1
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Deng J, Belyanskaya S, Prabhu N, Arico-Muendel C, Deng H, Phelps CB, Israel DI, Yang H, Boyer J, Franklin GJ, Yap JL, Lind KE, Tsai CH, Donahue C, Summerfield JD. Profiling cells with DELs: Small molecule fingerprinting of cell surfaces. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100171. [PMID: 38917882 DOI: 10.1016/j.slasd.2024.100171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
DNA-encoded small molecule library technology has recently emerged as a new paradigm for identifying ligands against drug targets. To date, it has been used to identify ligands against targets that are soluble or overexpressed on cell surfaces. Here, we report applying cell-based selection methods to profile surfaces of mouse C2C12 myoblasts and myotube cells in an unbiased, target agnostic manner. A panel of on-DNA compounds were identified and confirmed for cell binding selectivity. We optimized the cell selection protocol and employed a novel data analysis method to identify cell selective ligands against a panel of human B and T lymphocytes. We discuss the generality of using this workflow for DNA encoded small molecule library selection and data analysis against different cell types, and the feasibility of applying this method to profile cell surfaces for biomarker and target identification.
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Affiliation(s)
- Jason Deng
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Svetlana Belyanskaya
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Ninad Prabhu
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | | | - Hongfeng Deng
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Christopher B Phelps
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - David I Israel
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Hongfang Yang
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Joseph Boyer
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - G Joseph Franklin
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Jeremy L Yap
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Kenneth E Lind
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Ching-Hsuan Tsai
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Christine Donahue
- GSK Molecular Modalities Discovery, 200 Cambridgepark Drive, Cambridge, MA, 02140, USA
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2
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Keller M, Petrov D, Gloger A, Dietschi B, Jobin K, Gradinger T, Martinelli A, Plais L, Onda Y, Neri D, Scheuermann J. Highly pure DNA-encoded chemical libraries by dual-linker solid-phase synthesis. Science 2024; 384:1259-1265. [PMID: 38870307 DOI: 10.1126/science.adn3412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
The first drugs discovered using DNA-encoded chemical library (DEL) screens have entered late-stage clinical development. However, DEL technology as a whole still suffers from poor chemical purity resulting in suboptimal performance. In this work, we report a technique to overcome this issue through self-purifying release of the DEL after magnetic bead-based synthesis. Both the first and last building blocks of each assembled library member were linked to the beads by tethers that could be cleaved by mutually orthogonal chemistry. Sequential cleavage of the first and last tether, with washing in between, ensured that the final library comprises only the fully complete compounds. The outstanding purity attained by this approach enables a direct correlation of chemical display and encoding, allows for an increased chemical reaction scope, and facilitates the use of more diversity elements while achieving greatly improved signal-to-noise ratios in selections.
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Affiliation(s)
- Michelle Keller
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dimitar Petrov
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Gloger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Bastien Dietschi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Kilian Jobin
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Timon Gradinger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Yuichi Onda
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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3
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Coppola C, Greco M, Munir A, Musarò D, Quarta S, Massaro M, Lionetto MG, Maffia M. Osteoarthritis: Insights into Diagnosis, Pathophysiology, Therapeutic Avenues, and the Potential of Natural Extracts. Curr Issues Mol Biol 2024; 46:4063-4105. [PMID: 38785519 PMCID: PMC11119992 DOI: 10.3390/cimb46050251] [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: 02/28/2024] [Revised: 04/05/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Osteoarthritis (OA) stands as a prevalent and progressively debilitating clinical condition globally, impacting joint structures and leading to their gradual deterioration through inflammatory mechanisms. While both non-modifiable and modifiable factors contribute to its onset, numerous aspects of OA pathophysiology remain elusive despite considerable research strides. Presently, diagnosis heavily relies on clinician expertise and meticulous differential diagnosis to exclude other joint-affecting conditions. Therapeutic approaches for OA predominantly focus on patient education for self-management alongside tailored exercise regimens, often complemented by various pharmacological interventions primarily targeting pain alleviation. However, pharmacological treatments typically exhibit short-term efficacy and local and/or systemic side effects, with prosthetic surgery being the ultimate resolution in severe cases. Thus, exploring the potential integration or substitution of conventional drug therapies with natural compounds and extracts emerges as a promising frontier in enhancing OA management. These alternatives offer improved safety profiles and possess the potential to target specific dysregulated pathways implicated in OA pathogenesis, thereby presenting a holistic approach to address the condition's complexities.
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Affiliation(s)
- Chiara Coppola
- Department of Mathematics and Physics “E. De Giorgi”, University of Salento, Via Lecce-Arnesano, 73100 Lecce, Italy; (C.C.); (A.M.)
| | - Marco Greco
- Department of Biological and Environmental Science and Technology, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy; (M.G.); (D.M.); (S.Q.); (M.G.L.)
| | - Anas Munir
- Department of Mathematics and Physics “E. De Giorgi”, University of Salento, Via Lecce-Arnesano, 73100 Lecce, Italy; (C.C.); (A.M.)
| | - Debora Musarò
- Department of Biological and Environmental Science and Technology, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy; (M.G.); (D.M.); (S.Q.); (M.G.L.)
| | - Stefano Quarta
- Department of Biological and Environmental Science and Technology, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy; (M.G.); (D.M.); (S.Q.); (M.G.L.)
| | - Marika Massaro
- Institute of Clinical Physiology (IFC), National Research Council (CNR), 73100 Lecce, Italy;
| | - Maria Giulia Lionetto
- Department of Biological and Environmental Science and Technology, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy; (M.G.); (D.M.); (S.Q.); (M.G.L.)
| | - Michele Maffia
- Department of Experimental Medicine, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy
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4
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Ye Y, Berry M, Bock WJ, Cheng K, Nair SK, Park CS, Patman RL, Sakata S, Tran-Dubé M, Donaldson JS, Yang G, Liu G. Construction of Isoquinolone Scaffolds on DNA via Rhodium(III)-Catalyzed C-H Activation. Org Lett 2024; 26:3338-3342. [PMID: 38608176 DOI: 10.1021/acs.orglett.4c00604] [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: 04/14/2024]
Abstract
Isoquinolone is one of the most common heterocyclic core structures in countless natural products and many bioactive compounds. Here, a highly efficient approach to synthesize isoquinolone scaffolds on DNA via rhodium(III)-catalyzed C-H activation has been described. This chemistry transformation is robust and has shown good compatibility with DNA, which is suitable for DNA-encoded library synthesis.
