially activity-based protein profiling, that have been applied to unravel the chemical mechanisms of interkingdom interactions.
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Affiliation(s)
- R Gregor
- Department of Chemistry and National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, 84105, Israel.
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29
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Yaragorla S, Pareek A. Regioselective intramolecular annulations of ambident β-enamino esters: A diversity-oriented synthesis of nitrogen-containing privileged molecules. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.01.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Rugen MD, Rejzek M, Naested H, Svensson B, Field RA. High-Throughput In Vitro Screening for Inhibitors of Cereal α-Glucosidase. Methods Mol Biol 2018; 1795:101-115. [PMID: 29846922 DOI: 10.1007/978-1-4939-7874-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The hydrolysis of starch is a key step in plant germination, which also has relevance in the malting and brewing processes for beer and spirit production. Gaps in knowledge about this metabolic process exist that cannot easily be addressed using traditional genetic techniques, due to functional redundancy in many of the enzyme activities required for alpha-glucan metabolism in cereal crop species. Chemical inhibitors provide opportunities to probe the role of carbohydrate-active enzymes and the phenotypes associated with inhibition of specific enzymes. Iminosugars are the largest group of carbohydrate-active enzyme inhibitors and represent an underused resource for the dissection of plant carbohydrate metabolism. Herein we report a method for carrying out a reverse chemical genetic screen on α-glucosidase, the enzyme that catalyzes the final step in starch degradation during plant germination, namely the hydrolysis of maltose to release glucose. This chapter outlines the use of a high-throughput screen of small molecules for inhibition of α-glucosidase using a colorimetric assay which involves the substrate p-nitrophenyl α-D-glucopyranoside. Identified inhibitors can be further utilized in phenotypic screens to probe the roles played by amylolytic enzymes. Furthermore this 96-well plate-based method can be adapted to assay exo-glycosidase activities involved in other aspects of carbohydrate metabolism.
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Affiliation(s)
- Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Henrik Naested
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich, UK.
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31
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Niwetmarin W, Rego Campello H, Sparkes HA, Aggarwal VK, Gallagher T. (−)-Cytisine: Access to a stereochemically defined and functionally flexible piperidine scaffold. Org Biomol Chem 2018; 16:5823-5832. [DOI: 10.1039/c8ob01456f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cytisine undergoes ready fragmentation to provide a highly flexible (and “privileged”) piperidine scaffold capable of exploring a diversity of chemical space.
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32
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Jin G, Lee J, Lee K. Chemical genetics-based development of small molecules targeting hepatitis C virus. Arch Pharm Res 2017; 40:1021-1036. [PMID: 28856597 DOI: 10.1007/s12272-017-0949-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/20/2017] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni®, Zepatier®, Technivie®, and Epclusa®. A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.
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Affiliation(s)
- Guanghai Jin
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jisu Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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33
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Identification of aminosulfonylarylisoxazole as microRNA-31 regulators. PLoS One 2017; 12:e0182331. [PMID: 28783765 PMCID: PMC5544221 DOI: 10.1371/journal.pone.0182331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/17/2017] [Indexed: 12/28/2022] Open
Abstract
The discovery of small-molecule regulators of microRNAs remains challenging, but a few have been reported. Herein, we describe small-molecule inhibitors of miR-31, a tumor-associated microRNA (miRNA), identified by high-throughput screening using a cell-based reporter assay. Aminosulfonylarylisoxazole compounds exhibited higher specificity for miR-31 than for six other miRNAs, i.e., miR-15a, miR-16, miR-21, miR-92a-1, miR-146a, and miR-155, and increased the expression of miR-31 target genes. The down-regulation of mature miR-31 was observed, while its precursor form increased following treatment with the compounds. Thus, the compounds may target the processing of pre-miR-31 into mature miR-31 and thereby inhibit the production of mature miR-31.
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34
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Abstract
The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking. We discuss different strategies for uncovering the modes of action of such compounds and their use in unraveling membrane trafficking regulators. We also discuss how the bioactive chemicals that are currently used as probes to interrogate endomembrane trafficking were discovered and analyze the results regarding membrane trafficking and pathway crosstalk. The integration of different expertises and the rational implementation of chemical genetic strategies will improve the identification of molecular mechanisms that drive intracellular trafficking and our understanding of how trafficking interfaces with plant physiology and development.
