1
|
Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem 2024:10.1038/s41557-024-01601-1. [PMID: 39138346 DOI: 10.1038/s41557-024-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds-termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.
Collapse
Affiliation(s)
- Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | | | | | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | | | | | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | | |
Collapse
|
2
|
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.
Collapse
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
| | | |
Collapse
|
3
|
Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
Collapse
Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| |
Collapse
|
4
|
Siripuram V, Sunkari YK, Ma F, Nguyen TL, Flajolet M. Reversible and Fully Controllable Generation of Organo-Soluble DNA (osDNA). ACS OMEGA 2024; 9:14771-14780. [PMID: 38585059 PMCID: PMC10993399 DOI: 10.1021/acsomega.3c06755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 04/09/2024]
Abstract
The present work describes a complete and reversible transformation of DNA's properties allowing solubilization in organic solvents and subsequent chemical modifications that are otherwise not possible in an aqueous medium. Organo-soluble DNA (osDNA) moieties are generated by covalently linking a dsDNA fragment to a polyether moiety with a built-in mechanism, rendering the process perfectly reversible and fully controllable. The precise removal of the polyether moiety frees up the initial DNA fragment, unaltered, both in sequence and nature. The solubility of osDNA was confirmed in six organic solvents of decreasing polarity and six types of osDNAs. As a proof of concept, in the context of DNA-encoded library (DEL) technology, an amidation reaction was successfully performed on osDNA in 100% DMSO. The development of osDNA opens up entirely new avenues for any DNA applications that could benefit from working in nonaqueous solutions, including chemical transformations.
Collapse
Affiliation(s)
- Vijay
Kumar Siripuram
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Yashoda Krishna Sunkari
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Fei Ma
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Thu-Lan Nguyen
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Marc Flajolet
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| |
Collapse
|
5
|
An Y, Lee J, Seo H, Bae S, Kang J, Lee J, Kim J, Nam MH, Song M, Hwang GT. Groebke-Blackburn-Bienaymé Reaction for DNA-Encoded Library Technology. Org Lett 2023; 25:4445-4450. [PMID: 37310879 DOI: 10.1021/acs.orglett.3c01366] [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: 06/15/2023]
Abstract
This study presents a DNA-compatible synthesis of diverse 5-arylimidazo[1,2-a]pyridin-3-amine derivatives using the Suzuki-Miyaura reaction, followed by a Groebke-Blackburn-Bienaymé (GBB) reaction. The GBB reaction demonstrates a wide substrate scope, mild one-pot reaction conditions, and compatibility with subsequent enzymatic ligation, highlighting its potential in DNA-encoded library technology.
Collapse
Affiliation(s)
- Yujin An
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Juyeon Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyewon Seo
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Seri Bae
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jihee Kang
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jieon Lee
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jinwoo Kim
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
6
|
Hu Z, Zhang Y, Yu W, Li J, Yao J, Zhang J, Wang J, Wang C. Transient receptor potential ankyrin 1 (TRPA1) modulators: Recent update and future perspective. Eur J Med Chem 2023; 257:115392. [PMID: 37269667 DOI: 10.1016/j.ejmech.2023.115392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 06/05/2023]
Abstract
The transient receptor potential ankyrin 1 (TRPA1) channel is a non-selective cation channel that senses irritant chemicals. Its activation is closely associated with pain, inflammation, and pruritus. TRPA1 antagonists are promising treatments for these diseases, and there has been a recent upsurge in their application to new areas such as cancer, asthma, and Alzheimer's disease. However, due to the generally disappointing performance of TRPA1 antagonists in clinical studies, scientists must pursue the development of antagonists with higher selectivity, metabolic stability, and solubility. Moreover, TRPA1 agonists provide a deeper understanding of activation mechanisms and aid in antagonist screening. Therefore, we summarize the TRPA1 antagonists and agonists developed in recent years, with a particular focus on structure-activity relationships (SARs) and pharmacological activity. In this perspective, we endeavor to keep abreast of cutting-edge ideas and provide inspiration for the development of more effective TRPA1-modulating drugs.
Collapse
Affiliation(s)
- Zelin Hu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Ya Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Wenhan Yu
- College of Letters & Science, University of California, Berkeley, Berkeley, 94720, California, United States
| | - Junjie Li
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaqi Yao
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jifa Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
7
|
Adamik R, Buchholcz B, Darvas F, Sipos G, Novák Z. The Potential of Micellar Media in the Synthesis of DNA-Encoded Libraries. Chemistry 2022; 28:e202103967. [PMID: 35019168 PMCID: PMC9305553 DOI: 10.1002/chem.202103967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/17/2022]
Abstract
DNA‐encoded library (DEL) technology has become widely used in drug discovery research. The construction of DELs requires robust organic transformations that proceed in aqueous media under mild conditions. Unfortunately, the application of water as reaction medium for organic synthesis is not evident due to the generally limited solubility of organic reagents. However, the use of surfactants can offer a solution to this issue. Oil‐in‐water microemulsions formed by surfactant micelles are able to localize hydrophobic reagents inside them, resulting in high local concentrations of the organic substances in an otherwise poorly solvated environment. This review provides a conceptual and critical summary of micellar synthesis possibilities that are well suited to DEL synthesis. Existing examples of micellar DEL approaches, together with a selection of micellar organic transformations fundamentally suitable for DEL are discussed.
