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Huang Y, Hou R, Lam FS, Jia Y, Zhou Y, He X, Li G, Xiong F, Cao Y, Wang D, Li X. Agonist Discovery for Membrane Proteins on Live Cells by Using DNA-encoded Libraries. J Am Chem Soc 2024; 146:24638-24653. [PMID: 39171830 DOI: 10.1021/jacs.4c08624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Identifying biologically active ligands for membrane proteins is an important task in chemical biology. We report an approach to directly identify small molecule agonists against membrane proteins by selecting DNA-encoded libraries (DELs) on live cells. This method connects extracellular ligand binding with intracellular biochemical transformation, thereby biasing the selection toward agonist identification. We have demonstrated the methodology with three membrane proteins: epidermal growth factor receptor (EGFR), thrombopoietin receptor (TPOR), and insulin receptor (INSR). A ∼30 million and a 1.033 billion-compound DEL were selected against these targets, and novel agonists with subnanomolar affinity and low micromolar cellular activities have been discovered. The INSR agonists activated the receptor by possibly binding to an allosteric site, exhibited clear synergistic effects with insulin, and activated the downstream signaling pathways. Notably, the agonists did not activate the insulin-like growth factor 1 receptor (IGF-1R), a highly homologous receptor whose activation may lead to tumor progression. Collectively, this work has developed an approach toward "functional" DEL selections on the cell surface and may provide a widely applicable method for agonist discovery for membrane proteins.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Rui Hou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Yunxuan Jia
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
| | - Xun He
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen 518110, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Feng Xiong
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen 518110, China
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Dongyao Wang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
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Fitzgerald P, Dixit A, Zhang C, Mobley DL, Paegel BM. Building Block-Centric Approach to DNA-Encoded Library Design. J Chem Inf Model 2024; 64:4661-4672. [PMID: 38860710 PMCID: PMC11200258 DOI: 10.1021/acs.jcim.4c00232] [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: 02/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Anjali Dixit
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Chris Zhang
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
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Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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4
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Tian Y, Seifermann M, Bauer L, Luchena C, Wiedmann JJ, Schmidt S, Geisel A, Afonin S, Höpfner J, Brehm M, Liu X, Hopf C, Popova AA, Levkin PA. High-Throughput Miniaturized Synthesis of PROTAC-Like Molecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307215. [PMID: 38258390 DOI: 10.1002/smll.202307215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/03/2024] [Indexed: 01/24/2024]
Abstract
The development of miniaturized high-throughput in situ screening platforms capable of handling the entire process of drug synthesis to final screening is essential for advancing drug discovery in the future. In this study, an approach based on combinatorial solid-phase synthesis, enabling the efficient synthesis of libraries of proteolysis targeting chimeras (PROTACs) in an array format is presented. This on-chip platform allows direct biological screening without the need for transfer steps. UV-induced release of target molecules into individual droplets facilitates further on-chip experimentation. Utilizing a mitogen-activated protein kinase kinases (MEK1/2) degrader as a template, a series of 132 novel PROTAC-like molecules is synthesized using solid-phase Ugi reaction. These compounds are further characterized using various methods, including matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) imaging, while consuming only a few milligrams of starting materials in total. Furthermore, the feasibility of culturing cancer cells on the modified spots and quantifying the effect of MEK suppression is demonstrated. The miniaturized synthesis platform lays a foundation for high-throughput in situ biological screening of potent PROTACs for potential anticancer activity and offers the potential for accelerating the drug discovery process by integrating miniaturized synthesis and biological steps on the same array.
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Affiliation(s)
- Ye Tian
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
- Department of Immunology, Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Provincial Key Laboratory of Infection & Immunology, School of Basic Medical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Maximilian Seifermann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Liana Bauer
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Janne J Wiedmann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Alexander Geisel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Julius Höpfner
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Marius Brehm
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 280, 69117, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Theodor Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Anna A Popova
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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5
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Madasu C, Liao Z, Parks SE, Sharma KL, Bohren KM, Ye Q, Li F, Palaniappan M, Tan Z, Yuan F, Creighton CJ, Tang S, Masand RP, Guan X, Young DW, Monsivais D, Matzuk MM. Identification of potent pan-ephrin receptor kinase inhibitors using DNA-encoded chemistry technology. Proc Natl Acad Sci U S A 2024; 121:e2322934121. [PMID: 38701119 PMCID: PMC11087803 DOI: 10.1073/pnas.2322934121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
EPH receptors (EPHs), the largest family of tyrosine kinases, phosphorylate downstream substrates upon binding of ephrin cell surface-associated ligands. In a large cohort of endometriotic lesions from individuals with endometriosis, we found that EPHA2 and EPHA4 expressions are increased in endometriotic lesions relative to normal eutopic endometrium. Because signaling through EPHs is associated with increased cell migration and invasion, we hypothesized that chemical inhibition of EPHA2/4 could have therapeutic value. We screened DNA-encoded chemical libraries (DECL) to rapidly identify EPHA2/4 kinase inhibitors. Hit compound, CDD-2693, exhibited picomolar/nanomolar kinase activity against EPHA2 (Ki: 4.0 nM) and EPHA4 (Ki: 0.81 nM). Kinome profiling revealed that CDD-2693 bound to most EPH family and SRC family kinases. Using NanoBRET target engagement assays, CDD-2693 had nanomolar activity versus EPHA2 (IC50: 461 nM) and EPHA4 (IC50: 40 nM) but was a micromolar inhibitor of SRC, YES, and FGR. Chemical optimization produced CDD-3167, having picomolar biochemical activity toward EPHA2 (Ki: 0.13 nM) and EPHA4 (Ki: 0.38 nM) with excellent cell-based potency EPHA2 (IC50: 8.0 nM) and EPHA4 (IC50: 2.3 nM). Moreover, CDD-3167 maintained superior off-target cellular selectivity. In 12Z endometriotic epithelial cells, CDD-2693 and CDD-3167 significantly decreased EFNA5 (ligand) induced phosphorylation of EPHA2/4, decreased 12Z cell viability, and decreased IL-1β-mediated expression of prostaglandin synthase 2 (PTGS2). CDD-2693 and CDD-3167 decreased expansion of primary endometrial epithelial organoids from patients with endometriosis and decreased Ewing's sarcoma viability. Thus, using DECL, we identified potent pan-EPH inhibitors that show specificity and activity in cellular models of endometriosis and cancer.