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Affiliation(s)
- Yusong Ye
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan P. R. China
| | - Madeline Berry
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - William J Bock
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Kunpeng Cheng
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan P. R. China
| | - Sajiv K Nair
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Christiana S Park
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Ryan L Patman
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sylvie Sakata
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Michelle Tran-Dubé
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Joyann S Donaldson
- Pfizer Oncology Medicinal Chemistry, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Guanyu Yang
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan P. R. China
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan P. R. China
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5
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Zeng H, Li Y, Wu R, Liu D, Zhang Y, Xu S, Niu D. Carbohydrate-DNA Conjugation Enabled by Glycosyl Radicals Generated from Glycosyl Sulfinates. Org Lett 2024; 26:2686-2690. [PMID: 37125782 DOI: 10.1021/acs.orglett.3c00833] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Herein, we report a method that enables the synthesis of carbohydrate-DNA conjugates by radical addition. Key to the success is the use of readily available, bench-stable, and unprotected glycosyl sulfinates as precursors to glycosyl radicals. The redox neutral reaction proceeds under mild and simple conditions and tolerates a broad substrate scope. A small library of carbohydrate-DNA conjugates was prepared.
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Affiliation(s)
- Hongxin Zeng
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Yanjing Li
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Rongfeng Wu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Daqi Liu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Yang Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Shiyang Xu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
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6
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Montoya AL, Glavatskikh M, Halverson BJ, Yuen LH, Schüler H, Kireev D, Franzini RM. Combining pharmacophore models derived from DNA-encoded chemical libraries with structure-based exploration to predict Tankyrase 1 inhibitors. Eur J Med Chem 2023; 246:114980. [PMID: 36495630 PMCID: PMC9805525 DOI: 10.1016/j.ejmech.2022.114980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
DNA-encoded chemical libraries (DECLs) interrogate the interactions of a target of interest with vast numbers of molecules. DECLs hence provide abundant information about the chemical ligand space for therapeutic targets, and there is considerable interest in methods for exploiting DECL screening data to predict novel ligands. Here we introduce one such approach and demonstrate its feasibility using the cancer-related poly-(ADP-ribose)transferase tankyrase 1 (TNKS1) as a model target. First, DECL affinity selections resulted in structurally diverse TNKS1 inhibitors with high potency including compound 2 with an IC50 value of 0.8 nM. Additionally, TNKS1 hits from four DECLs were translated into pharmacophore models, which were exploited in combination with docking-based screening to identify TNKS1 ligand candidates in databases of commercially available compounds. This computational strategy afforded TNKS1 inhibitors that are outside the chemical space covered by the DECLs and yielded the drug-like lead compound 12 with an IC50 value of 22 nM. The study further provided insights in the reliability of screening data and the effect of library design on hit compounds. In particular, the study revealed that while in general DECL screening data are in good agreement with off-DNA ligand binding, unpredictable interactions of the DNA-attachment linker with the target protein contribute to the noise in the affinity selection data.
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Affiliation(s)
- Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Brayden J Halverson
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Lik Hang Yuen
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100, Lund, Sweden.
| | - Dmitri Kireev
- Department of Chemistry, 36 Schlundt Hall, University of Missouri, Columbia, MO, 65211, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, UT, 84112, USA.
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7
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Cuffaro D, Ciccone L, Rossello A, Nuti E, Santamaria S. Targeting Aggrecanases for Osteoarthritis Therapy: From Zinc Chelation to Exosite Inhibition. J Med Chem 2022; 65:13505-13532. [PMID: 36250680 PMCID: PMC9620172 DOI: 10.1021/acs.jmedchem.2c01177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Indexed: 11/30/2022]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease. In 1999, two members of the A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) family of metalloproteinases, ADAMTS4 and ADAMTS5, or aggrecanases, were identified as the enzymes responsible for aggrecan degradation in cartilage. The first aggrecanase inhibitors targeted the active site by chelation of the catalytic zinc ion. Due to the generally disappointing performance of zinc-chelating inhibitors in preclinical and clinical studies, inhibition strategies tried to move away from the active-site zinc in order to improve selectivity. Exosite inhibitors bind to proteoglycan-binding residues present on the aggrecanase ancillary domains (called exosites). While exosite inhibitors are generally more selective than zinc-chelating inhibitors, they are still far from fulfilling their potential, partly due to a lack of structural and functional data on aggrecanase exosites. Filling this gap will inform the design of novel potent, selective aggrecanase inhibitors.
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Affiliation(s)
- Doretta Cuffaro
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Lidia Ciccone
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Elisa Nuti
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Salvatore Santamaria
- Department
of Immunology and Inflammation, Imperial
College London, Du Cane Road, London W12
0NN, U.K.
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8
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Li L, Su M, Lu W, Song H, Liu J, Wen X, Suo Y, Qi J, Luo X, Zhou YB, Liao XH, Li J, Lu X. Triazine-Based Covalent DNA-Encoded Libraries for Discovery of Covalent Inhibitors of Target Proteins. ACS Med Chem Lett 2022; 13:1574-1581. [PMID: 36262386 PMCID: PMC9575176 DOI: 10.1021/acsmedchemlett.2c00127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/10/2022] [Indexed: 11/28/2022] Open
Abstract
Since ibrutinib was approved by the FDA as an effective monotherapy for chronic lymphocytic leukemia (CLL) and multilymphoma, more and more FDA-approved covalent drugs are coming back into the market. On this occasion, the resurgence of interest in covalent drugs calls for more hit discovery techniques. However, the limited numbers of covalent libraries prevent the development of this area. Herein, we report the design of covalent DNA-encoded library (DEL) and its selection method for the discovery of covalent inhibitors for target proteins. These triazine-based covalent DELs yielded potent compounds after covalent selection against target proteins, including Bruton's Tyrosine Kinase (BTK), Janus kinase 3 (JAK3), and peptidyl-prolyl cis/trans isomerase NIMA-interacting-1 (Pin1).