Collapse
Affiliation(s)
- Réka Adamik
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
| | | | - Ferenc Darvas
- Innostudio Inc., Záhony u. 7, 1031, Budapest, Hungary
| | | | - Zoltán Novák
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
| |
Collapse
|
8
|
Plais L, Scheuermann J. Macrocyclic DNA-encoded chemical libraries: a historical perspective. RSC Chem Biol 2022; 3:7-17. [PMID: 35128404 PMCID: PMC8729180 DOI: 10.1039/d1cb00161b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
While macrocyclic peptides are extensively researched for therapeutically relevant protein targets, DNA-encoded chemical libraries (DELs) are developed at a quick pace to discover novel small molecule binders. The combination of both fields has been explored since 2004 and the number of macrocyclic peptide DELs is steadily increasing. Macrocycles with high affinity and potency were identified for diverse classes of proteins, revealing DEL's huge potential. By giving a historical perspective, we would like to review the methods which permitted the rise of macrocyclic peptide DELs, describe the different DELs which were created and discuss the achievements and challenges of this emerging field.
Collapse
Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| |
Collapse
|
9
|
Zhou Y, Shen W, Peng J, Deng Y, Li X. Identification of isoform/domain-selective fragments from the selection of DNA-encoded dynamic library. Bioorg Med Chem 2021; 45:116328. [PMID: 34364223 DOI: 10.1016/j.bmc.2021.116328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged to be a powerful ligand screening technology in drug discovery. Recently, we reported a DNA-encoded dynamic library (DEDL) approach that combines the principle of traditional dynamic combinatorial library (DCL) with DEL. DEDL has shown excellent potential in fragment-based ligand discovery with a variety of protein targets. Here, we further tested the utility of DEDL in identifying low molecular weight fragments that are selective for different isoforms or domains of the same protein family. A 10,000-member DEDL was selected against sirtuin-1, 2, and 5 (SIRT1, 2, 5) and the BD1 and BD2 domains of bromodomain 4 (BRD4), respectively. Albeit with modest potency, a series of isoform/domain-selective fragments were identified and the corresponding inhibitors were derived by fragment linking.
Collapse
Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Innovation and Technology Commission, Hong Kong Special Administrative Region
| |
Collapse
|
10
|
Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
| |
Collapse
|
11
|
Abstract
![]()
Sirtuin 6 (SIRT6)
is an NAD+-dependent protein deacylase
and mono-ADP-ribosyltransferase of the sirtuin family with a wide
substrate specificity. In vitro and in vivo studies have indicated that SIRT6 overexpression or activation has
beneficial effects for cellular processes such as DNA repair, metabolic
regulation, and aging. On the other hand, SIRT6 has contrasting roles
in cancer, acting either as a tumor suppressor or promoter in a context-specific
manner. Given its central role in cellular homeostasis, SIRT6 has
emerged as a promising target for the development of small-molecule
activators and inhibitors possessing a therapeutic potential in diseases
ranging from cancer to age-related disorders. Moreover, specific modulators
allow the molecular details of SIRT6 activity to be scrutinized and
further validate the enzyme as a pharmacological target. In this Perspective,
we summarize the current knowledge about SIRT6 pharmacology and medicinal
chemistry and describe the features of the activators and inhibitors
identified so far.
Collapse
Affiliation(s)
- Francesco Fiorentino
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Antonello Mai
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, P.le A Moro 5, 00185 Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, P.le A Moro 5, 00185 Rome, Italy
| |
Collapse
|
12
|
Matulevičiūtė G, Arbačiauskienė E, Kleizienė N, Kederienė V, Ragaitė G, Dagilienė M, Bieliauskas A, Milišiūnaitė V, Sløk FA, Šačkus A. Synthesis and Characterization of Novel Methyl (3)5-( N-Boc-piperidinyl)-1 H-pyrazole-4-carboxylates. Molecules 2021; 26:molecules26133808. [PMID: 34206593 PMCID: PMC8270337 DOI: 10.3390/molecules26133808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/13/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Series of methyl 3- and 5-(N-Boc-piperidinyl)-1H-pyrazole-4-carboxylates were developed and regioselectively synthesized as novel heterocyclic amino acids in their N-Boc protected ester form for achiral and chiral building blocks. In the first stage of the synthesis, piperidine-4-carboxylic and (R)- and (S)-piperidine-3-carboxylic acids were converted to the corresponding β-keto esters, which were then treated with N,N-dimethylformamide dimethyl acetal. The subsequent reaction of β-enamine diketones with various N-mono-substituted hydrazines afforded the target 5-(N-Boc-piperidinyl)-1H-pyrazole-4-carboxylates as major products, and tautomeric NH-pyrazoles prepared from hydrazine hydrate were further N-alkylated with alkyl halides to give 3-(N-Boc-piperidinyl)-1H-pyrazole-4-carboxylates. The structures of the novel heterocyclic compounds were confirmed by 1H-, 13C-, and 15N-NMR spectroscopy and HRMS investigation.