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Affiliation(s)
- Chandrashekhar Madasu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Zian Liao
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
| | - Sydney E. Parks
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Kiran L. Sharma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Kurt M. Bohren
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Qiuji Ye
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Feng Li
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Murugesan Palaniappan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Zhi Tan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Fei Yuan
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX77030
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX77030
- Department of Medicine, Baylor College of Medicine, Houston, TX77030
| | - Suni Tang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Ramya P. Masand
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX77030
| | - Xiaoming Guan
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX77030
| | - Damian W. Young
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Diana Monsivais
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - Martin M. Matzuk
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX77030
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
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6
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Siripuram V, Sunkari YK, Ma F, Nguyen TL, Flajolet M. Reversible and Fully Controllable Generation of Organo-Soluble DNA (osDNA). ACS OMEGA 2024; 9:14771-14780. [PMID: 38585059 PMCID: PMC10993399 DOI: 10.1021/acsomega.3c06755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 04/09/2024]
Abstract
The present work describes a complete and reversible transformation of DNA's properties allowing solubilization in organic solvents and subsequent chemical modifications that are otherwise not possible in an aqueous medium. Organo-soluble DNA (osDNA) moieties are generated by covalently linking a dsDNA fragment to a polyether moiety with a built-in mechanism, rendering the process perfectly reversible and fully controllable. The precise removal of the polyether moiety frees up the initial DNA fragment, unaltered, both in sequence and nature. The solubility of osDNA was confirmed in six organic solvents of decreasing polarity and six types of osDNAs. As a proof of concept, in the context of DNA-encoded library (DEL) technology, an amidation reaction was successfully performed on osDNA in 100% DMSO. The development of osDNA opens up entirely new avenues for any DNA applications that could benefit from working in nonaqueous solutions, including chemical transformations.
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Affiliation(s)
- Vijay
Kumar Siripuram
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Yashoda Krishna Sunkari
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Fei Ma
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Thu-Lan Nguyen
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Marc Flajolet
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
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7
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Wallach I, Bernard D, Nguyen K, Ho G, Morrison A, Stecula A, Rosnik A, O’Sullivan AM, Davtyan A, Samudio B, Thomas B, Worley B, Butler B, Laggner C, Thayer D, Moharreri E, Friedland G, Truong H, van den Bedem H, Ng HL, Stafford K, Sarangapani K, Giesler K, Ngo L, Mysinger M, Ahmed M, Anthis NJ, Henriksen N, Gniewek P, Eckert S, de Oliveira S, Suterwala S, PrasadPrasad SVK, Shek S, Contreras S, Hare S, Palazzo T, O’Brien TE, Van Grack T, Williams T, Chern TR, Kenyon V, Lee AH, Cann AB, Bergman B, Anderson BM, Cox BD, Warrington JM, Sorenson JM, Goldenberg JM, Young MA, DeHaan N, Pemberton RP, Schroedl S, Abramyan TM, Gupta T, Mysore V, Presser AG, Ferrando AA, Andricopulo AD, Ghosh A, Ayachi AG, Mushtaq A, Shaqra AM, Toh AKL, Smrcka AV, Ciccia A, de Oliveira AS, Sverzhinsky A, de Sousa AM, Agoulnik AI, Kushnir A, Freiberg AN, Statsyuk AV, Gingras AR, Degterev A, Tomilov A, Vrielink A, Garaeva AA, Bryant-Friedrich A, Caflisch A, Patel AK, Rangarajan AV, Matheeussen A, Battistoni A, Caporali A, Chini A, Ilari A, Mattevi A, Foote AT, Trabocchi A, Stahl A, Herr AB, Berti A, Freywald A, Reidenbach AG, Lam A, Cuddihy AR, White A, Taglialatela A, Ojha AK, Cathcart AM, Motyl AAL, Borowska A, D’Antuono A, Hirsch AKH, Porcelli AM, Minakova A, Montanaro A, Müller A, Fiorillo A, Virtanen A, O’Donoghue AJ, Del Rio Flores A, Garmendia AE, Pineda-Lucena A, Panganiban AT, Samantha A, Chatterjee AK, Haas AL, Paparella AS, John ALS, Prince A, ElSheikh A, Apfel AM, Colomba A, O’Dea A, Diallo BN, Ribeiro BMRM, Bailey-Elkin BA, Edelman BL, Liou B, Perry B, Chua BSK, Kováts B, Englinger B, Balakrishnan B, Gong B, Agianian B, Pressly B, Salas BPM, Duggan BM, Geisbrecht BV, Dymock BW, Morten BC, Hammock BD, Mota BEF, Dickinson BC, Fraser C, Lempicki C, Novina CD, Torner C, Ballatore C, Bon C, Chapman CJ, Partch CL, Chaton CT, Huang C, Yang CY, Kahler CM, Karan C, Keller C, Dieck CL, Huimei C, Liu C, Peltier C, Mantri CK, Kemet CM, Müller CE, Weber C, Zeina CM, Muli CS, Morisseau C, Alkan C, Reglero C, Loy CA, Wilson CM, Myhr C, Arrigoni C, Paulino C, Santiago C, Luo D, Tumes DJ, Keedy DA, Lawrence DA, Chen D, Manor D, Trader DJ, Hildeman DA, Drewry DH, Dowling DJ, Hosfield DJ, Smith DM, Moreira D, Siderovski DP, Shum D, Krist DT, Riches DWH, Ferraris DM, Anderson