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Affiliation(s)
- Linjie Li
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Mingbo Su
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Weiwei Lu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Hongzhi Song
- School
of Medicine, Shanghai University, Shanghai 200444, P. R. China
| | - Jiaxiang Liu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Xin Wen
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
| | - Yanrui Suo
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
| | - Jingjing Qi
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Xiaomin Luo
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Yu-Bo Zhou
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400,P. R. China
| | - Xin-Hua Liao
- School of
Life Sciences, Shanghai University, Shanghai200444, P. R. China
| | - Jia Li
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400,P. R. China
| | - Xiaojie Lu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
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9
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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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10
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Sun Z, Zhang J, Zhang H, Cao H, Xiao L, Yang K, Hu YJ. DNA Compatible Oxidization and Amidation of Terminal Alkynes. Bioconjug Chem 2022; 33:1585-1594. [PMID: 36001094 DOI: 10.1021/acs.bioconjchem.2c00340] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Through a modified Kinugasa reaction, a novel method of amidation on terminal oligo alkyne conjugates by copper-promoted oxidation with nitrones has been developed. Unprotected bifunctional carboxylic acid-amine reagents can be transformed directly to the respective amide products under these edited Kinugasa reaction conditions. 3-Cycle DNA-encoded libraries (DELs) can be built in three steps of chemical conversion.
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Affiliation(s)
- Zhaomei Sun
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Jie Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Huanqing Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Hongli Cao
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Lingqian Xiao
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing, 100176, China
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, China
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11
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Dakhel S, Galbiati A, Migliorini F, Comacchio C, Oehler S, Prati L, Scheuermann J, Cazzamalli S, Neri D, Bassi G, Favalli N. Isolation of a Natural Killer Group 2D Small-Molecule Ligand from DNA-Encoded Chemical Libraries. ChemMedChem 2022; 17:e202200350. [PMID: 35929380 DOI: 10.1002/cmdc.202200350] [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: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/11/2022]
Abstract
Natural Killer Group 2D (NKG2D) is a homo-dimeric transmembrane protein which is typically expressed on the surface of natural killer (NK) cells, natural killer T (NKT) cells, gamma delta T (γδT) cells, activated CD8 positive T-cells and activated macrophages. Bispecific molecules, capable of bridging NKG2D with a target protein expressed on the surface of tumor cells, may be used to redirect the cytotoxic activity of NK-cells towards antigen-positive malignanT-cells. In this work, we report the discovery of a novel NKG2D small molecule binder [K D = (410±60) nM], isolated from a DNA-Encoded Chemical Library (DEL). The discovery of small organic NKG2D ligands may facilitate the generation of fully synthetic bispecific adaptors, which may serve as an alternative to bispecific antibody products and which may benefit from better tumor targeting properties.
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Affiliation(s)
| | | | | | | | | | - Luca Prati
- Philogen SpA, R&D (Philochem), SWITZERLAND
| | - Jörg Scheuermann
- ETH Zürich: Eidgenossische Technische Hochschule Zurich, chemistry and applied biosciences, SWITZERLAND
| | | | | | | | - Nicholas Favalli
- Philogen SpA, R&D (Philochem), Libernstrasse 3, 8112, Otelfingen, SWITZERLAND
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12
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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Affiliation(s)
- Paddy R. A. Melsen
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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13
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Castan IFSF, Madin A, Pairaudeau G, Waring MJ. Scope of on-DNA nucleophilic aromatic substitution on weakly-activated heterocyclic substrates for the synthesis of DNA-encoded libraries. Bioorg Med Chem 2022; 63:116688. [PMID: 35430536 DOI: 10.1016/j.bmc.2022.116688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022]
Abstract
DNA-Encoded Libraries (DEL) represent a promising hit finding strategy for drug discovery. Nonetheless, the available DNA-compatible chemistry remains of limited scope. Nucleophilic aromatic substitution (SNAr) has been extensively used in DEL synthesis but has generally been restricted to highly activated (hetero)arenes. Herein, we report an optimised procedure for SNAr reactions through the use of factorial experimental design (FED) on-DNA using 15% THF as a co-solvent. This method gave conversions of >95% for pyridine and pyrazine scaffolds for 36 secondary cyclic amines. This analysis provides a new DNA-compatible SNAr reaction to produce high yielding libraries. The scope of this reaction on other amines is described. This work identifies challenges for the further development for DNA-compatible SNAr reactions. 2009 Elsevier Ltd. All rights reserved.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | | | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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14
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Hua Y, Fang X, Xing G, Xu Y, Liang L, Deng C, Dai X, Liu H, Lu T, Zhang Y, Chen Y. Effective Reaction-Based De Novo Strategy for Kinase Targets: A Case Study on MERTK Inhibitors. J Chem Inf Model 2022; 62:1654-1668. [PMID: 35353505 DOI: 10.1021/acs.jcim.2c00068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reaction-based de novo design is the computational generation of novel molecular structures by linking building blocks using reaction vectors derived from chemistry knowledge. In this work, we first adopted a recurrent neural network (RNN) model to generate three groups of building blocks with different functional groups and then constructed an in silico target-focused combinatorial library based on chemical reaction rules. Mer tyrosine kinase (MERTK) was used as a study case. Combined with a scaffold enrichment analysis, 15 novel MERTK inhibitors covering four scaffolds were achieved. Among them, compound 5a obtained an IC50 value of 53.4 nM against MERTK without any further optimization. The efficiency of hit identification could be significantly improved by shrinking the compound library with the fragment iterative optimization strategy and enriching the dominant scaffold in the hinge region. We hope that this strategy can provide new insights for accelerating the drug discovery process.
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Affiliation(s)
- Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Xiaobao Fang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Guomeng Xing
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yuan Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Li Liang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chenglong Deng
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Xiaowen Dai
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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15
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Sun ZM, Yang SG, Xue LJ, Zhang J, Yang K, Hu YJ. N-Alkyl Linkers for DNA-Encoded Chemical Libraries. Chem Asian J 2022; 17:e202200016. [PMID: 35254005 DOI: 10.1002/asia.202200016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/14/2022] [Indexed: 11/06/2022]
Abstract
A series of novel N-alkyl linkers that connect small-molecule library members with their encoding DNA oligonucleotides has been developed. In comparison with the standard amide linker (usually constructed with oligo-AOP-NH2 ), the N-alkyl linker is not only more chemically stable, but also provides better structural diversity at the linkage point. Chemical variety in the vicinity of the polyglycol terminus, in particular, could affect binding interactions with the target protein. It could have been neglected in previous DNA-encoded chemical library (DEL) synthesis and screening studies due to the limited linkage alternatives. With these linkers, one can produce versatile key intermediates as Cycle 1 products directly amenable to Cycle 2 chemistry without the use of protecting groups. As a result, a DEL synthesis process that uses the fewest chemical conversions, such as 3-step, 3-cycle DELs, can achieve higher synthetic efficiency while creating less DNA tag degradation, resulting in higher quality DELs.