Collapse
Affiliation(s)
- Gita Matulevičiūtė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, LT-50254 Kaunas, Lithuania;
| | - Eglė Arbačiauskienė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, LT-50254 Kaunas, Lithuania;
- Correspondence: (E.A.); (A.Š.); Tel.: +370-37-451-401 (A.Š.)
| | - Neringa Kleizienė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
| | - Vilija Kederienė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, LT-50254 Kaunas, Lithuania;
| | - Greta Ragaitė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
| | - Miglė Dagilienė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
| | - Aurimas Bieliauskas
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
| | - Vaida Milišiūnaitė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
| | - Frank A. Sløk
- Vipergen ApS, Gammel Kongevej 23A, V DK-1610 Copenhagen, Denmark;
| | - Algirdas Šačkus
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, LT-51423 Kaunas, Lithuania; (G.M.); (N.K.); (G.R.); (M.D.); (A.B.); (V.M.)
- Correspondence: (E.A.); (A.Š.); Tel.: +370-37-451-401 (A.Š.)
| |
Collapse
|
13
|
Saarbach J, Barluenga S, Winssinger N. PNA-Encoded Synthesis (PES) and DNA Display of Small Molecule Libraries. Methods Mol Biol 2021; 2105:119-139. [PMID: 32088867 DOI: 10.1007/978-1-0716-0243-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DNA-encoded library technologies have emerged as a powerful platform to rapidly screen for binders to a protein of interest. These technologies are underpinned by the ability to encode a rich diversity of small molecules. While large libraries are accessible by cycles of mix and split synthesis, libraries based on single chemistries tend to be redundant. Furthermore, the quality of libraries generally decreases with the number of synthetic transformations performed in its synthesis. An alternative approach is to use hybridization to program the combinatorial assembly of fragment pairs onto a library of DNA templates. A broad molecular diversity is more easily sampled since it arises from the pairing of diverse fragments. Upon identification of productive fragment pairs, a focused library covalently linking the fragments is prepared. This focused library includes linker of different length and geometry and offers the opportunity to enrich the selected fragment set with close neighbors. Herein we describe detailed protocols to covalently link diverse fragments and screen fragment-based libraries using commercially available microarray platform.
Collapse
Affiliation(s)
- Jacques Saarbach
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
14
|
Liu S, Qi J, Lu W, Wang X, Lu X. Synthetic Studies toward DNA-Encoded Heterocycles Based on the On-DNA Formation of α,β-Unsaturated Ketones. Org Lett 2021; 23:908-913. [PMID: 33444029 DOI: 10.1021/acs.orglett.0c04118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Taking advantage of the diversity-oriented synthesis strategy with α,β-unsaturated carbonyl compounds, we have successfully established the DNA-compatible transformations for various heterocyclic scaffolds. The ring-closure reactions for pyrrole, pyrrolidine, pyrazole, pyrazoline, isoxazoline, pyridine, piperidine, cyclohexenone, and 5,8-dihydroimidazo[1,2-a]pyrimidine were elegantly demonstrated in a DNA-compatible format. These efforts paved the way for preparing DNA-encoded libraries with more extensive chemical space.