DH, Coombe DR, Welsbie DS, Hu D, Ortiz D, Alramadhani D, Zhang D, Chaudhuri D, Slotboom DJ, Ronning DR, Lee D, Dirksen D, Shoue DA, Zochodne DW, Krishnamurthy D, Duncan D, Glubb DM, Gelardi ELM, Hsiao EC, Lynn EG, Silva EB, Aguilera E, Lenci E, Abraham ET, Lama E, Mameli E, Leung E, Giles E, Christensen EM, Mason ER, Petretto E, Trakhtenberg EF, Rubin EJ, Strauss E, Thompson EW, Cione E, Lisabeth EM, Fan E, Kroon EG, Jo E, García-Cuesta EM, Glukhov E, Gavathiotis E, Yu F, Xiang F, Leng F, Wang F, Ingoglia F, van den Akker F, Borriello F, Vizeacoumar FJ, Luh F, Buckner FS, Vizeacoumar FS, Bdira FB, Svensson F, Rodriguez GM, Bognár G, Lembo G, Zhang G, Dempsey G, Eitzen G, Mayer G, Greene GL, Garcia GA, Lukacs GL, Prikler G, Parico GCG, Colotti G, De Keulenaer G, Cortopassi G, Roti G, Girolimetti G, Fiermonte G, Gasparre G, Leuzzi G, Dahal G, Michlewski G, Conn GL, Stuchbury GD, Bowman GR, Popowicz GM, Veit G, de Souza GE, Akk G, Caljon G, Alvarez G, Rucinski G, Lee G, Cildir G, Li H, Breton HE, Jafar-Nejad H, Zhou H, Moore HP, Tilford H, Yuan H, Shim H, Wulff H, Hoppe H, Chaytow H, Tam HK, Van Remmen H, Xu H, Debonsi HM, Lieberman HB, Jung H, Fan HY, Feng H, Zhou H, Kim HJ, Greig IR, Caliandro I, Corvo I, Arozarena I, Mungrue IN, Verhamme IM, Qureshi IA, Lotsaris I, Cakir I, Perry JJP, Kwiatkowski J, Boorman J, Ferreira J, Fries J, Kratz JM, Miner J, Siqueira-Neto JL, Granneman JG, Ng J, Shorter J, Voss JH, Gebauer JM, Chuah J, Mousa JJ, Maynes JT, Evans JD, Dickhout J, MacKeigan JP, Jossart JN, Zhou J, Lin J, Xu J, Wang J, Zhu J, Liao J, Xu J, Zhao J, Lin J, Lee J, Reis J, Stetefeld J, Bruning JB, Bruning JB, Coles JG, Tanner JJ, Pascal JM, So J, Pederick JL, Costoya JA, Rayman JB, Maciag JJ, Nasburg JA, Gruber JJ, Finkelstein JM, Watkins J, Rodríguez-Frade JM, Arias JAS, Lasarte JJ, Oyarzabal J, Milosavljevic J, Cools J, Lescar J, Bogomolovas J, Wang J, Kee JM, Kee JM, Liao J, Sistla JC, Abrahão JS, Sishtla K, Francisco KR, Hansen KB, Molyneaux KA, Cunningham KA, Martin KR, Gadar K, Ojo KK, Wong KS, Wentworth KL, Lai K, Lobb KA, Hopkins KM, Parang K, Machaca K, Pham K, Ghilarducci K, Sugamori KS, McManus KJ, Musta K, Faller KME, Nagamori K, Mostert KJ, Korotkov KV, Liu K, Smith KS, Sarosiek K, Rohde KH, Kim KK, Lee KH, Pusztai L, Lehtiö L, Haupt LM, Cowen LE, Byrne LJ, Su L, Wert-Lamas L, Puchades-Carrasco L, Chen L, Malkas LH, Zhuo L, Hedstrom L, Hedstrom L, Walensky LD, Antonelli L, Iommarini L, Whitesell L, Randall LM, Fathallah MD, Nagai MH, Kilkenny ML, Ben-Johny M, Lussier MP, Windisch MP, Lolicato M, Lolli ML, Vleminckx M, Caroleo MC, Macias MJ, Valli M, Barghash MM, Mellado M, Tye MA, Wilson MA, Hannink M, Ashton MR, Cerna MVC, Giorgis M, Safo MK, Maurice MS, McDowell MA, Pasquali M, Mehedi M, Serafim MSM, Soellner MB, Alteen MG, Champion MM, Skorodinsky M, O’Mara ML, Bedi M, Rizzi M, Levin M, Mowat M, Jackson MR, Paige M, Al-Yozbaki M, Giardini MA, Maksimainen MM, De Luise M, Hussain MS, Christodoulides M, Stec N, Zelinskaya N, Van Pelt N, Merrill NM, Singh N, Kootstra NA, Singh N, Gandhi NS, Chan NL, Trinh NM, Schneider NO, Matovic N, Horstmann N, Longo N, Bharambe N, Rouzbeh N, Mahmoodi N, Gumede NJ, Anastasio NC, Khalaf NB, Rabal O, Kandror O, Escaffre O, Silvennoinen O, Bishop OT, Iglesias P, Sobrado P, Chuong P, O’Connell P, Martin-Malpartida P, Mellor P, Fish PV, Moreira POL, Zhou P, Liu P, Liu P, Wu P, Agogo-Mawuli P, Jones PL, Ngoi P, Toogood P, Ip P, von Hundelshausen P, Lee PH, Rowswell-Turner RB, Balaña-Fouce R, Rocha REO, Guido RVC, Ferreira RS, Agrawal RK, Harijan RK, Ramachandran R, Verma R, Singh RK, Tiwari RK, Mazitschek R, Koppisetti RK, Dame RT, Douville RN, Austin RC, Taylor RE, Moore RG, Ebright RH, Angell RM, Yan R, Kejriwal R, Batey RA, Blelloch R, Vandenberg RJ, Hickey RJ, Kelm RJ, Lake RJ, Bradley RK, Blumenthal RM, Solano R, Gierse RM, Viola RE, McCarthy RR, Reguera RM, Uribe RV, do Monte-Neto RL, Gorgoglione R, Cullinane RT, Katyal S, Hossain S, Phadke S, Shelburne SA, Geden SE, Johannsen S, Wazir S, Legare S, Landfear SM, Radhakrishnan SK, Ammendola S, Dzhumaev S, Seo SY, Li S, Zhou S, Chu S, Chauhan S, Maruta S, Ashkar SR, Shyng SL, Conticello SG, Buroni S, Garavaglia S, White SJ, Zhu S, Tsimbalyuk S, Chadni SH, Byun SY, Park S, Xu SQ, Banerjee S, Zahler S, Espinoza S, Gustincich S, Sainas S, Celano SL, Capuzzi SJ, Waggoner SN, Poirier S, Olson SH, Marx SO, Van Doren SR, Sarilla S, Brady-Kalnay SM, Dallman S, Azeem SM, Teramoto T, Mehlman T, Swart T, Abaffy T, Akopian T, Haikarainen T, Moreda TL, Ikegami T, Teixeira TR, Jayasinghe TD, Gillingwater TH, Kampourakis T, Richardson TI, Herdendorf TJ, Kotzé TJ, O’Meara TR, Corson TW, Hermle T, Ogunwa TH, Lan T, Su T, Banjo T, O’Mara TA, Chou T, Chou TF, Baumann U, Desai UR, Pai VP, Thai VC, Tandon V, Banerji V, Robinson VL, Gunasekharan V, Namasivayam V, Segers VFM, Maranda V, Dolce V, Maltarollo VG, Scoffone VC, Woods VA, Ronchi VP, Van Hung Le V, Clayton WB, Lowther WT, Houry WA, Li W, Tang W, Zhang W, Van Voorhis WC, Donaldson WA, Hahn WC, Kerr WG, Gerwick WH, Bradshaw WJ, Foong WE, Blanchet X, Wu X, Lu X, Qi X, Xu X, Yu X, Qin X, Wang X, Yuan X, Zhang X, Zhang YJ, Hu Y, Aldhamen YA, Chen Y, Li Y, Sun Y, Zhu Y, Gupta YK, Pérez-Pertejo Y, Li Y, Tang Y, He Y, Tse-Dinh YC, Sidorova YA, Yen Y, Li Y, Frangos ZJ, Chung Z, Su Z, Wang Z, Zhang Z, Liu Z, Inde Z, Artía Z, Heifets A. AI is a viable alternative to high throughput screening: a 318-target study. Sci Rep 2024; 14:7526. [PMID: 38565852 PMCID: PMC10987645 DOI: 10.1038/s41598-024-54655-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.