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Affiliation(s)
- Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
| | - Ricardo Tejos
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024 Santiago, Chile;
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, 111093 Iquique, Chile
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35
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Hau M, Zenk F, Ganesan A, Iovino N, Jung M. Cellular analysis of the action of epigenetic drugs and probes. Epigenetics 2017; 12:308-322. [PMID: 28071961 DOI: 10.1080/15592294.2016.1274472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small molecule drugs and probes are important tools in drug discovery, pharmacology, and cell biology. This is of course also true for epigenetic inhibitors. Important examples for the use of established epigenetic inhibitors are the study of the mechanistic role of a certain target in a cellular setting or the modulation of a certain phenotype in an approach that aims toward therapeutic application. Alternatively, cellular testing may aim at the validation of a new epigenetic inhibitor in drug discovery approaches. Cellular and eventually animal models provide powerful tools for these different approaches but certain caveats have to be recognized and taken into account. This involves both the selectivity of the pharmacological tool as well as the specificity and the robustness of the cellular system. In this article, we present an overview of different methods that are used to profile and screen for epigenetic agents and comment on their limitations. We describe not only diverse successful case studies of screening approaches using different assay formats, but also some problematic cases, critically discussing selected applications of these systems.
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Affiliation(s)
- Mirjam Hau
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany
| | - Fides Zenk
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - A Ganesan
- c School of Pharmacy, University of East Anglia , Norwich NR4 7TJ , United Kingdom.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
| | - Nicola Iovino
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Manfred Jung
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
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36
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Martinez-Amezaga M, Delpiccolo CML, Mata EG. Immobilized boronic acid for Suzuki–Miyaura coupling: application to the generation of pharmacologically relevant molecules. RSC Adv 2017. [DOI: 10.1039/c7ra06662g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An efficient Suzuki–Miyaura coupling of immobilized boronic acid for the generation of a variety of biaryl biologically interesting derivatives is reported.
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Affiliation(s)
- M. Martinez-Amezaga
- Instituto de Química Rosario (CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- 2000 Rosario
- Argentina
| | - C. M. L. Delpiccolo
- Instituto de Química Rosario (CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- 2000 Rosario
- Argentina
| | - E. G. Mata
- Instituto de Química Rosario (CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- 2000 Rosario
- Argentina
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37
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Kim J, Jung J, Koo J, Cho W, Lee WS, Kim C, Park W, Park SB. Diversity-oriented synthetic strategy for developing a chemical modulator of protein-protein interaction. Nat Commun 2016; 7:13196. [PMID: 27774980 PMCID: PMC5078997 DOI: 10.1038/ncomms13196] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/09/2016] [Indexed: 12/24/2022] Open
Abstract
Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase-RagD protein-protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.
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Affiliation(s)
- Jonghoon Kim
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Jinjoo Jung
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Jaeyoung Koo
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Wansang Cho
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Won Seok Lee
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Chanwoo Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Wonwoo Park
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, CRI Center for Chemical Proteomics, Seoul National University, Seoul 151-747, Korea
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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Abbasov ME, Hudson BM, Tantillo DJ, Romo D. Stereodivergent, Diels-Alder-initiated organocascades employing α,β-unsaturated acylammonium salts: scope, mechanism, and application. Chem Sci 2016; 8:1511-1524. [PMID: 28616147 PMCID: PMC5460596 DOI: 10.1039/c6sc04273b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/24/2016] [Indexed: 12/16/2022] Open
Abstract
Chiral α,β-unsaturated acylammonium salts are novel dienophiles enabling enantioselective Diels–Alder-lactonization (DAL) organocascades leading to cis- and trans-fused, bicyclic γ- and δ-lactones.
Chiral α,β-unsaturated acylammonium salts are novel dienophiles enabling enantioselective Diels–Alder-lactonization (DAL) organocascades leading to cis- and trans-fused, bicyclic γ- and δ-lactones from readily prepared dienes, commodity acid chlorides, and a chiral isothiourea organocatalyst under mild conditions. We describe extensions of stereodivergent DAL organocascades to other racemic dienes bearing pendant secondary and tertiary alcohols, and application to a formal synthesis of (+)-dihydrocompactin is described. A combined experimental and computational investigation of unsaturated acylammonium salt formation and the entire DAL organocascade pathway provide a rationalization of the effect of Brønsted base additives and enabled a controllable, diastereodivergent DAL process leading to a full complement of possible stereoisomeric products. Evaluation of free energy and enthalpy barriers in conjunction with experimentally observed temperature effects revealed that the DAL is a rare case of an entropy-controlled diastereoselective process. NMR analysis of diene alcohol–Brønsted base interactions and computational studies provide a plausible explanation of observed stabilization of exo transition-state structures through hydrogen-bonding effects.