Collapse
Affiliation(s)
- Sixiu 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, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingjing Qi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Weiwei 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, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| |
Collapse
|
15
|
Wen H, Ge R, Qu Y, Sun J, Shi X, Cui W, Yan H, Zhang Q, An Y, Su W, Yang H, Kuai L, Satz AL, Peng X. Synthesis of 1,2-Amino Alcohols by Photoredox-Mediated Decarboxylative Coupling of α-Amino Acids and DNA-Conjugated Carbonyls. Org Lett 2020; 22:9484-9489. [DOI: 10.1021/acs.orglett.0c03461] [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)
- Huanan Wen
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Rui Ge
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yi Qu
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jialin Sun
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hao Yan
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L. Satz
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| |
Collapse
|
16
|
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.![]()
Collapse
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
| |
Collapse
|
17
|
Catalano M, Moroglu M, Balbi P, Mazzieri F, Clayton J, Andrews KH, Bigatti M, Scheuermann J, Conway SJ, Neri D. Selective Fragments for the CREBBP Bromodomain Identified from an Encoded Self-assembly Chemical Library. ChemMedChem 2020; 15:1752-1756. [PMID: 32686307 DOI: 10.1002/cmdc.202000528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/21/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i. e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i. e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore encoded self-assembly chemical (ESAC) library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from library selection showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
Collapse
Affiliation(s)
- Marco Catalano
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Petra Balbi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Federica Mazzieri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - James Clayton
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katrina H Andrews
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Stuart J Conway
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Péter Kómár
- Totient, Inc., 1 Alewife Center, Cambridge Massachusetts 02140 United States
| | - Marko Kalinić
- Totient, Inc., Sinđelićeva 9, 11000 Belgrade, Serbia
| |
Collapse
|
19
|
Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| |
Collapse
|
20
|
Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020; 59:14965-14972. [PMID: 32436364 DOI: 10.1002/anie.202005070] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Indexed: 11/11/2022]
Abstract
Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.
Collapse
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China.,Department of Chemistry, Southern University of Science and Technology China, 1088 Xueyuan Road, Shenzhen, China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
21
|
Xie J, Wang S, Ma P, Ma F, Li J, Wang W, Lu F, Xiong H, Gu Y, Zhang S, Xu H, Yang G, Lerner RA. Selection of Small Molecules that Bind to and Activate the Insulin Receptor from a DNA-Encoded Library of Natural Products. iScience 2020; 23:101197. [PMID: 32544667 PMCID: PMC7298650 DOI: 10.1016/j.isci.2020.101197] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/21/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
Although insulin is a life-saving medicine, administration by daily injection remains problematic. Our goal was to exploit the power of DNA-encoded libraries to identify molecules with insulin-like activity but with the potential to be developed as oral drugs. Our strategy involved using a 104-member DNA-encoded library containing 160 Traditional Chinese Medicines (nDEL) to identify molecules that bind to and activate the insulin receptor. Importantly, we used the natural ligand, insulin, to liberate bound molecules. Using this selection method on our relatively small, but highly diverse, nDEL yielded a molecule capable of both binding to and activating the insulin receptor. Chemical analysis showed this molecule to be a polycyclic analog of the guanidine metformin, a known drug used to treat diabetes. By using our protocol with other, even larger, DELs we can expect to identify additional organic molecules capable of binding to and activating the insulin receptor. Annotation of natural products via complementary bifunctional linkers Function-guided DEL selection using the natural ligand for competitive elution Identification of Rutaecarpine as a binder and activator of insulin receptor
Collapse
Affiliation(s)
- Jia Xie
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Fei Ma
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
22
|
An YL, Li K, Shen Y, Hong Z, Chen L, Hu Y, Zhou L, Wang D, Shi X, Liu S, Su W, Cui W, Kuai L, Yang H, Peng X. DNA Compatible Intermolecular Wittig Olefination for the Construction of α, β-Unsaturated Carbonyl Compounds. Org Lett 2020; 22:3931-3935. [DOI: 10.1021/acs.orglett.0c01215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| |
Collapse
|
23
|
Zhou Y, Peng J, Shen W, Li X. Psoralen as an interstrand DNA crosslinker in the selection of DNA-Encoded dynamic chemical library. Biochem Biophys Res Commun 2020; 533:215-222. [PMID: 32359876 DOI: 10.1016/j.bbrc.2020.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/04/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful technology for ligand discovery in biomedical research. Recently, we have developed a DNA-encoded dynamic library (DEDL) approach by incorporating the concept of dynamic combinatorial library (DCL) with DELs. DEDL has shown excellent potential in ligand discovery towards a variety of protein targets. However, the requirement of having a pair of unnatural p-stilbazoles as the interstrand DNA crosslinker has limited the chemical diversity of DEDLs. Here, we replaced p-stilbazole with psoralen (PS) and tested the feasibility of psoralen as the crosslinker in DEDL selection. Since psoralen is commercially available and does not require any special crosslinking partner, existing DELs may be directly used to create high-diversity DEDLs. This study is expected to greatly facilitate the development of DEDLs as a versatile tool in drug discovery.
Collapse
Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, 518055, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| |
Collapse
|
24
|
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.
Collapse
|
25
|
Farrera-Soler L, Daguer JP, Raunft P, Barluenga S, Imberty A, Winssinger N. PNA-Based Dynamic Combinatorial Libraries (PDCL) and screening of lectins. Bioorg Med Chem 2020; 28:115458. [PMID: 32241620 DOI: 10.1016/j.bmc.2020.115458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 11/16/2022]
Abstract
Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used with small molecules interacting with each other through reversible covalent interaction. However, application of this technology in biomedical research and drug discovery has been limited by the reversibility of covalent exchange and the analytical deconvolution of small molecule fragments. Here we report a supramolecular approach based on the use of a constant short PNA tag to direct the combinatorial pairing of fragment. This PNA tag yields fast exchange kinetics, while still delivering the benefits of cooperativity, and provides favourable properties for analytical deconvolution by MALDI. A selection from >6,000 assemblies of glycans (mono-, di-, tri-saccharides) targeting AFL, a lectin from pathogenic fungus, yielded a 95 nM assembly, nearly three orders of magnitude better in affinity than the corresponding glycan alone (41 µM).
