1
|
Zhou Y, Shen W, Gao Y, Peng J, Li Q, Wei X, Liu S, Lam FS, Mayol-Llinàs J, Zhao G, Li G, Li Y, Sun H, Cao Y, Li X. Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries. Nat Chem 2024; 16:543-555. [PMID: 38326646 DOI: 10.1038/s41557-024-01442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.
Collapse
Grants
- AoE/P-705/16, 17301118, 17111319, 17303220, 17300321, 17318322, C7005-20G, C7016-22G, and 2122-7S04 Research Grants Council, University Grants Committee (RGC, UGC)
- 21877093, 22222702, and 91953119 National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
- Health@InnoHK Innovation and Technology Commission (ITF)
Collapse
Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Gao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qingrong Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shihao Liu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Joan Mayol-Llinàs
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Hongzhe Sun
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
| |
Collapse
|
2
|
Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
Collapse
Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
3
|
Lessing A, Petrov D, Scheuermann J. Advancing small-molecule drug discovery by encoded dual-display technologies. Trends Pharmacol Sci 2023; 44:817-831. [PMID: 37739829 DOI: 10.1016/j.tips.2023.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023]
Abstract
DNA-encoded chemical library technology (DECL or DEL) has become an important pillar for small-molecule drug discovery. The technology rapidly identifies small-molecule hits for relevant target proteins at low cost and with a high success rate, including ligands for targeted protein degradation (TPD). More recently, the setup of DNA- or peptide nucleic acid (PNA)-encoded chemical libraries based on the simultaneous display of ligand pairs, termed dual-display, allows for more sophisticated applications which will be reviewed herein. Both stable and dynamic dual-display DEL technologies enable innovative affinity-based selection modalities, even on and in cells. Novel methods for a seamless conversion between single- and double-stranded library formats allow for even more versatility. We present the first candidates emerging from dual-display technologies and discuss the future potential of dual-display for drug discovery.
Collapse
Affiliation(s)
- Alice Lessing
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Dimitar Petrov
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Jörg Scheuermann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland.
| |
Collapse
|
4
|
Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
Collapse
Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
5
|
Hou R, Xie C, Gui Y, Li G, Li X. Machine-Learning-Based Data Analysis Method for Cell-Based Selection of DNA-Encoded Libraries. ACS OMEGA 2023; 8:19057-19071. [PMID: 37273617 PMCID: PMC10233830 DOI: 10.1021/acsomega.3c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is a powerful ligand discovery technology that has been widely adopted in the pharmaceutical industry. DEL selections are typically performed with a purified protein target immobilized on a matrix or in solution phase. Recently, DELs have also been used to interrogate the targets in the complex biological environment, such as membrane proteins on live cells. However, due to the complex landscape of the cell surface, the selection inevitably involves significant nonspecific interactions, and the selection data are much noisier than the ones with purified proteins, making reliable hit identification highly challenging. Researchers have developed several approaches to denoise DEL datasets, but it remains unclear whether they are suitable for cell-based DEL selections. Here, we report the proof-of-principle of a new machine-learning (ML)-based approach to process cell-based DEL selection datasets by using a Maximum A Posteriori (MAP) estimation loss function, a probabilistic framework that can account for and quantify uncertainties of noisy data. We applied the approach to a DEL selection dataset, where a library of 7,721,415 compounds was selected against a purified carbonic anhydrase 2 (CA-2) and a cell line expressing the membrane protein carbonic anhydrase 12 (CA-12). The extended-connectivity fingerprint (ECFP)-based regression model using the MAP loss function was able to identify true binders and also reliable structure-activity relationship (SAR) from the noisy cell-based selection datasets. In addition, the regularized enrichment metric (known as MAP enrichment) could also be calculated directly without involving the specific machine-learning model, effectively suppressing low-confidence outliers and enhancing the signal-to-noise ratio. Future applications of this method will focus on de novo ligand discovery from cell-based DEL selections.
Collapse
Affiliation(s)
- Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| |
Collapse
|
6
|
Cui M, Nguyen D, Gaillez MP, Heiden S, Lin W, Thompson M, Reddavide FV, Chen Q, Zhang Y. Trio-pharmacophore DNA-encoded chemical library for simultaneous selection of fragments and linkers. Nat Commun 2023; 14:1481. [PMID: 36932079 PMCID: PMC10023787 DOI: 10.1038/s41467-023-37071-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The split-and-pool method has been widely used to synthesize chemical libraries of a large size for early drug discovery, albeit without the possibility of meaningful quality control. In contrast, a self-assembled DNA-encoded chemical library (DEL) allows us to construct an m x n-member library by mixing an m-member and an n-member pre-purified sub-library. Herein, we report a trio-pharmacophore DEL (T-DEL) of m x l x n members through assembling three pre-purified and validated sub-libraries. The middle sub-library is synthesized using DNA-templated synthesis with different reaction mechanisms and designed as a linkage connecting the fragments displayed on the flanking two sub-libraries. Despite assembling three fragments, the resulting compounds do not exceed the up-to-date standard of molecular weight regarding drug-likeness. We demonstrate the utility of T-DEL in linker optimization for known binding fragments against trypsin and carbonic anhydrase II and by de novo selections against matrix metalloprotease-2 and -9.