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Affiliation(s)
- Mikail E Abbasov
- Department of Chemistry and Biochemistry , Baylor University , One Bear Place 97348 , Waco , Texas 76798 , USA
| | - Brandi M Hudson
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , USA .
| | - Dean J Tantillo
- Department of Chemistry , University of California-Davis , One Shields Avenue , Davis , California 95616 , USA .
| | - Daniel Romo
- Department of Chemistry and Biochemistry , Baylor University , One Bear Place 97348 , Waco , Texas 76798 , USA
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39
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Bansode AH, Chimala P, Patil NT. Catalytic Branching Cascades in Diversity Oriented Synthesis. ChemCatChem 2016. [DOI: 10.1002/cctc.201600766] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Avinash H. Bansode
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road Pune - 411 008 India
| | - Prathyusha Chimala
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road Pune - 411 008 India
| | - Nitin T. Patil
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road Pune - 411 008 India
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40
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Ai Y, Yu L, Tan X, Chai X, Liu S. Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a "Steric-Clashes Alleviating Receptor (SCAR)" Strategy. J Chem Inf Model 2016; 56:1563-75. [PMID: 27411028 DOI: 10.1021/acs.jcim.6b00334] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covalent ligands modulating protein activities/signals have attracted unprecedented attention in recent years, but the insufficient understanding of their advantages in the early days of drug discovery has hindered their rational discovery and development. This also left us inadequate knowledge on the rational design of covalent ligands, e.g., how to balance the contribution from the covalent group and the noncovalent group, respectively. In this work, we dissected the noncovalent docking from covalent docking by creating SCARs (steric-clashes alleviating receptors). We showed that the SCAR method outperformed those specifically developed but more complicated covalent docking protocols. We furthermore provided a "proof-of-principle" example by implementing this method in the first high-throughput screening and discovery of novel covalent inhibitors of S-adenosylmethionine decarboxylase. This work demonstrated that noncovalent groups play a predeterminate role in the design of covalent ligands, and would be of great value in accelerating the discovery and development of covalent ligands.
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Affiliation(s)
- Yuanbao Ai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University , Yichang 443002, China.,College of Medical Science, China Three Gorges University , Yichang 443002, China
| | - Lingling Yu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University , Yichang 443002, China.,College of Medical Science, China Three Gorges University , Yichang 443002, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University , Yichang 443002, China.,College of Medical Science, China Three Gorges University , Yichang 443002, China
| | - Xiaoying Chai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University , Yichang 443002, China.,College of Medical Science, China Three Gorges University , Yichang 443002, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University , Yichang 443002, China.,College of Medical Science, China Three Gorges University , Yichang 443002, China
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41
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Welsh MA, Blackwell HE. Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 2016; 40:774-94. [PMID: 27268906 DOI: 10.1093/femsre/fuw009] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.
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Affiliation(s)
- Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
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42
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Gerüstdiversitätsbasierte Synthese und ihre Anwendung bei der Sonden- und Wirkstoffsuche. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508818] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Stefan Zimmermann
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Muthukumar G. Sankar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Kamal Kumar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
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43
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Scaffold Diversity Synthesis and Its Application in Probe and Drug Discovery. Angew Chem Int Ed Engl 2016; 55:7586-605. [DOI: 10.1002/anie.201508818] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/19/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Stefan Zimmermann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Muthukumar G. Sankar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Kamal Kumar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
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44
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Morin MD, Wang Y, Jones BT, Su L, Surakattula MMRP, Berger M, Huang H, Beutler EK, Zhang H, Beutler B, Boger DL. Discovery and Structure-Activity Relationships of the Neoseptins: A New Class of Toll-like Receptor-4 (TLR4) Agonists. J Med Chem 2016; 59:4812-30. [PMID: 27050713 DOI: 10.1021/acs.jmedchem.6b00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we report studies leading to the discovery of the neoseptins and a comprehensive examination of the structure-activity relationships (SARs) of this new class of small-molecule mouse Toll-like receptor 4 (mTLR4) agonists. The compounds in this class, which emerged from screening an α-helix mimetic library, stimulate the immune response, act by a well-defined mechanism (mouse TLR4 agonist), are easy to produce and structurally manipulate, exhibit exquisite SARs, are nontoxic, and elicit improved and qualitatively different responses compared to lipopolysaccharide, even though they share the same receptor.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lijing Su
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Murali M R P Surakattula