Collapse
Affiliation(s)
- Lluc Farrera-Soler
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Patrick Raunft
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Nicolas Winssinger
- Department of Organic Chemistry, National Centre of Competence in Research (NCCR) in Chemical Biology, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
26
|
Potowski M, Esken R, Brunschweiger A. Translation of the copper/bipyridine-promoted Petasis reaction to solid phase-coupled DNA for encoded library synthesis. Bioorg Med Chem 2020; 28:115441. [PMID: 32222338 DOI: 10.1016/j.bmc.2020.115441] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/28/2020] [Accepted: 03/12/2020] [Indexed: 11/28/2022]
Abstract
The Petasis three-component reaction gives rise to diverse substituted α-aryl glycines from readily available amines, boronic acids and glyoxalic acid. Thus, this reaction is highly attractive for DNA-encoded small molecule screening library synthesis. The Petasis reaction is for instance promoted by a potentially DNA damaging copper(I)/bipyridine reagent system in dry organic solvents. We found that solid phase-coupled DNA strands tolerated this reagent system at elevated temperature allowing for synthesis of diverse substituted DNA-tagged α-aryl glycines from DNA-conjugated secondary amines.
Collapse
Affiliation(s)
- Marco Potowski
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Robin Esken
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany.
| |
Collapse
|
27
|
Bobers J, Škopić MK, Dinter R, Sakthithasan P, Neukirch L, Gramse C, Weberskirch R, Brunschweiger A, Kockmann N. Design of an Automated Reagent-Dispensing System for Reaction Screening and Validation with DNA-Tagged Substrates. ACS COMBINATORIAL SCIENCE 2020; 22:101-108. [PMID: 32053337 DOI: 10.1021/acscombsci.9b00207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Laboratory automation strategies have vast potential for accelerating discovery processes. They enable higher efficiency and throughput for time-consuming screening procedures and reduce error-prone manual steps. Automating repetitive procedures can for instance support chemists in optimizing chemical reactions. Particularly, the technology of DNA-encoded libraries (DELs) may benefit from automation techniques, since translation of chemical reactions to DNA-tagged reactants often requires screening of multiple reaction parameters and evaluation of large numbers of reactants. Here, we describe a portable, automated system for reagent dispensing that was designed from open source materials. The system was validated by performing amide coupling of carboxylic acids to DNA-linked amine and a micelle-mediated Povarov reaction to DNA-tagged hexahydropyrroloquinolines. The latter reaction required accurate pipetting of multiple components including different solvents and a surface-active reagent. Analysis of reactions demonstrated that the robotic system achieved high accuracy comparable to experimentation by an experienced chemist with the potential of higher throughput.
Collapse
Affiliation(s)
- Jens Bobers
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Mateja Klika Škopić
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Robin Dinter
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Piriyanth Sakthithasan
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Laura Neukirch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Christian Gramse
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Ralf Weberskirch
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Norbert Kockmann
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Flood DT, Kingston C, Vantourout JC, Dawson PE, Baran PS. DNA Encoded Libraries: A Visitor's Guide. Isr J Chem 2020. [DOI: 10.1002/ijch.201900133] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dillon T. Flood
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Cian Kingston
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Julien C. Vantourout
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Philip E. Dawson
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Phil S. Baran
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| |
Collapse
|
30
|
Zhu H, Flanagan ME, Stanton RV. Designing DNA Encoded Libraries of Diverse Products in a Focused Property Space. J Chem Inf Model 2019; 59:4645-4653. [DOI: 10.1021/acs.jcim.9b00729] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
31
|
Potowski M, Losch F, Wünnemann E, Dahmen JK, Chines S, Brunschweiger A. Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions. Chem Sci 2019; 10:10481-10492. [PMID: 32055372 PMCID: PMC7003951 DOI: 10.1039/c9sc04708e] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022] Open
Abstract
DNA-encoded compound libraries are widely used in drug discovery. Screening of catalysts for compatibility with solid phase-coupled DNA sequences guided the selection of encoded reactions, exemplified by a Zn(II)-mediated aza-Diels–Alder reaction.