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8
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Zhang J, Liu J, Zhang G, He X, Xiong F, Fan X, Li Y, Li Y. Synthesis of Diacylhydrazine Derivatives Based on Tetrazole-Focused DNA-Encoded Library. Org Lett 2024; 26:1094-1099. [PMID: 38277138 DOI: 10.1021/acs.orglett.3c04374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Utilizing already existing DNA-encoded libraries (DELs) for the generation of a distinct DEL represents an expedited strategy for expanding the chemical space. Herein, we leverage the unique photoreactivity of tetrazoles to synthesize diacylhydrazines on DNA. Widely available carboxylic acids serving as building blocks were employed under the mild photomediated reaction conditions, affording diverse DNA-conjugated diacylhydrazines. This methodology also demonstrates robustness in DEL-compatible synthesis and facilitates the preparation of oligonucleotide-based chemical probes.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jinlu Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xun He
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Xiaohong Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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9
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Zhang S, Zhang H, Liu X, Qi P, Tan T, Wang S, Gao H, Xu H, Zhou Z, Yi W. Mask and Release Strategy-Enabled Diversity-Oriented Synthesis for DNA-Encoded Library. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307049. [PMID: 38044314 PMCID: PMC10853742 DOI: 10.1002/advs.202307049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Indexed: 12/05/2023]
Abstract
An ideal DNA-encoded library (DEL) selection requires the library to consist of diverse core skeletons and cover chemical space as much as possible. However, the lack of efficient on-DNA synthetic approaches toward core skeletons has greatly restricted the diversity of DEL. To mitigate this issue, this work disclosed a "Mask & Release" strategy to streamline the challenging on-DNA core skeleton synthesis. N-phenoxyacetamide is used as a masked phenol and versatile directing group to mediate diversified DNA-compatible C-H functionalization, introducing the 1st-dimensional diversity at a defined site, and simultaneously releasing the phenol functionality, which can facilitate the introduction of the 2nd diversity. This work not only provides a set of efficient syntheses toward DNA-conjugated drug-like core skeletons such as ortho-alkenyl/sulfiliminyl/cyclopropyl phenol, benzofuran, dihydrobenzofuran but also provides a paradigm for on-DNA core skeleton synthetic method development.
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Affiliation(s)
- Silin Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Haiman Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Xiawen Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Ping Qi
- Guangzhou Institute for Food InspectionGuangzhou511400China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Shengdong Wang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Hui Gao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
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10
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Fang X, Zhang T, Fang W, Zhang G, Li Y, Li Y. Synthesis of Functionalized Triazoles on DNA via Azide-Acetonitrile "Click" Reaction. Org Lett 2023; 25:8326-8331. [PMID: 37943666 DOI: 10.1021/acs.orglett.3c03404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Triazoles are privileged structural motifs that are embedded in a number of molecules with interesting biological activities. In this work, we developed a practical and general synthetic strategy to construct a medicinally important 5-amino-1,2,3-triazole moiety on DNA by coupling DNA-conjugated azides and monosubstituted acetonitriles via azide-acetonitrile "click" reaction. Under mild reaction conditions, this reaction displayed a broad substrate scope. Most substrates gave moderate-to-excellent conversions. Thus, this DNA-compatible reaction could be employed in practical DNA-encoded library (DEL) construction and potentially expand the chemical space of DNA-encoded libraries.