Collapse
Affiliation(s)
- Meiying Cui
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Michelle Patino Gaillez
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Weilin Lin
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | | | - Qinchang Chen
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, China.
- School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yixin Zhang
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
7
|
Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
Collapse
Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| |
Collapse
|
8
|
Cai B, Mhetre AB, Krusemark CJ. Selection methods for proximity-dependent enrichment of ligands from DNA-encoded libraries using enzymatic fusion proteins. Chem Sci 2023; 14:245-250. [PMID: 36687357 PMCID: PMC9811540 DOI: 10.1039/d2sc05495g] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we report a selection approach to enrich ligands from DNA-encoded libraries (DELs) based on proximity to an enzymatic tag on the target protein. This method involves uncaging or installation of a biotin purification tag on the DNA construct either through photodeprotection of a protected biotin group using a light emitting protein tag (nanoluciferase) or by acylation using an engineered biotin ligase (UltraID). This selection does not require purification of the target protein and results in improved recovery and enrichment of DNA-linked ligands. This approach should serve as a general and convenient tool for molecular discovery with DELs.
Collapse
Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Amol B. Mhetre
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| |
Collapse
|
9
|
Wu X, Chen Y, Lu W, Jin R, Lu X. Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries. Bioconjug Chem 2022; 33:1818-1824. [PMID: 36197318 DOI: 10.1021/acs.bioconjchem.2c00421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries.
Collapse
Affiliation(s)
- Xinyuan Wu
- 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
| | - Yujie Chen
- 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
| | - 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
| | - Rui Jin
- 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.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
10
|
Gui Y, Wong CS, Zhao G, Xie C, Hou R, Li Y, Li G, Li X. Converting Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded Libraries for More Versatile Selections. ACS OMEGA 2022; 7:11491-11500. [PMID: 35415338 PMCID: PMC8992267 DOI: 10.1021/acsomega.2c01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is an efficient high-throughput screening technology platform in drug discovery and is also gaining momentum in academic research. Today, the majority of DELs are assembled and encoded with double-stranded DNA tags (dsDELs) and has been selected against numerous biological targets; however, dsDELs are not amendable to some of the recently developed selection methods, such as the cross-linking-based selection against immobilized targets and live-cell-based selections, which require DELs encoded with single-stranded DNAs (ssDELs). Herein, we present a simple method to convert dsDELs to ssDELs using exonuclease digestion without library redesign and resynthesis. We show that dsDELs could be efficiently converted to ssDELs and used for affinity-based selections either with purified proteins or on live cells.
Collapse
Affiliation(s)
- Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Clara Shania Wong
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Rui Hou
- Department
of Chemistry and 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
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Xiaoyu Li
- Department
of Chemistry and 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
|
Li Y, Zhao G, Fan X, Li Y, Zhang G. Switchable DNA-Encoded Chemical Library: Interconversion between Double- and Single-Stranded DNA Formats. Chembiochem 2022; 23:e202200025. [PMID: 35352452 DOI: 10.1002/cbic.202200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/10/2022] [Indexed: 11/07/2022]
Abstract
DNA-Encoded Chemical Library (DEL) has attracted substantial attention due to the infinite possibility for hit discovery in both pharmaceutical companies and academia. The encoding method is the initial step of DEL construction and one of the cornerstones of DEL applications. Classified by the DNA format, the existing DEL encoding strategies could be categorized into single-stranded DNA-based strategies and double-stranded DNA-based strategies. The two DEL formats have their unique advantages but are usually incompatible with each other. To address this issue, we proposed the concept of interconversion between double- and single-stranded DEL based on the "reversible covalent headpiece (RCHP)" design, which combined maximum robustness of synthesis with extraordinary flexibility of applications in distinct setups. Future opportunities in this field were also proposed to advance DEL technology to a comprehensive drug discovery platform.