DNA-encoded compound libraries are a widely used technology for target-based small molecule screening. Generally, these libraries are synthesized by solution phase combinatorial chemistry requiring aqueous solvent mixtures and reactions that are orthogonal to DNA reactivity. Initiating library synthesis with readily available controlled pore glass-coupled DNA barcodes benefits from enhanced DNA stability due to nucleobase protection and choice of dry organic solvents for encoded compound synthesis. We screened the compatibility of solid-phase coupled DNA sequences with 53 metal salts and organic reagents. This screening experiment suggests design of encoded library synthesis. Here, we show the reaction optimization and scope of three sp3-bond containing heterocyclic scaffolds synthesized on controlled pore glass-connected DNA sequences. A ZnCl2-promoted aza-Diels–Alder reaction with Danishefsky's diene furnished diverse substituted DNA-tagged pyridones, and a phosphoric acid organocatalyst allowed for synthesis of tetrahydroquinolines by the Povarov reaction and pyrimidinones by the Biginelli reaction, respectively. These three reactions caused low levels of DNA depurination and cover broad and only partially overlapping chemical space though using one set of DNA-coupled starting materials.
Collapse
Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Elena Wünnemann
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Janina K Dahmen
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Silvia Chines
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| |
Collapse
|
32
|
Iškauskienė M, Ragaitė G, Sløk FA, Šačkus A. Facile synthesis of novel amino acid-like building blocks by N-alkylation of heterocyclic carboxylates with N-Boc-3-iodoazetidine. Mol Divers 2019; 24:1235-1251. [PMID: 31420788 DOI: 10.1007/s11030-019-09987-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/08/2019] [Indexed: 01/11/2023]
Abstract
An efficient protocol providing easy access to highly functionalized heterocyclic compounds as novel organic building blocks was developed by coupling alkyl pyrazole-, indazole- and indolecarboxylates with N-Boc-3-iodoazetidine. The synthesized compounds are representatives of constrained non-chiral synthetic azole carboxylates in their N-Boc protected ester forms. Diversification of the prepared heterocyclic building blocks was achieved via application of palladium-catalyzed Suzuki-Miyaura cross-coupling reactions. In total, 34 building blocks were obtained to form a highly diversified small molecule collection. The structure of the novel heterocyclic compounds was investigated and verified by advanced NMR spectroscopy methods.
Collapse
Affiliation(s)
- Monika Iškauskienė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, 50254, Kaunas, Lithuania. .,Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, 51423, Kaunas, Lithuania.
| | - Greta Ragaitė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, 51423, Kaunas, Lithuania
| | - Frank A Sløk
- Vipergen ApS, Gammel Kongevej 23A, 1610, Copenhagen V, Denmark
| | - Algirdas Šačkus
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, 50254, Kaunas, Lithuania.,Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, 51423, Kaunas, Lithuania
| |
Collapse
|
33
|
Li JY, Miklossy G, Modukuri RK, Bohren KM, Yu Z, Palaniappan M, Faver JC, Riehle K, Matzuk MM, Simmons N. Palladium-Catalyzed Hydroxycarbonylation of (Hetero)aryl Halides for DNA-Encoded Chemical Library Synthesis. Bioconjug Chem 2019; 30:2209-2215. [PMID: 31329429 PMCID: PMC6706801 DOI: 10.1021/acs.bioconjchem.9b00447] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A strategy
for DNA-compatible, palladium-catalyzed hydroxycarbonylation
of (hetero)aryl halides on DNA–chemical conjugates has been
developed. This method generally provided the corresponding carboxylic
acids in moderate to very good conversions for (hetero)aryl iodides
and bromides, and in poor to moderate conversions for (hetero)aryl
chlorides. These conditions were further validated by application
within a DNA-encoded chemical library synthesis and subsequent discovery
of enriched features from the library in selection experiments against
two protein targets.
Collapse
Affiliation(s)
- Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Gabriella Miklossy
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Ram K Modukuri
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - John C Faver
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kevin Riehle
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| |
Collapse
|
34
|
Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
35
|
Shi B, Deng Y, Li X. Polymerase-Extension-Based Selection Method for DNA-Encoded Chemical Libraries against Nonimmobilized Protein Targets. ACS COMBINATORIAL SCIENCE 2019; 21:345-349. [PMID: 30920794 DOI: 10.1021/acscombsci.9b00011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) have become an important ligand discovery technology in biomedical research and drug discovery. DELs can be comprised of hundreds of millions to billions of candidate molecules and provide outstanding chemical diversity for discovering novel ligands and inhibitors for a large variety of biological targets. However, in most cases, DELs are selected against purified and immobilized proteins based on binding affinity. The development and application of DELs to more complex biological targets requires selection methods compatible with nonimmobilized and unpurified proteins. Here, we describe an approach using polymerase-based extension and target-directed photo-cross-linking and its application to the interrogation of a solution-phase protein target, carbonic anhydrase II.