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Affiliation(s)
- Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, P. R. China
| | - Tianyang Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Wei Fang
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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11
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Sunkari YK, Nguyen TL, Siripuram VK, Flajolet M. Impact of organic chemistry conditions on DNA durability in the context of DNA-encoded library technology. iScience 2023; 26:107573. [PMID: 37664608 PMCID: PMC10470182 DOI: 10.1016/j.isci.2023.107573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
High-power screening (HPS) technologies, such as DNA-encoded library (DEL) technology, could exponentially increase the dimensions of the chemical space accessible for drug discovery. The intrinsic fragile nature of DNA is associated with cumbersome limitations and DNA durability (e.g., depurination, loss of phosphate groups, adduct formation) is compromised in numerous organic chemistry conditions that require empirical testing. An atlas of reaction conditions (temperature, pH, solvent/buffer, ligands, oxidizing reagents, catalysts, scavengers in function of time) that have been systematically tested in multiple combinations, indicates precisely limits useful for DEL construction. More importantly, this approach could be used broadly to effectively evaluate DNA-compatibility of any novel on-DNA chemical reaction, and it is compatible with different molecular methodologies. This atlas and the general approach presented, by allowing novel reaction conditions to be performed in presence of DNA, should greatly help in expanding the DEL chemical space as well as any field involving DNA durability.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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12
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Fitzgerald P, Cochrane WG, Paegel BM. Dose-Response Activity-Based DNA-Encoded Library Screening. ACS Med Chem Lett 2023; 14:1295-1303. [PMID: 37736190 PMCID: PMC10510511 DOI: 10.1021/acsmedchemlett.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Dose-response, or "conforming" behavior, increases confidence in a screening hit's authenticity. Here, we demonstrate dose-response solid-phase DNA-encoded library (DEL) screening. Compound dose in microfluidic droplets is modulated via the UV intensity of photocleavage from DEL beads. A 55,296-member DEL was screened at different UV intensities against model enzyme drug targets factor Xa (FXa) and autotaxin (ATX). Both screens yielded photochemical dose-dependent hit rates (FXa hit rates of 0.08/0.05% at 100/30% UV exposure; ATX hit rates of 0.24/0.08% at 100/20% UV exposure). FXa hits contained structures reflective of FXa inhibitors and four hits inhibited FXa (IC50 = 4.2 ± 0.1, 7.4 ± 0.3, 9.0 ± 0.3, and 19 ± 2 μM.) The top ATX hits (two dihydrobenzamidazolones and a tetrahydroisoquinoline) were validated as inhibitors (IC50 = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Wesley G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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13
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Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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14
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Singh S, Tian W, Severance ZC, Chaudhary SK, Anokhina V, Mondal B, Pergu R, Singh P, Dhawa U, Singha S, Choudhary A. Proximity-inducing modalities: the past, present, and future. Chem Soc Rev 2023; 52:5485-5515. [PMID: 37477631 DOI: 10.1039/d2cs00943a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Living systems use proximity to regulate biochemical processes. Inspired by this phenomenon, bifunctional modalities that induce proximity have been developed to redirect cellular processes. An emerging example of this class is molecules that induce ubiquitin-dependent proteasomal degradation of a protein of interest, and their initial development sparked a flurry of discovery for other bifunctional modalities. Recent advances in this area include modalities that can change protein phosphorylation, glycosylation, and acetylation states, modulate gene expression, and recruit components of the immune system. In this review, we highlight bifunctional modalities that perform functions other than degradation and have great potential to revolutionize disease treatment, while also serving as important tools in basic research to explore new aspects of biology.
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Affiliation(s)
- Sameek Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Wenzhi Tian
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Zachary C Severance
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Viktoriya Anokhina
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Basudeb Mondal
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Prashant Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Uttam Dhawa
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santanu Singha
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
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15
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Seydimemet M, Yang Y, Lv Y, Liu J, Yan Z, Zhao Y, Wang X, Lu X. Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries. ACS Med Chem Lett 2023; 14:1073-1078. [PMID: 37583819 PMCID: PMC10424316 DOI: 10.1021/acsmedchemlett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.
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Affiliation(s)
- Mengnisa Seydimemet
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yixuan Yang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yuhan Lv
- School
of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong P.R. China
| | - Jiaxiang Liu
- Alphama
Biotechnology Suzhou Co., Ltd., 108 Yuxin Road, Suzhou City, Jiangsu Province 215123, China
| | - Ziqin Yan
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yujun Zhao
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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16
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Luo A, Duchemin N, Wang X, Zhou H, Zeng F, Zhao X, Yu W, Yang K, Jin Hu Y. Development of On-DNA Thiophene Synthesis for DEL Construction. Chem Asian J 2023; 18:e202300458. [PMID: 37339942 DOI: 10.1002/asia.202300458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
Thiophene and its substituted derivatives are a highly important class of heterocyclic compounds, with noteworthy applications in pharmaceutical ingredients. In this study, we leverage the unique reactivity of alkynes to generate thiophenes on-DNA, using a cascade iodination, Cadiot-Chodkiewicz coupling and heterocyclization. This approach, tackling on-DNA thiophene synthesis for the first time, generates diverse, and unprecedented structural and chemical features, which could be significant motifs in DEL screening as molecular recognition agents for drug discovery.
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Affiliation(s)
- Ayun Luo
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Nicolas Duchemin
- Pharmaron UK, Ltd., Innovation Park, West Cl, Hertford Rd, Hoddesdon, EN11 9FH, UK
| | - Xiuming Wang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Fanming Zeng
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Xue Zhao
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Weina Yu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd, 6 Taihe Road, BDA, Beijing, 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
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17
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Hou R, Xie C, Gui Y, Li G, Li X. Machine-Learning-Based Data Analysis Method for Cell-Based Selection of DNA-Encoded Libraries. ACS OMEGA 2023; 8:19057-19071. [PMID: 37273617 PMCID: PMC10233830 DOI: 10.1021/acsomega.3c02152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is a powerful ligand discovery technology that has been widely adopted in the pharmaceutical industry. DEL selections are typically performed with a purified protein target immobilized on a matrix or in solution phase. Recently, DELs have also been used to interrogate the targets in the complex biological environment, such as membrane proteins on live cells. However, due to the complex landscape of the cell surface, the selection inevitably involves significant nonspecific interactions, and the selection data are much noisier than the ones with purified proteins, making reliable hit identification highly challenging. Researchers have developed several approaches to denoise DEL datasets, but it remains unclear whether they are suitable for cell-based DEL selections. Here, we report the proof-of-principle of a new machine-learning (ML)-based approach to process cell-based DEL selection datasets by using a Maximum A Posteriori (MAP) estimation loss function, a probabilistic framework that can account for and quantify uncertainties of noisy data. We applied the approach to a DEL selection dataset, where a library of 7,721,415 compounds was selected against a purified carbonic anhydrase 2 (CA-2) and a cell line expressing the membrane protein carbonic anhydrase 12 (CA-12). The extended-connectivity fingerprint (ECFP)-based regression model using the MAP loss function was able to identify true binders and also reliable structure-activity relationship (SAR) from the noisy cell-based selection datasets. In addition, the regularized enrichment metric (known as MAP enrichment) could also be calculated directly without involving the specific machine-learning model, effectively suppressing low-confidence outliers and enhancing the signal-to-noise ratio. Future applications of this method will focus on de novo ligand discovery from cell-based DEL selections.