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Affiliation(s)
- Zhao-Mei Sun
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Shao-Guang Yang
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Li-Jun Xue
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Jie Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Kexin Yang
- Taihe Road, Pharmaron Beijing Co., Ltd., 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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16
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Gao Y, Zhao G, He P, Zhang G, Li Y, Li Y. DNA-Compatible Synthesis of α,β-Epoxyketones for DNA-Encoded Chemical Libraries. Bioconjug Chem 2022; 33:105-110. [PMID: 34927428 DOI: 10.1021/acs.bioconjchem.1c00567] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As a powerful platform in drug discovery, the DNA-encoded chemical library technique enables the generation of numerous chemical members with high structural diversity. Epoxides widely exist in a variety of approved drugs and clinical candidates, eliciting multiple pharmaceutical activities. Herein, we report a non-oxidative DNA-compatible synthesis of di-/trisubstituted α,β-epoxyketones by implementing aldehydes and α-chlorinated ketones as abundant building blocks. This methodology was demonstrated to cover a broad substrate scope with medium-to-excellent conversions. Further structural diversification and transformation were also successfully explored to fully leverage α,β-epoxyketone moiety.
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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
| | - 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
| | - 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
| | - 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
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17
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Sunkari YK, Siripuram VK, Nguyen TL, Flajolet M. High-power screening (HPS) empowered by DNA-encoded libraries. Trends Pharmacol Sci 2021; 43:4-15. [PMID: 34782164 DOI: 10.1016/j.tips.2021.10.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023]
Abstract
The world is totally dependent on medications. As science progresses, new, better, and cheaper drugs are needed more than ever. The pharmaceutical industry has been predominantly dependent on high-throughput screening (HTS) for the past three decades. Considering that the discovery rate has been relatively constant, can one hope for a much-needed sudden trend uptick? DNA-encoded libraries (DELs) and similar technologies, that have several orders of magnitude more screening power than HTS, and that we propose to group together under the umbrella term of high-power screening (HPS), are very well positioned to do exactly that. HPS also offers novel screening options such as parallel screening, ex vivo and in vivo screening, as well as a new path to druggable alternatives such as proteolysis targeting chimeras (PROTACs). Altogether, HPS unlocks novel powerful drug discovery avenues.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA.
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18
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Gironda-Martínez A, Donckele EJ, Samain F, Neri D. DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges. ACS Pharmacol Transl Sci 2021; 4:1265-1279. [PMID: 34423264 PMCID: PMC8369695 DOI: 10.1021/acsptsci.1c00118] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) represent a versatile and powerful technology platform for the discovery of small-molecule ligands to protein targets of biological and pharmaceutical interest. DELs are collections of molecules, individually coupled to distinctive DNA tags serving as amplifiable identification barcodes. Thanks to advances in DNA-compatible reactions, selection methodologies, next-generation sequencing, and data analysis, DEL technology allows the construction and screening of libraries of unprecedented size, which has led to the discovery of highly potent ligands, some of which have progressed to clinical trials. In this Review, we present an overview of diverse approaches for the generation and screening of DEL molecular repertoires. Recent success stories are described, detailing how novel ligands were isolated from DEL screening campaigns and were further optimized by medicinal chemistry. The goal of the Review is to capture some of the most recent developments in the field, while also elaborating on future challenges to further improve DEL technology as a therapeutic discovery platform.
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Affiliation(s)
| | | | - Florent Samain
- Philochem
AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss
Federal Institute of Technology, CH-8093 Zürich, Switzerland
- Philogen
S.p.A, 53100 Siena, Italy
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19
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Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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20
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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Liu W, Huang W, Lin Q, Tsai MH, Zhang R, Fan L, Scott JD, Liu G, Wan J. Development of DNA-compatible hydroxycarbonylation reactions using chloroform as a source of carbon monoxide. Bioorg Med Chem 2021; 38:116118. [PMID: 33839592 DOI: 10.1016/j.bmc.2021.116118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 11/26/2022]
Abstract
A robust palladium-catalyzed hydroxycarbonylation of aryl halides on DNA has been developed. Instead of Mo(CO)6 as a source of carbon monoxide as previously described in the literature, chloroform was used as a surrogate in this report for the purpose of avoiding to use a large excess of molybdenum reagent which is not totally soluble in aqueous reaction mixtures.
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Affiliation(s)
- Wentao Liu
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China
| | - Wei Huang
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China
| | - Qian Lin
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China
| | - Mei-Hsuan Tsai
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China
| | - Rui Zhang
- New Jersey Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States
| | - Lijun Fan
- New Jersey Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States.
| | - Jack D Scott
- New Jersey Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, United States.
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China.
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu 1(st) East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, PR China.
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22
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Ding Y, Belyanskaya S, DeLorey JL, Messer JA, Joseph Franklin G, Centrella PA, Morgan BA, Clark MA, Skinner SR, Dodson JW, Li P, Marino JP, Israel DI. Discovery of soluble epoxide hydrolase inhibitors through DNA-encoded library technology (ELT). Bioorg Med Chem 2021; 41:116216. [PMID: 34023664 DOI: 10.1016/j.bmc.2021.116216] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 10/21/2022]
Abstract
Inhibition of soluble epoxide hydrolase (sEH) has recently emerged as a new approach to treat cardiovascular disease and respiratory disease. Inhibitors based on 1,3,5-triazine chemotype were discovered through affinity selection against two triazine-based DNA-encoded libraries. The structure and activity relationship study led to the expansion of the original 1,4-cycloalkyl series to related aniline, piperidine, quinoline, aryl-ether and benzylic series. The 1,3-cycloalkyl chemotype led to the discovery of a clinical candidate (GSK2256294) for COPD.