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael Berger
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hua Huang
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elliot K Beutler
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hong Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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45
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Moore JD, Rossi FM, Welsh MA, Nyffeler KE, Blackwell HE. A Comparative Analysis of Synthetic Quorum Sensing Modulators in Pseudomonas aeruginosa: New Insights into Mechanism, Active Efflux Susceptibility, Phenotypic Response, and Next-Generation Ligand Design. J Am Chem Soc 2015; 137:14626-39. [PMID: 26491787 PMCID: PMC4665086 DOI: 10.1021/jacs.5b06728] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quorum sensing (QS) is a chemical signaling mechanism that allows bacterial populations to coordinate gene expression in response to social and environmental cues. Many bacterial pathogens use QS to initiate infection at high cell densities. Over the past two decades, chemical antagonists of QS in pathogenic bacteria have attracted substantial interest for use both as tools to further elucidate QS mechanisms and, with further development, potential anti-infective agents. Considerable recent research has been devoted to the design of small molecules capable of modulating the LasR QS receptor in the opportunistic pathogen Pseudomonas aeruginosa. These molecules hold significant promise in a range of contexts; however, as most compounds have been developed independently, comparative activity data for these compounds are scarce. Moreover, the mechanisms by which the bulk of these compounds act are largely unknown. This paucity of data has stalled the choice of an optimal chemical scaffold for further advancement. Herein, we submit the best-characterized LasR modulators to standardized cell-based reporter and QS phenotypic assays in P. aeruginosa, and we report the first comprehensive set of comparative LasR activity data for these compounds. Our experiments uncovered multiple interesting mechanistic phenomena (including a potential alternative QS-modulatory ligand binding site/partner) that provide new, and unexpected, insights into the modes by which many of these LasR ligands act. The lead compounds, data trends, and mechanistic insights reported here will significantly aid the design of new small molecule QS inhibitors and activators in P. aeruginosa, and in other bacteria, with enhanced potencies and defined modes of action.
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Affiliation(s)
- Joseph D Moore
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Francis M Rossi
- Department of Chemistry, SUNY Cortland , Cortland, New York 13045, United States
| | - Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kayleigh E Nyffeler
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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46
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Stratton CF, Newman DJ, Tan DS. Cheminformatic comparison of approved drugs from natural product versus synthetic origins. Bioorg Med Chem Lett 2015; 25:4802-4807. [PMID: 26254944 PMCID: PMC4607632 DOI: 10.1016/j.bmcl.2015.07.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/08/2015] [Indexed: 11/27/2022]
Abstract
Despite the recent decline of natural product discovery programs in the pharmaceutical industry, approximately half of all new drug approvals still trace their structural origins to a natural product. Herein, we use principal component analysis to compare the structural and physicochemical features of drugs from natural product-based versus completely synthetic origins that were approved between 1981 and 2010. Drugs based on natural product structures display greater chemical diversity and occupy larger regions of chemical space than drugs from completely synthetic origins. Notably, synthetic drugs based on natural product pharmacophores also exhibit lower hydrophobicity and greater stereochemical content than drugs from completely synthetic origins. These results illustrate that structural features found in natural products can be successfully incorporated into synthetic drugs, thereby increasing the chemical diversity available for small-molecule drug discovery.
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Affiliation(s)
- Christopher F Stratton
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA
| | - David J Newman
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, PO Box B, Frederick, MD 21702, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA; Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA
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47
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Eibergen NR, Moore JD, Mattmann ME, Blackwell HE. Potent and Selective Modulation of the RhlR Quorum Sensing Receptor by Using Non-native Ligands: An Emerging Target for Virulence Control in Pseudomonas aeruginosa. Chembiochem 2015; 16:2348-56. [PMID: 26460240 DOI: 10.1002/cbic.201500357] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/10/2022]
Abstract
Pseudomonas aeruginosa uses N-acylated L-homoserine lactone signals and a triumvirate of LuxR-type receptor proteins--LasR, RhlR, and QscR--for quorum sensing (QS). Each of these receptors can contribute to QS activation or repression and, thereby, the control of myriad virulence phenotypes in this pathogen. LasR has traditionally been considered to be at the top of the QS receptor hierarchy in P. aeruginosa; however, recent reports suggest that RhlR plays a more prominent role in infection than originally predicted, in some circumstances superseding that of LasR. Herein, we report the characterization of a set of synthetic, small-molecule agonists and antagonists of RhlR. Using E. coli reporter strains, we demonstrated that many of these compounds can selectively activate or inhibit RhlR instead of LasR and QscR. Moreover, several molecules maintain their activities in P. aeruginosa at concentrations analogous to native RhlR signal levels. These compounds represent useful chemical probes to study the role of RhlR in the complex QS circuitry of P. aeruginosa, its direct (and indirect) effects on virulence, and its overall merit as a target for anti-infective therapy.