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Affiliation(s)
- Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
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18
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Luo A, Zhou H, Hua Q, An Y, Ma H, Zhao X, Yang K, Hu YJ. Development of the Inverse Sonogashira Reaction for DEL Synthesis. ACS Med Chem Lett 2023; 14:270-277. [PMID: 36923912 PMCID: PMC10009795 DOI: 10.1021/acsmedchemlett.2c00477] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
An efficient approach for aryl acetylene DNA-encoded library (DEL) synthesis was developed in this study by transition-metal-mediated inverse Sonogashira reaction of 1-iodoalkyne with boronic acid under ambient conditions, with moderate to excellent conversions and broad substrate adaptability for the first time. Compared to palladium-phosphine, copper iodide performed better in the on-DNA inverse Sonogashira reaction. Interestingly, substrate diversity can be enhanced by first interrogating coupling reagents under copper-promoted conditions, and then revalidating them under palladium-facilitated conditions for those reagents which failed under the former. This complementary validation strategy is particularly well-fitted to any DEL validation studies.
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Affiliation(s)
- Ayun Luo
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Qini Hua
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Yufang An
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hangke Ma
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Xue Zhao
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Kexin Yang
- Pharmaron
Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
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19
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Sala D, Batebi H, Ledwitch K, Hildebrand PW, Meiler J. Targeting in silico GPCR conformations with ultra-large library screening for hit discovery. Trends Pharmacol Sci 2023; 44:150-161. [PMID: 36669974 PMCID: PMC9974811 DOI: 10.1016/j.tips.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
The use of deep machine learning (ML) in protein structure prediction has made it possible to easily access a large number of annotated conformations that can potentially compensate for missing experimental structures in structure-based drug discovery (SBDD). However, it is still unclear whether the accuracy of these predicted conformations is sufficient for screening chemical compounds that will effectively interact with a protein target for pharmacological purposes. In this opinion article, we examine the potential benefits and limitations of using state-annotated conformations for ultra-large library screening (ULLS) in light of the growing size of ultra-large libraries (ULLs). We believe that targeting different conformational states of common drug targets like G-protein-coupled receptors (GPCRs), which can regulate human physiology by switching between different conformations, can offer multiple advantages.
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Affiliation(s)
- D Sala
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - H Batebi
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - K Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - P W Hildebrand
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - J Meiler
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
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20
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Krishna Sunkari Y, Kumar Siripuram V, Flajolet M. Diversity-Oriented Synthesis (DOS) of On-DNA Peptidomimetics from Acid-Derived Phosphonium Ylides. Chemistry 2023; 29:e202203037. [PMID: 36653313 DOI: 10.1002/chem.202203037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 01/20/2023]
Abstract
The DNA-encoded library (DEL) technology represents a revolutionary drug-discovery tool with unprecedented screening power originating from the association of combinatorial chemistry and DNA barcoding. The chemical diversity of DELs and its chemical space will be further expanded as new DNA-compatible reactions are introduced. This work introduces the use of DOS in the context of on-DNA peptidomimetics. Wittig olefination of aspartic acid-derived on-DNA Wittig ylide, combined with a broad substrate scope of aldehydes, led to formation of on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated ketones. The synthesis of on-DNA multi-peptidyl-ylides was performed by incorporating sequential amino acids onto a monomeric ylide. Di-, tri- and tetrameric peptidyl-ylides were validated for Wittig olefination and led to on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated-based peptidomimetics, an important class of intermediates. One on-DNA aryl Wittig ylide was also developed and applied to Wittig olefination for synthesis of on-DNA chalcone-based molecules. Furthermore, DOS was used successfully with electron-deficient peptidomimetics and led to the development of different heterocyclic cores containing on-DNA peptidomimetics.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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21
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Zhao G, Wang H, Luo J, He X, Xiong F, Li Y, Zhang G, Li Y. Multicomponent DNA-Compatible Synthesis of an Annelated Benzodiazepine Scaffold for Focused Chemical Libraries. Org Lett 2023; 25:665-670. [PMID: 36693020 DOI: 10.1021/acs.orglett.2c04293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Annelated benzodiazepines are attractive drug-like scaffolds with a broad spectrum of biological activities. Incorporation of this heterocyclic core into DNA-encoded chemical libraries (DELs) via multicomponent assembly is highly demanded. Herein, we developed a DNA-compatible method to generate the tricyclic benzodiazepine scaffold via catalyst-free three-component condensation using a broad range of aldehyde, o-phenylenediamine, and diketone sources. With either aldehyde or o-phenylenediamine conjugated with DNA tags, functionalized 1,5-benzodiazepine scaffolds were efficiently forged, expanding the chemical space of the diazepine-centered drug-like DEL.
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Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Huihong Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Pharmaceutical Department of Chongqing Three Gorges Central Hospital, Chongqing University Three Gorges Hospital, 404100 Chongqing, P. R. China
| | - Jie Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xun He
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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22
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Chen Q, Liu C, Wang W, Meng X, Cheng X, Li X, Cai L, Luo L, He X, Qu H, Luo J, Wei H, Gao S, Liu G, Wan J, Israel DI, Li J, Dou D. Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach. ACS Chem Biol 2023; 18:25-33. [PMID: 36606710 PMCID: PMC9872815 DOI: 10.1021/acschembio.2c00797] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023]
Abstract
The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.
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Affiliation(s)
- Qiuxia Chen
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Chuan Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Wei Wang
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xiaoyun Meng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xuemin Cheng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xianyang Li
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Longying Cai
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Linfu Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xu He
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Huan Qu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jing Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Hong Wei
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Sen Gao
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Guansai Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jinqiao Wan
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | | | - Jin Li
- HitGen
Inc., Chengdu, Sichuan 610200, China
| | - Dengfeng Dou
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
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23
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Nie Q, Sun J, Fang X, He X, Xiong F, Zhang G, Li Y, Li Y. Antimony salt-promoted cyclization facilitating on-DNA syntheses of dihydroquinazolinone derivatives and its applications. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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Chines S, Ehrt C, Potowski M, Biesenkamp F, Grützbach L, Brunner S, van den Broek F, Bali S, Ickstadt K, Brunschweiger A. Navigating chemical reaction space - application to DNA-encoded chemistry. Chem Sci 2022; 13:11221-11231. [PMID: 36320474 PMCID: PMC9517168 DOI: 10.1039/d2sc02474h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Databases contain millions of reactions for compound synthesis, rendering selection of reactions for forward synthetic design of small molecule screening libraries, such as DNA-encoded libraries (DELs), a big data challenge. To support reaction space navigation, we developed the computational workflow Reaction Navigator. Reaction files from a large chemistry database were processed using the open-source KNIME Analytics Platform. Initial processing steps included a customizable filtering cascade that removed reactions with a high probability to be incompatible with DEL, as they would e.g. damage the genetic barcode, to arrive at a comprehensive list of transformations for DEL design with applicability potential. These reactions were displayed and clustered by user-defined molecular reaction descriptors which are independent of reaction core substitution patterns. Thanks to clustering, these can be searched manually to identify reactions for DEL synthesis according to desired reaction criteria, such as ring formation or sp3 content. The workflow was initially applied for mapping chemical reaction space for aromatic aldehydes as an exemplary functional group often used in DEL synthesis. Exemplary reactions have been successfully translated to DNA-tagged substrates and can be applied to library synthesis. The versatility of the Reaction Navigator was then shown by mapping reaction space for different reaction conditions, for amines as a second set of starting materials, and for data from a second database.