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Affiliation(s)
- Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
| | - Svetlana Belyanskaya
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jennifer L DeLorey
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jeffrey A Messer
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - G Joseph Franklin
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Paolo A Centrella
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Barry A Morgan
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Matthew A Clark
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Steven R Skinner
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jason W Dodson
- Department of Chemistry, Heart Failure Disease Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area Unit, GSK, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Peng Li
- Department of Chemistry, Heart Failure Disease Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area Unit, GSK, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Joseph P Marino
- Department of Chemistry, Heart Failure Disease Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area Unit, GSK, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - David I Israel
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
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23
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Ji Y, Dai D, Luo H, Shen S, Fan J, Wang Z, Chen M, Wan J, Li J, Ma H, Liu G. C-S Coupling of DNA-Conjugated Aryl Iodides for DNA-Encoded Chemical Library Synthesis. Bioconjug Chem 2021; 32:685-689. [PMID: 33720689 DOI: 10.1021/acs.bioconjchem.1c00076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Thioethers have been widely found in biologically active compounds, including pharmaceuticals. In this report, a highly efficient approach to on-DNA construction of thioethers via Cu-promoted Ullmann cross-coupling between DNA-conjugated aryl iodides and thiols is developed. This methodology was demonstrated with medium to high yields, without obvious DNA damage. This reported reaction has strong potential for application in DNA-encoded chemical library synthesis.
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Affiliation(s)
- Yue Ji
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Dongliang Dai
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Huadong Luo
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Simin Shen
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jing Fan
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Zhao Wang
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Min Chen
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Huiyong Ma
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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24
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Reiher CA, Schuman DP, Simmons N, Wolkenberg SE. Trends in Hit-to-Lead Optimization Following DNA-Encoded Library Screens. ACS Med Chem Lett 2021; 12:343-350. [PMID: 33738060 DOI: 10.1021/acsmedchemlett.0c00615] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/28/2021] [Indexed: 12/16/2022] Open
Abstract
DNA-encoded library (DEL) screens have emerged as a powerful hit-finding tool for a number of biological targets. In this Innovations article, we review published hit-to-lead optimization studies following DEL screens. Trends in molecular property changes from hit to lead are identified, and specific optimization tactics are exemplified in case studies. Across the studies, physicochemical property and structural changes post-DEL screening are similar to those which occur during hit-to-lead optimization following high throughputscreens (HTS). However, unique aspects of DEL-the combinatorial synthetic methods which enable DEL synthesis and the linker effects at the DNA attachment point-impact the strategies and outcomes of hit-to-lead optimizations.
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Affiliation(s)
- Christopher A. Reiher
- Discovery Chemistry, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - David P. Schuman
- Discovery Chemistry, Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Nicholas Simmons
- Discovery Chemistry, Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Scott E. Wolkenberg
- Discovery Chemistry, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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25
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Yang G, He D, Zhu Y, Zhu W, Tan Y, Long X, Wan J, Shi Z, Schuman D, Chheda P, Simmons N, Liu G. Cholesterol-Modified Oligonucleotides as Internal Reaction Controls during DNA-Encoded Chemical Library Synthesis. Bioconjug Chem 2021; 32:667-671. [PMID: 33689295 DOI: 10.1021/acs.bioconjchem.1c00045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report two cholesterol-modified oligonucleotides for use as internal controls for on-DNA reactions during the pooled stages of a DNA-encoded chemical library (DECL) synthesis. As these cholesterol-tagged oligonucleotides are chromatographically separable from normal DECL intermediates, they can be directly monitored by mass spectrometry to track reaction progression within a complex pool of DNA. We observed similar product conversions for reactions on substrates linked to a standard DECL DNA headpiece, to the cholesterol-modified oligonucleotides, and to the cholesterol-modified oligonucleotides while in the presence of pooled DECL synthetic intermediates-validating their use as a representative control. We also highlight an example from a DECL production in which the use of the cholesterol-modified oligonucleotides provided quality control information that guided synthetic decisions. We conclude that the use of cholesterol-modified oligonucleotides as a regular control will significantly improve the quality of DECL productions.
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Affiliation(s)
- Guanyu Yang
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Dou He
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Yijun Zhu
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Weiwei Zhu
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Yang Tan
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Xingwen Long
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Zhicai Shi
- Discovery Chemistry, Janssen Research and Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - David Schuman
- Discovery Chemistry, Janssen Research and Development, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Pratik Chheda
- Discovery Chemistry, Janssen Research and Development, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Nicholas Simmons
- Discovery Chemistry, Janssen Research and Development, 3210 Merryfield Row, San Diego, California 92121, United States
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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26
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Kölmel DK, Zhu H, Flanagan ME, Sakata SK, Harris AR, Wan J, Morgan BA. Employing Photocatalysis for the Design and Preparation of DNA‐Encoded Libraries: A Case Study. CHEM REC 2021; 21:616-630. [DOI: 10.1002/tcr.202000148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Dominik K. Kölmel
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Hongyao Zhu
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Mark E. Flanagan
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Sylvie K. Sakata
- Worldwide Research and Development Pfizer Inc 10770 Science Center Drive San Diego CA 92121 United States
| | - Anthony R. Harris
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Jinqiao Wan
- HitGen Inc Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District Chengdu City Sichuan Province P. R. China
| | - Barry A. Morgan
- HitGen Inc Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District Chengdu City Sichuan Province P. R. China
- HitGen Pharmaceuticals Inc PO Box 88240 Houston TX 77288 United States
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27
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Yuen J, Chai J, Ding Y. Condensation of DNA-Conjugated Imines with Homophthalic Anhydride for the Synthesis of Isoquinolones on DNA. Bioconjug Chem 2020; 31:2712-2718. [DOI: 10.1021/acs.bioconjchem.0c00508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Josephine Yuen
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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28
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Fan Z, Zhao S, Liu T, Shen PX, Cui ZN, Zhuang Z, Shao Q, Chen JS, Ratnayake AS, Flanagan ME, Kölmel DK, Piotrowski DW, Richardson P, Yu JQ. Merging C(sp 3)-H activation with DNA-encoding. Chem Sci 2020; 11:12282-12288. [PMID: 34094436 PMCID: PMC8162953 DOI: 10.1039/d0sc03935g] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA-encoded library (DEL) technology has the potential to dramatically expedite hit identification in drug discovery owing to its ability to perform protein affinity selection with millions or billions of molecules in a few experiments. To expand the molecular diversity of DEL, it is critical to develop different types of DNA-encoded transformations that produce billions of molecules with distinct molecular scaffolds. Sequential functionalization of multiple C–H bonds provides a unique avenue for creating diversity and complexity from simple starting materials. However, the use of water as solvent, the presence of DNA, and the extremely low concentration of DNA-encoded coupling partners (0.001 M) have hampered the development of DNA-encoded C(sp3)–H activation reactions. Herein, we report the realization of palladium-catalyzed C(sp3)–H arylation of aliphatic carboxylic acids, amides and ketones with DNA-encoded aryl iodides in water. Notably, the present method enables the use of alternative sets of monofunctional building blocks, providing a linchpin to facilitate further setup for DELs. Furthermore, the C–H arylation chemistry enabled the on-DNA synthesis of structurally-diverse scaffolds containing enriched C(sp3) character, chiral centers, cyclopropane, cyclobutane, and heterocycles. DNA-compatible C(sp3)–H activation reactions of aliphatic carboxylic acids, amides, and ketones were developed for efficient access to DEL synthesis.![]()