Collapse
Affiliation(s)
- Bingbing Shi
- Department of Food Science, Tibet Agriculture and Animal Husbandry University, 100 Yucai Road West, Nyingchi, China 860000
| | - Yuqing Deng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
36
|
Du HC, Bangs MC, Simmons N, Matzuk MM. Multistep Synthesis of 1,2,4-Oxadiazoles via DNA-Conjugated Aryl Nitrile Substrates. Bioconjug Chem 2019; 30:1304-1308. [PMID: 30964278 DOI: 10.1021/acs.bioconjchem.9b00188] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A multistep protocol for the synthesis of 3,5-disubstituted 1,2,4-oxadiazoles on DNA-chemical conjugates has been developed. A set of six DNA-connected aryl nitriles were converted to corresponding amidoximes with hydroxylamine followed by the O-acylation with a series of aryl and aliphatic carboxylic acids. After cyclodehydration of the O-acyl amidoximes by heating at 90 °C in pH 9.5 borate buffer for 2 h, the desired oxadiazole products were observed in 51-92% conversion with the cleavage of O-acylamidoximes as the major side-product. The reported protocol paves the way for the synthesis of oxadiazole core-focused DNA-encoded chemical libraries.
Collapse
Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Madison C Bangs
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| |
Collapse
|
37
|
Nicholas F, Bassi G, Zanetti T, Scheuermann J, Neri D. Screening of copper and palladium-mediated reactions compatible with DNA-encoded chemical libraries. Helv Chim Acta 2019; 102. [PMID: 32292208 DOI: 10.1002/hlca.201900033] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The construction of DNA-encoded chemical libraries (DECLs) crucially relies on the availability of chemical reactions, which are DNA-compatible and which exhibit high conversion rates for a large number of diverse substrates. In this work, we present our optimization and validation procedures for three copper and palladium-catalyzed reactions (Suzuki cross-coupling, Sonogashira cross-coupling and copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC)), which have been successfully used by our group for the construction of large encoded libraries.
Collapse
Affiliation(s)
- Favalli Nicholas
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich (Switzerland)
| | - Tania Zanetti
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich (Switzerland)
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich (Switzerland)
| |
Collapse
|
38
|
Yuen LH, Dana S, Liu Y, Bloom SI, Thorsell AG, Neri D, Donato AJ, Kireev D, Schüler H, Franzini RM. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes. J Am Chem Soc 2019; 141:5169-5181. [DOI: 10.1021/jacs.8b08039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Srikanta Dana
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Yu Liu
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Samuel I. Bloom
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Dario Neri
- Department of Pharmaceutical Sciences, ETH Zürich, Vladimir Prelog Weg 3, 8093 Zürich, Switzerland
| | - Anthony J. Donato
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| |
Collapse
|
39
|
Faver JC, Riehle K, Lancia DR, Milbank JBJ, Kollmann CS, Simmons N, Yu Z, Matzuk MM. Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections. ACS COMBINATORIAL SCIENCE 2019; 21:75-82. [PMID: 30672692 PMCID: PMC6372980 DOI: 10.1021/acscombsci.8b00116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA-encoded
chemical libraries (DELs) provide a high-throughput
and cost-effective route for screening billions of unique molecules
for binding affinity for diverse protein targets. Identifying candidate
compounds from these libraries involves affinity selection, DNA sequencing,
and measuring enrichment in a sample pool of DNA barcodes. Successful
detection of potent binders is affected by many factors, including
selection parameters, chemical yields, library amplification, sequencing
depth, sequencing errors, library sizes, and the chosen enrichment
metric. To date, there has not been a clear consensus about how enrichment
from DEL selections should be measured or reported. We propose a normalized z-score enrichment metric using a binomial distribution
model that satisfies important criteria that are relevant for analysis
of DEL selection data. The introduced metric is robust with respect
to library diversity and sampling and allows for quantitative comparisons
of enrichment of n-synthons from parallel DEL selections.
These features enable a comparative enrichment analysis strategy that can
provide valuable information about hit compounds in early stage drug
discovery.