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Affiliation(s)
- Silvia Chines
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | | | - Marco Potowski
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Felix Biesenkamp
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Lars Grützbach
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Susanne Brunner
- TU Dortmund University, Department of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | | | - Shilpa Bali
- Elsevier B.V. Radarweg 29 1043 NX Amsterdam The Netherlands
| | - Katja Ickstadt
- TU Dortmund University, Department of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
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25
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Chen Y, Li W, Xing H. Chemistries and applications of DNA-natural product conjugate. Front Chem 2022; 10:984916. [PMID: 36147254 PMCID: PMC9489112 DOI: 10.3389/fchem.2022.984916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022] Open
Abstract
Natural products and their derivatives have made great contributions to chemotherapy, especially for the treatment of tumors and infections. Despite the achievements, natural product-based small molecule drugs usually suffer from side effects, short circulation time, and solubility issue. To overcome these drawbacks, a common approach is to integrate another bio-functional motif into a natural product compound, enabling targeted or synergistic therapy. One of the most promising strategies is to form a DNA-natural product conjugate to improve therapeutic purposes. The incorporated DNA molecules can serve as an aptamer, a nucleic-acid-based congener of antibody, to specifically bind to the disease target of interest, or function as a gene therapy agent, such as immuno-adjuvant or antisense, to enable synergistic chemo-gene therapy. DNA-natural product conjugate can also be incorporated into other DNA nanostructures to improve the administration and delivery of drugs. This minireview aims to provide the chemistry community with a brief overview on this emerging topic of DNA-natural product conjugates for advanced therapeutics. The basic concepts to use the conjugation, the commonly used robust conjugation chemistries, as well as applications in targeted therapy and synergistic therapy of using DNA-natural product conjugates, are highlighted in this minireview. Future perspectives and challenges of this field are also discussed in the discussion and perspective section.
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26
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Gao Y, Sun Y, Zhao G, Zhang G, Li Y, Li Y. On-DNA Synthesis of Functionalized 4 H-Pyran Scaffolds for Focused DNA-Encoded Chemical Libraries. Org Lett 2022; 24:6664-6669. [PMID: 36053053 DOI: 10.1021/acs.orglett.2c02714] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionalized 4H-pyran scaffold has aroused synthetic attention because it is widely found in many interesting pharmacologically relevant compounds. We here disclose its incorporation into DNA-encoded chemical libraries, combining this scaffold with the merits of scaffold architecture in drug design. Under the optimized DNA-compatible conditions, functionalized 4H-pyrans were efficiently formed with a broad substrate scope. Among the 4H-pyrans formed, the axial structure features rotational restriction, and the spirocyclic structure provides rigidity and three-dimensionality. These efforts open the door for the construction of DNA-encoded chemical libraries with more consideration for this structural architecture.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.,Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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27
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Eom S, Kwon T, Lee DY, Park CH, Kim HJ. Copper-Mediated Three-Component Reaction for the Synthesis of N-Acylsulfonamide on DNA. Org Lett 2022; 24:4881-4885. [PMID: 35775977 DOI: 10.1021/acs.orglett.2c01675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA-encoded library (DEL) technology is a new method for discovering hit compounds for target proteins in the pharmaceutical industry. The N-acylsulfonamide functional group has been reported to exhibit various pharmacological activities, and based on this, the demand for a method that allows its introduction into the DEL platform has increased. In this report, a procedure for synthesizing N-acylsulfonamide functional groups applicable to DEL construction was developed in the presence of a copper reagent and water as a nucleophile from simple alkynes or sulfonyl azides, which are widely commercially available. Furthermore, we prove that a new alternative procedure can be used to construct a DNA-encoded library.
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Affiliation(s)
- Solji Eom
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Taeyeon Kwon
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Da Yeon Lee
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Chi Hoon Park
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Hyun Jin Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
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28
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Sun J, Nie Q, Fang X, He Z, Zhang G, Li Y, Li Y. Vinyl azide as a synthon for DNA-compatible divergent transformations into N-heterocycles. Org Biomol Chem 2022; 20:5045-5049. [PMID: 35703385 DOI: 10.1039/d2ob00862a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Inspired by diversity-oriented synthesis, we have developed a series of DNA-compatible transformations utilizing on-DNA vinyl azide as a synthon to forge divergent N-heterocyclic scaffolds. Polysubstituted imidazoles and isoquinolines were efficiently obtained with moderate-to-excellent conversions. Besides, the "one-pot" strategy to prepare in-house on-DNA vinyl azides afforded synthons readily. Results from substrate scope exploration and enzymatic ligation further demonstrate the feasibility of these N-heterocycle syntheses in DNA-encoded chemical library construction.
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Affiliation(s)
- Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Zhiwei He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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29
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Siripuram VK, Sunkari YK, Nguyen TL, Flajolet M. DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries. Front Chem 2022; 10:894603. [PMID: 35774858 PMCID: PMC9237475 DOI: 10.3389/fchem.2022.894603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
An efficient method for the C-C bond formation via water soluble Na2PdCl4/sSPhos mediated Suzuki-Miyaura cross-coupling reaction of DNA-conjugated aryl iodide with (het)aryl boronic acids has been developed. This reaction proceeds at 37°C in water and acetonitrile (4:1) system. We also demonstrated that numerous aromatic and heteroaromatic boronic acids of different electronic natures, and harboring various functional groups, were highly compatible providing the desired coupling products in good to excellent yields. This DNA-compatible Suzuki-Miyaura cross-coupling reaction has strong potential to construct DNA-Encoded Libraries (DELs) in the context of drug discovery.