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Affiliation(s)
- Zhoulong Fan
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Shuai Zhao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Tao Liu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Peng-Xiang Shen
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zi-Ning Cui
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zhe Zhuang
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Qian Shao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Anokha S Ratnayake
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Mark E Flanagan
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Dominik K Kölmel
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - David W Piotrowski
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive San Diego CA 09121 USA
| | - Jin-Quan Yu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
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29
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Kómár P, Kalinić M. Denoising DNA Encoded Library Screens with Sparse Learning. ACS COMBINATORIAL SCIENCE 2020; 22:410-421. [PMID: 32531158 DOI: 10.1021/acscombsci.0c00007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded libraries (DELs) are large, pooled collections of compounds in which every library member is attached to a stretch of DNA encoding its complete synthetic history. DEL-based hit discovery involves affinity selection of the library against a protein of interest, whereby compounds retained by the target are subsequently identified by next-generation sequencing of the corresponding DNA tags. When analyzing the resulting data, one typically assumes that sequencing output (i.e., read counts) is proportional to the binding affinity of a given compound, thus enabling hit prioritization and elucidation of any underlying structure-activity relationships (SAR). This assumption, though, tends to be severely confounded by a number of factors, including variable reaction yields, presence of incomplete products masquerading as their intended counterparts, and sequencing noise. In practice, these confounders are often ignored, potentially contributing to low hit validation rates, and universally leading to loss of valuable information. To address this issue, we have developed a method for comprehensively denoising DEL selection outputs. Our method, dubbed "deldenoiser", is based on sparse learning and leverages inputs that are commonly available within a DEL generation and screening workflow. Using simulated and publicly available DEL affinity selection data, we show that "deldenoiser" is not only able to recover and rank true binders much more robustly than read count-based approaches but also that it yields scores, which accurately capture the underlying SAR. The proposed method can, thus, be of significant utility in hit prioritization following DEL screens.
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Affiliation(s)
- Péter Kómár
- Totient, Inc., 1 Alewife Center, Cambridge Massachusetts 02140 United States
| | - Marko Kalinić
- Totient, Inc., Sinđelićeva 9, 11000 Belgrade, Serbia
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30
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Bao Y, Deng Z, Feng J, Zhu W, Li J, Wan J, Liu G. A B 2(OH) 4-Mediated Synthesis of 2-Substituted Indazolone and Its Application in a DNA-Encoded Library. Org Lett 2020; 22:6277-6282. [PMID: 32806212 DOI: 10.1021/acs.orglett.0c02032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indazolone cores are among the most common structural components in medicinal chemistry and can be found in many biologically active molecules. In this report, a mild and efficient approach to 2-substituted indazolones via B2(OH)4-mediated reductive N-N bond formation is developed. This strategy features mild conditions, no request for a metal catalyst, and a wide scope for both aliphatic and aromatic amines. Meanwhile, this method was further successfully applied on DNA to construct indazolone cores for a DNA-encoded library. This will enable the production of a very attractive indazolone-cored library from simple amines and scaffolds, which will provide considerable diversity.
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Affiliation(s)
- Yapeng Bao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Zongfa Deng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Weiwei Zhu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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31
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Coley CW, Eyke NS, Jensen KF. Autonomous Discovery in the Chemical Sciences Part I: Progress. Angew Chem Int Ed Engl 2020; 59:22858-22893. [DOI: 10.1002/anie.201909987] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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32
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Coley CW, Eyke NS, Jensen KF. Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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33
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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34
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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35
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Badir SO, Sim J, Billings K, Csakai A, Zhang X, Dong W, Molander GA. Multifunctional Building Blocks Compatible with Photoredox-Mediated Alkylation for DNA-Encoded Library Synthesis. Org Lett 2020; 22:1046-1051. [PMID: 31940210 PMCID: PMC7060506 DOI: 10.1021/acs.orglett.9b04568] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-encoded library (DEL) technology has emerged as a novel interrogation modality for ligand discovery in the pharmaceutical industry. Given the increasing demand for a higher proportion of C(sp3)-hybridized centers in DEL platforms, a photoredox-mediated cross-coupling and defluorinative alkylation process is introduced using commercially available alkyl bromides and structurally diverse α-silylamines. Notably, no protecting group strategies for amines are necessary for the incorporation of a variety of amino-acid-based organosilanes, providing crucial branching points for further derivatization.
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Affiliation(s)
- Shorouk O. Badir
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Katelyn Billings
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, USA
| | - Adam Csakai
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, USA
| | - Xuange Zhang
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Weizhe Dong
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Gary A. Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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36
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Su L, Feng J, Peng T, Wan J, Fan J, Li J, O’Connell J, Lancia DR, Franklin GJ, Liu G. Synthesis of Multifunctional 2-Aminobenzimidazoles on DNA via Iodine-Promoted Cyclization. Org Lett 2020; 22:1290-1294. [DOI: 10.1021/acs.orglett.9b04578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liqiang Su
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Ting Peng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Fan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jonathan O’Connell
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - David R. Lancia
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - G. Joseph Franklin
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
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37
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Chen Q, Cheng X, Zhang L, Li X, Chen P, Liu J, Zhang L, Wei H, Li Z, Dou D. Exploring the Lower Limit of Individual DNA-Encoded Library Molecules in Selection. SLAS DISCOVERY 2019; 25:523-529. [DOI: 10.1177/2472555219893949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA-encoded library (DEL) technology has been used as an ultra-high-throughput screening approach for hit identification of drug targets. This process is an affinity-based selection and requires incubation of DEL molecules with the target. Currently, in most reported cases, the input (i.e., the copy number) of individual DEL molecules varies from 105 to 107. With the ever-increasing DEL size and screening cost, lowering the input of DEL molecules while maintaining an appropriate signal-to-noise ratio in a selection is of paramount importance. In this article, we varied the input of DEL ranging from 103 to 105 in selections with two different protein targets to explore the lower limit of DEL molecule input. The results could facilitate the optimization of the DEL selection process and reduce costs related to library consumption.