Collapse
Affiliation(s)
| | | | - David R. Lancia
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Jared B. J. Milbank
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Christopher S. Kollmann
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | | | | | | |
Collapse
|
40
|
Advances in Lead Generation. Bioorg Med Chem Lett 2019; 29:517-524. [DOI: 10.1016/j.bmcl.2018.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/28/2018] [Accepted: 12/01/2018] [Indexed: 11/21/2022]
|
41
|
Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery. J Am Chem Soc 2018; 140:15859-15867. [DOI: 10.1021/jacs.8b09277] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhou
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Chen Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
| | - Jianzhao Peng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Liangxu Xie
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Ling Meng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Qingrong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Jianfu Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water
Bay, Kowloon, Hong Kong, Hong Kong
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| |
Collapse
|
42
|
Kochmann S, Le ATH, Hili R, Krylov SN. Predicting efficiency of NECEEM‐based partitioning of protein binders from nonbinders in DNA‐encoded libraries. Electrophoresis 2018; 39:2991-2996. [DOI: 10.1002/elps.201800270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sven Kochmann
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| |
Collapse
|
43
|
Kolodny G, Li X, Balk S. Addressing Cancer Chemotherapeutic Toxicity, Resistance, and Heterogeneity: Novel Theranostic Use of DNA‐Encoded Small Molecule Libraries. Bioessays 2018; 40:e1800057. [DOI: 10.1002/bies.201800057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/08/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Gerald Kolodny
- Beth Israel Deaconess Medical Center − Radiology/Nuclear Medicine and Molecular Imaging330 Brookline AvenueBostonMA02215USA
| | - Xiaoyu Li
- Hong Kong University − ChemistryPokfulam RoadHong Kong
| | - Steven Balk
- Beth Israel Deaconess Medical Center − Medicine330 Brookline AvenueBostonMA02215USA
| |
Collapse
|
44
|
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.
Collapse
|
45
|
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.
Collapse
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;
| |
Collapse
|
46
|
Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery,
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hongbing Huang
- Center for Drug Discovery,
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| |
Collapse
|
47
|
Shi B, Deng Y, Zhao P, Li X. Selecting a DNA-Encoded Chemical Library against Non-immobilized Proteins Using a “Ligate–Cross-Link–Purify” Strategy. Bioconjug Chem 2017; 28:2293-2301. [PMID: 28742329 DOI: 10.1021/acs.bioconjchem.7b00343] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bingbing Shi
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yuqing Deng
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Peng Zhao
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute
of Nuclear Physics and Chemistry, China Academy of Engineering Physics, 64 Mianshan Road, Mianyang, Sichuan 621900, China
| | - Xiaoyu Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
48
|
Zimmermann G, Rieder U, Bajic D, Vanetti S, Chaikuad A, Knapp S, Scheuermann J, Mattarella M, Neri D. A Specific and Covalent JNK-1 Ligand Selected from an Encoded Self-Assembling Chemical Library. Chemistry 2017; 23:8152-8155. [PMID: 28485044 PMCID: PMC5557334 DOI: 10.1002/chem.201701644] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/05/2023]
Abstract
We describe the construction of a DNA-encoded chemical library comprising 148 135 members, generated through the self-assembly of two sub-libraries, containing 265 and 559 members, respectively. The library was designed to contain building blocks potentially capable of forming covalent interactions with target proteins. Selections performed with JNK1, a kinase containing a conserved cysteine residue close to the ATP binding site, revealed the preferential enrichment of a 2-phenoxynicotinic acid moiety (building block A82) and a 4-(3,4-difluorophenyl)-4-oxobut-2-enoic acid moiety (building block B272). When the two compounds were joined by a short PEG linker, the resulting bidentate binder (A82-L-B272) was able to covalently modify JNK1 in the presence of a large molar excess of glutathione (0.5 mm), used to simulate intracellular reducing conditions. By contrast, derivatives of the individual building blocks were not able to covalently modify JNK1 in the same experimental conditions. The A82-L-B272 ligand was selective over related kinases (BTK and GAK), which also contain targetable cysteine residues in the vicinity of the active site.
Collapse
Affiliation(s)
- Gunther Zimmermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Ulrike Rieder
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland)
| | - Davor Bajic
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Sara Vanetti
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland)
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt (Germany)
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt (Germany)
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | | | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| |
Collapse
|
49
|
Saarbach J, Masi D, Zambaldo C, Winssinger N. Facile access to modified and functionalized PNAs through Ugi-based solid phase oligomerization. Bioorg Med Chem 2017. [PMID: 28624242 DOI: 10.1016/j.bmc.2017.05.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide nucleic acids (PNAs) derivatized with functional molecules are increasingly used in diverse biosupramolecular applications. PNAs have proven to be highly tolerant to modifications and different applications benefit from the use of modified PNAs, in particular modifications at the γ position. Herein we report simple protocols to access modified PNAs from iterative Ugi couplings which allow modular modifications at the α, β or γ position of the PNA backbone from simple starting materials. We demonstrate the utility of the method with the synthesis of several bioactive small molecules (a peptide ligand, a kinase inhibitor and a glycan)-PNA conjugates.
Collapse
Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Daniela Masi
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Claudio Zambaldo
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland.
| |
Collapse
|
50
|
Lu X, Fan L, Phelps CB, Davie CP, Donahue CP. Ruthenium Promoted On-DNA Ring-Closing Metathesis and Cross-Metathesis. Bioconjug Chem 2017; 28:1625-1629. [DOI: 10.1021/acs.bioconjchem.7b00292] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaojie Lu
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Lijun Fan
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christopher B. Phelps
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christopher P. Davie
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christine P. Donahue
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| |
Collapse
|