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Affiliation(s)
| | | | | | - Marc Flajolet
- *Correspondence: Vijay Kumar Siripuram, ; Marc Flajolet,
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30
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Fang X, Wang Y, He P, Liao H, Zhang G, Li Y, Li Y. Visible Light-Promoted Divergent Benzoheterocyclization from Aldehydes for DNA-Encoded Chemical Libraries. Org Lett 2022; 24:3291-3296. [PMID: 35467894 DOI: 10.1021/acs.orglett.2c01187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Benzoheterocyclics have been widely adopted as drug-like core scaffolds that can be incorporated into DNA-encoded chemical library technology for high-throughput hit discovery. Here, we present a visible light-promoted divergent synthesis of on-DNA benzoheterocycles from aldehydes. Four types of DNA-conjugated benzoheterocyclics were obtained under mild conditions with a broad substrate scope. A cross substrate scope study, together with enzymatic ligation and subsequent chemical diversifications, were conducted, demonstrating the feasibility of this approach in DNA-encoded chemical library construction.
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Affiliation(s)
- Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Pengyang He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Huilin Liao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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31
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Warr WA, Nicklaus MC, Nicolaou CA, Rarey M. Exploration of Ultralarge Compound Collections for Drug Discovery. J Chem Inf Model 2022; 62:2021-2034. [PMID: 35421301 DOI: 10.1021/acs.jcim.2c00224] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Designing new medicines more cheaply and quickly is tightly linked to the quest of exploring chemical space more widely and efficiently. Chemical space is monumentally large, but recent advances in computer software and hardware have enabled researchers to navigate virtual chemical spaces containing billions of chemical structures. This review specifically concerns collections of many millions or even billions of enumerated chemical structures as well as even larger chemical spaces that are not fully enumerated. We present examples of chemical libraries and spaces and the means used to construct them, and we discuss new technologies for searching huge libraries and for searching combinatorially in chemical space. We also cover space navigation techniques and consider new approaches to de novo drug design and the impact of the "autonomous laboratory" on synthesis of designed compounds. Finally, we summarize some other challenges and opportunities for the future.
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Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, 6 Berwick Court, Holmes Chapel, Crewe, Cheshire CW4 7HZ, United Kingdom
| | - Marc C Nicklaus
- NCI, NIH, CADD Group, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Christos A Nicolaou
- Discovery Chemistry, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Matthias Rarey
- Universität Hamburg, ZBH Center for Bioinformatics, 20146 Hamburg, Germany
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32
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Shen Y, Yang G, Huang W, Shaginian A, Lin Q, Wan J, Li J, Deng Y, Liu G. Photoredox Deaminative Alkylation in DNA-Encoded Library Synthesis. Org Lett 2022; 24:2650-2654. [PMID: 35362987 DOI: 10.1021/acs.orglett.2c00697] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herein, we report an on-DNA photoredox-mediated deaminative alkylation method for diversifying DNA-tagged acrylamide substrate with amine-derived radicals. The radicals can be conveniently generated from sterically hindered primary amines, and the deaminative alkylation can tolerate a broad array of radical precursors. Furthermore, the methodology is applicable to Boc-protected diamines, free amino acids, and aryl halides, which bear functional groups enabling additional rounds of diversification. The method is believed to offer a high potential for constructing DNA-encoded libraries, as was demonstrated by the production of a mock library in a 2 × 3 matrix format and confirmation of DNA stability by UPLC-MS and qPCR experiments.
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Affiliation(s)
- Yurong Shen
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, P.R. China
| | - Guanyu Yang
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Wei Huang
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Alex Shaginian
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Qian Lin
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Jin Li
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Yun Deng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, P.R. China
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
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33
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Christensen TA, Lee KY, Gottlieb SZP, Carrier MB, Leconte AM. Mutant polymerases capable of 2′ fluoro-modified nucleic acid synthesis and amplification with improved accuracy. RSC Chem Biol 2022; 3:1044-1051. [PMID: 35975008 PMCID: PMC9347352 DOI: 10.1039/d2cb00064d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Nonnatural nucleic acids (xeno nucleic acids, XNA) can possess several useful properties such as expanded reactivity and nuclease resistance, which can enhance the utility of DNA as a biotechnological tool. Native DNA polymerases are unable to synthesize XNA, so, in recent years mutant XNA polymerases have been engineered with sufficient activity for use in processes such as PCR. While substantial improvements have been made, accuracy still needs to be increased by orders of magnitude to approach natural error rates and make XNA polymerases useful for applications that require high fidelity. Here, we systematically evaluate leading Taq DNA polymerase mutants for their fidelity during synthesis of 2′F XNA. To further improve their accuracy, we add mutations that have been shown to increase the fidelity of wild-type Taq polymerases, to some of the best current XNA polymerases (SFM4–3, SFM4–6, and SFP1). The resulting polymerases show significant improvements in synthesis accuracy. In addition to generating more accurate XNA polymerases, this study also informs future polymerase engineering efforts by demonstrating that mutations that improve the accuracy of DNA synthesis may also have utility in improving the accuracy of XNA synthesis. Polymerases that have been evolved to synthesize 2′F XNA are often inaccurate. Here, we show that you can improve the accuracy of 2′F XNA polymerase synthesis by adding mutations previously found to improve the accuracy of natural DNA synthesis.![]()
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Affiliation(s)
- Trevor A. Christensen
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Kristi Y. Lee
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Simone Z. P. Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Mikayla B. Carrier
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Aaron M. Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
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34
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Gao Y, Sun Y, Fang X, Zhao G, Li X, Zhang G, Li Y, Li Y. Development of on-DNA vinyl sulfone synthesis for DNA-encoded chemical libraries. Org Chem Front 2022. [DOI: 10.1039/d2qo00881e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present the development of an efficient synthetic route to generate a DNA-compatible vinyl sulfone functional group, and the subsequent chemical transformations demonstrated the feasibility of our method in DEL construction.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xufeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China
- Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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