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Affiliation(s)
- Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuemin Cheng
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Lifang Zhang
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Purui Chen
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Jian Liu
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Lanjun Zhang
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Hong Wei
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Zhonghan Li
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Dengfeng Dou
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
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38
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Ratnayake AS, Flanagan ME, Foley TL, Smith JD, Johnson JG, Bellenger J, Montgomery JI, Paegel BM. A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis. ACS COMBINATORIAL SCIENCE 2019; 21:650-655. [PMID: 31425646 PMCID: PMC6938256 DOI: 10.1021/acscombsci.9b00113] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA-encoded chemical library (DECL) synthesis must occur in aqueous media under conditions that preserve the integrity of the DNA encoding tag. While the identification of "DNA-compatible" reaction conditions is critical for the development of DECL designs that explore previously inaccessible chemical space, reports measuring such compatibility have been largely restricted to methods that do not faithfully capture the impact of reaction conditions on DNA fidelity in solution phase. Here we report a comprehensive methodology that uses soluble DNA substrates that exactly recapitulate DNA's exposure to the chemically reactive species of DECL synthesis. This approach includes the assessment of chemical fidelity (reaction yield and purity), encoding fidelity (ligation efficiency), and readability (DNA compatibility), revealing the fate of the DNA tag during DECL chemistry from a single platform.
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Affiliation(s)
- Anokha S. Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Timothy L. Foley
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin D. Smith
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jillian G. Johnson
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin I. Montgomery
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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39
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Cai P, Yang G, Zhao L, Wan J, Li J, Liu G. Synthesis of C3-Alkylated Indoles on DNA via Indolyl Alcohol Formation Followed by Metal-Free Transfer Hydrogenation. Org Lett 2019; 21:6633-6637. [DOI: 10.1021/acs.orglett.9b02132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pinwen Cai
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guanyu Yang
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Lanzhou Zhao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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40
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Ma P, Xu H, Li J, Lu F, Ma F, Wang S, Xiong H, Wang W, Buratto D, Zonta F, Wang N, Liu K, Hua T, Liu Z, Yang G, Lerner RA. Functionality‐Independent DNA Encoding of Complex Natural Products. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Kaiwen Liu
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Tian Hua
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Zhi‐Jie Liu
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of ChemistryScripps Research Institute La Jolla CA 92037 USA
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41
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Ma P, Xu H, Li J, Lu F, Ma F, Wang S, Xiong H, Wang W, Buratto D, Zonta F, Wang N, Liu K, Hua T, Liu ZJ, Yang G, Lerner RA. Functionality-Independent DNA Encoding of Complex Natural Products. Angew Chem Int Ed Engl 2019; 58:9254-9261. [PMID: 31020752 DOI: 10.1002/anie.201901485] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 01/06/2023]
Abstract
DNA encoded chemical libraries (DELs) link the powers of genetics and chemical synthesis via combinatorial optimization. Through combinatorial chemistry, DELs can grow to the unprecedented size of billions to trillions. To take full advantage of the DEL approach, linking the power of genetics directly to chemical structures would offer even greater diversity in a finite chemical world. Natural products have evolved an incredible structural diversity along with their biological evolution. Herein, we used traditional Chinese medicines (TCMs) as examples in a late-stage modification toolbox approach to annotate these complex organic compounds with amplifiable DNA barcodes, which could be easily incorporated into a DEL. The method of end-products labeling also generates a cluster of isomers with a single DNA tag at different sites. These isomers provide an additional spatial diversity for multiple accessible pockets of targeted proteins. Notably, a novel PARP1 inhibitor from TCM has been identified from the natural products enriched DEL (nDEL).
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Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kaiwen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, 92037, USA
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42
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Phelan JP, Lang SB, Sim J, Berritt S, Peat AJ, Billings K, Fan L, Molander GA. Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis. J Am Chem Soc 2019; 141:3723-3732. [PMID: 30753065 DOI: 10.1021/jacs.9b00669] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA-encoded library (DEL) technology is a powerful tool commonly used by the pharmaceutical industry for the identification of compounds with affinity to biomolecular targets. Success in this endeavor lies in sampling diverse chemical libraries. However, current DELs tend to be deficient in C(sp3) carbon counts. We report unique solutions to the challenge of increasing both the chemical diversity of these libraries and their C(sp3) carbon counts by merging Ni/photoredox dual catalytic C(sp2)-C(sp3) cross-coupling as well as photoredox-catalyzed radical/polar crossover alkylation protocols with DELs. The successful integration of multiple classes of radical sources enables the rapid incorporation of a diverse set of alkyl fragments.
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Affiliation(s)
- James P Phelan
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon B Lang
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon Berritt
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Andrew J Peat
- GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Katelyn Billings
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Lijun Fan
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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43
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de Pedro Beato E, Priego J, Gironda-Martínez A, González F, Benavides J, Blas J, Martín-Ortega MD, Toledo MÁ, Ezquerra J, Torrado A. Mild and Efficient Palladium-Mediated C-N Cross-Coupling Reaction between DNA-Conjugated Aryl Bromides and Aromatic Amines. ACS COMBINATORIAL SCIENCE 2019; 21:69-74. [PMID: 30615417 DOI: 10.1021/acscombsci.8b00142] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA-encoded library technology (ELT) has emerged in the pharmaceutical industry as a powerful tool for hit and lead generation. Over the last 10 years, a number of DNA-compatible chemical reactions have been published and used to synthesize libraries. Among the most commonly used reactions in medicinal chemistry is the C-N bond formation, and its application to DNA-encoded library technology affords an alternative approach to identify high-affinity binders for biologically relevant protein targets. Herein we report a newly developed Pd-promoted C-N cross coupling reaction between DNA-conjugated aryl bromides and a wide scope of arylamines in good to excellent yields. The mild reaction conditions should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
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Affiliation(s)
| | - Julián Priego
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | - Fernando González
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Benavides
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Blas
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | | | - Jesús Ezquerra
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Alicia Torrado
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
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44
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Wang X, Sun H, Liu J, Dai D, Zhang M, Zhou H, Zhong W, Lu X. Ruthenium-Promoted C–H Activation Reactions between DNA-Conjugated Acrylamide and Aromatic Acids. Org Lett 2018; 20:4764-4768. [DOI: 10.1021/acs.orglett.8b01837] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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, P. R. China
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Hui Sun
- 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, P. R. China
| | - Jiaxiang Liu
- 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, P. R. China
| | - Dongcheng Dai
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Mingqiang Zhang
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Hu Zhou
- 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, P. R. China
| | - Wenge Zhong
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Xiaojie Lu
- 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, P. R. China
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45
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Ruff Y, Berst F. Efficient copper-catalyzed amination of DNA-conjugated aryl iodides under mild aqueous conditions. MEDCHEMCOMM 2018; 9:1188-1193. [PMID: 30109007 PMCID: PMC6072498 DOI: 10.1039/c8md00185e] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
Herein, we describe the development of copper-catalyzed cross-coupling of DNA-conjugated aryl iodides with aliphatic amines. This protocol leverages a novel ligand, 2-((2,6-dimethoxyphenyl)amino)-2-oxoacetic acid, to effect the transformation in aqueous DMSO, under mild conditions and in air, making it an ideal candidate for the synthesis of DNA-encoded libraries.