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Affiliation(s)
- Nora R Eibergen
- Dow Microbial Control, The Dow Chemical Company, 400 Arcola Road, Collegeville, PA, 19426, USA
| | - Joseph D Moore
- Dow Microbial Control, The Dow Chemical Company, 400 Arcola Road, Collegeville, PA, 19426, USA
| | | | - Helen E Blackwell
- Department of Chemistry, The University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA.
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48
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Chemical genetics and its application to moonlighting in glycolytic enzymes. Biochem Soc Trans 2015; 42:1756-61. [PMID: 25399602 DOI: 10.1042/bst20140201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycolysis is an ancient biochemical pathway that breaks down glucose into pyruvate to produce ATP. The structural and catalytic properties of glycolytic enzymes are well-characterized. However, there is growing appreciation that these enzymes participate in numerous moonlighting functions that are unrelated to glycolysis. Recently, chemical genetics has been used to discover novel moonlighting functions in glycolytic enzymes. In the present mini-review, we introduce chemical genetics and discuss how it can be applied to the discovery of protein moonlighting. Specifically, we describe the application of chemical genetics to uncover moonlighting in two glycolytic enzymes, enolase and glyceraldehyde dehydrogenase. This led to the discovery of moonlighting roles in glucose homoeostasis, cancer progression and diabetes-related complications. Finally, we also provide a brief overview of the latest progress in unravelling the myriad moonlighting roles for these enzymes.
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49
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Barette C, Soleilhac E, Charavay C, Cochet C, Fauvarque MO. [Strength and specificity of the CMBA screening platform for bioactive molecules discovery]. Med Sci (Paris) 2015; 31:423-31. [PMID: 25958761 DOI: 10.1051/medsci/20153104017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Used as powerful chemical probes in Life science fundamental research, the application potential of new bioactive molecular entities includes but extends beyond their development as therapeutic drugs in pharmacology. In this review, we wish to point out the methodology of chemical libraries screening on living cells or purified proteins at the CMBA academic platform of Grenoble Alpes University, and strategies employed to further characterize the selected bioactive molecules by phenotypic profiling on human cells. Multiple application fields are concerned by the screening activity developed at CMBA with bioactive molecules previously selected for their potential as tools for fundamental research purpose, therapeutic candidates to treat cancer or infection, or promising compounds for production of bioenergy.
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Affiliation(s)
- Caroline Barette
- Université Grenoble Alpes ; CEA-Direction des sciences du vivant, Institut de recherches en technologies et sciences pour le vivant, iRTSV-BGE-CMBA, CEA-Grenoble; Inserm UMRS_1038, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Emmanuelle Soleilhac
- Université Grenoble Alpes ; CEA-Direction des sciences du vivant, Institut de recherches en technologies et sciences pour le vivant, iRTSV-BGE-CMBA, CEA-Grenoble; Inserm UMRS_1038, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Céline Charavay
- Université Grenoble Alpes ; CEA-Direction des sciences du vivant, Institut de recherches en technologies et sciences pour le vivant, iRTSV-BGE-CMBA, CEA-Grenoble; Inserm UMRS_1038, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Claude Cochet
- Université Grenoble Alpes ; CEA-Direction des sciences du vivant, Institut de recherches en technologies et sciences pour le vivant, BCI ; Inserm UMRS_1036, iRTSV-BCI-KIN, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Marie-Odile Fauvarque
- Université Grenoble Alpes ; CEA-Direction des sciences du vivant, Institut de recherches en technologies et sciences pour le vivant, iRTSV-BGE-CMBA, CEA-Grenoble; Inserm UMRS_1038, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
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50
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Diversity oriented synthesis for novel anti-malarials. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:49-53. [PMID: 26702309 DOI: 10.1007/s11693-015-9171-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/30/2015] [Indexed: 01/26/2023]
Abstract
Malaria a global pandemic has engulfed nearly 0.63 million people globally. It is high time that a cure for malaria is required to stop its ever increasing menace. Our commentary discusses the advent and contribution of diversity oriented synthesis (DOS) in the drug discovery efforts towards developing cure for malaria. DOS based on chemical genetics focusses on design and synthesis of molecular libraries which covers large tracts of biologically relevant chemical space. Herein we will discuss the applications, advantages, disadvantages and future directions of DOS with respect to malaria.
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