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Affiliation(s)
- Yves Ruff
- Novartis Institutes for BioMedical Research , Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland .
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research , Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland .
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46
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Kinetically guided radical-based synthesis of C(sp 3)-C(sp 3) linkages on DNA. Proc Natl Acad Sci U S A 2018; 115:E6404-E6410. [PMID: 29946037 DOI: 10.1073/pnas.1806900115] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA-encoded libraries (DEL)-based discovery platforms have recently been widely adopted in the pharmaceutical industry, mainly due to their powerful diversity and incredible number of molecules. In the two decades since their disclosure, great strides have been made to expand the toolbox of reaction modes that are compatible with the idiosyncratic aqueous, dilute, and DNA-sensitive parameters of this system. However, construction of highly important C(sp3)-C(sp3) linkages on DNA through cross-coupling remains unexplored. In this article, we describe a systematic approach to translating standard organic reactions to a DEL setting through the tactical combination of kinetic analysis and empirical screening with information captured from data mining. To exemplify this model, implementation of the Giese addition to forge high value C-C bonds on DNA was studied, which represents a radical-based synthesis in DEL.
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47
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Neri D, Lerner RA. DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information. Annu Rev Biochem 2018; 87:479-502. [PMID: 29328784 PMCID: PMC6080696 DOI: 10.1146/annurev-biochem-062917-012550] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.
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Affiliation(s)
- Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), 8093 Zürich, Switzerland;
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA;
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48
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Ding Y, Chai J, Centrella PA, Gondo C, DeLorey JL, Clark MA. Development and Synthesis of DNA-Encoded Benzimidazole Library. ACS COMBINATORIAL SCIENCE 2018; 20:251-255. [PMID: 29648439 DOI: 10.1021/acscombsci.8b00009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Encoded library technology (ELT) is an effective approach to the discovery of novel small-molecule ligands for biological targets. A key factor for the success of the technology is the chemical diversity of the libraries. Here we report the development of DNA-conjugated benzimidazoles. Using 4-fluoro-3-nitrobenzoic acid as a key synthon, we synthesized a 320 million-member DNA-encoded benzimidazole library using Fmoc-protected amino acids, amines and aldehydes as diversity elements. Affinity selection of the library led to the discovery of a novel, potent and specific antagonist of the NK3 receptor.
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Affiliation(s)
- Yun Ding
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jing Chai
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Paolo A. Centrella
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Chenaimwoyo Gondo
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jennifer L. DeLorey
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Matthew A. Clark
- GlaxoSmithKline, Platform Technology & Science, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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49
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Opassi G, Gesù A, Massarotti A. The hitchhiker’s guide to the chemical-biological galaxy. Drug Discov Today 2018; 23:565-574. [DOI: 10.1016/j.drudis.2018.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/25/2017] [Accepted: 01/04/2018] [Indexed: 12/21/2022]
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50
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Zhang W, Zhong B, Zhang C, Wang Y, Guo S, Luo C, Zhan Y. Structural modeling of osteoarthritis ADAMTS4 complex with its cognate inhibitory protein TIMP3 and rational derivation of cyclic peptide inhibitors from the complex interface to target ADAMTS4. Bioorg Chem 2017; 76:13-22. [PMID: 29102725 DOI: 10.1016/j.bioorg.2017.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
The ADAMTS4 (a disintegrin and metalloproteinase with thrombospondin motifs 4) enzyme is a matrix-associated zinc metalloendopeptidase that plays an essential role in the degradation of cartilage aggrecan in arthritic diseases and has been recognized as one of the most primary targets for therapeutic intervention in osteoarthritis (OA). Here, we reported computational modeling of the atomic-level complex structure of ADAMTS4 with its cognate inhibitory protein TIMP3 based on high-resolution crystal template. By systematically examining the modeled complex structure we successfully identified a short inhibitory loop (62EASESLC68) in TIMP3 N-terminal inhibitory domain (NID) that directly participates in blocking the enzyme's active site, which, and its extended versions, were then broken from the full-length protein to serve as the peptide inhibitor candidates of ADAMTS4. Atomistic molecular dynamics simulation, binding energetic analysis, and fluorescence-based assay revealed that the TIMP3-derived linear peptides can only bind weakly to the enzyme (Kd = 74 ± 8 μM), which would incur a considerable entropy penalty due to the high conformational flexibility and intrinsic disorder of these linear peptides. In this respect, we proposed a cyclization strategy to improve enzyme-peptide binding affinity by, instead of traditionally maximizing enthalpy contribution, minimizing entropy cost of the binding, where a disulfide bond was added across the two terminal residues of linear peptides, resulting in a number of TIMP3-derived cyclic peptides. Our studies confirmed that the cyclization, as might be expected, can promote peptide binding capability against ADAMTS4 substantially, with affinity increase by 3-fold, 9-fold and 7-fold for cyclic peptides , and , respectively.
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Affiliation(s)
- Wei Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Biao Zhong
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Chi Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yukai Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shang Guo
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Congfeng Luo
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yulin Zhan
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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