Collapse
Affiliation(s)
- Yizhou Li
- Chongqing University, School of Pharmaceutical Sciences, Chongqing College Town, Shapingba, 401331, Chongqing, CHINA
| | - Guixian Zhao
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Xiaohong Fan
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Yangfeng Li
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Gong Zhang
- Chongqing University, School of Pharmaceutical Science, CHINA
| |
Collapse
|
12
|
Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double‐ and Single‐Stranded DNA‐Encoded Chemical Libraries. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University 400044 Chongqing P. R. China
| |
Collapse
|
13
|
Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
| |
Collapse
|
14
|
Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
Collapse
Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
| |
Collapse
|
15
|
Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double- and Single-Stranded DNA-Encoded Chemical Libraries. Angew Chem Int Ed Engl 2021; 61:e202115157. [PMID: 34904335 DOI: 10.1002/anie.202115157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The use of a proper encoding methodology is one of the most important aspects when practicing DEL technology. A "headpiece"-based double-stranded DEL encoding method is currently the most widely used for productive DEL. However, the robustness of double-stranded DEL construction conflicts with the versatility presented by single-stranded DEL applications. We here report a novel encoding method, which is based on a "reversible covalent headpiece (RCHP)". The RCHP allows reversible interconversion between double- and single-stranded DNA formats, providing an avenue to robust synthesis and allowing for the applications in distinct setups. We have validated the versatility of this encoding method with encoded self-assembled chemical library and DNA-encoded dynamic library technology. Notably, based on the RCHP-settled library construction, a unique "ternary covalent complex" mediating ligand isolation methodology against non-immobilized targets was developed.
Collapse
Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044, Chongqing, P. R. China
| |
Collapse
|
16
|
Abstract
In the past two decades, a DNA-encoded chemical library (DEL or DECL) has emerged and has become a major technology platform for ligand discovery in drug discovery as well as in chemical biology research. Although based on a simple concept, i.e., encoding each compound with a unique DNA tag in a combinatorial chemical library, DEL has been proven to be a powerful tool for interrogating biological targets by accessing vast chemical space at a fraction of the cost of traditional high-throughput screening (HTS). Moreover, the recent technological advances and rapid developments of DEL-compatible reactions have greatly enhanced the chemical diversity of DELs. Today, DELs have been adopted by nearly all major pharmaceutical companies and are also gaining momentum in academia. However, this field is heavily biased toward library encoding and synthesis, and an underexplored aspect of DEL research is the selection methods. Generally, DEL selection is considered to be a massive binding assay conducted over an immobilized protein to identify the physical binders using the typical bind-wash-elute procedure. In recent years, we and other research groups have developed new approaches that can perform DEL selections in the solution phase, which has enabled the selection against complex biological targets beyond purified proteins. On the one hand, these methods have significantly widened the target scope of DELs; on the other hand, they have enabled the functional and potentially phenotypic assays of DELs beyond simple binding. An overview of these methods is provided in this Account.Our laboratory has been using DNA-programmed affinity labeling (DPAL) as the main strategy to develop new DEL selection methods. DPAL is based on DNA-templated synthesis; by using a known ligand to guide the target binding, DPAL is able to specifically establish a stable linkage between the target protein and the ligand. The DNA tag of the target-ligand conjugates serves as a programmable handle for protein characterization or hit compound decoding in the case of DEL selections. DPAL also takes advantage of the fast reaction kinetics of photo-cross-linking to achieve high labeling specificity and fidelity, especially in the selection of DNA-encoded dynamic libraries (DEDLs). DPAL has enabled DEL selections not only in buffer and cell lysates but also with complex biological systems, such as large protein complexes and live cells. Moreover, this strategy has also been employed in other biological applications, such as site-specific protein labeling, protein detection, protein profiling, and target identification. In the Account, we describe these methods, highlight their underlying principles, and conclude with perspectives of the development of the DEL technology.
Collapse
Affiliation(s)
- Yinan Song
- 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
|
17
|
Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.09.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
18
|
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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [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
|
19
|
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: 26] [Impact Index Per Article: 8.7] [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
|
20
|
Conole D, H Hunter J, J Waring M. The maturation of DNA encoded libraries: opportunities for new users. Future Med Chem 2021; 13:173-191. [PMID: 33275046 DOI: 10.4155/fmc-2020-0285] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA-encoded combinatorial libraries (DECLs) represent an exciting new technology for high-throughput screening, significantly increasing its capacity and cost-effectiveness. Historically, DECLs have been the domain of specialized academic groups and industry; however, there has recently been a shift toward more drug discovery academic centers and institutes adopting this technology. Key to this development has been the simplification, characterization and standardization of various DECL subprotocols, such as library design, affinity screening and data analysis of hits. This review examines the feasibility of implementing DECL screening technology as a first-time user, particularly in academia, exploring the some important considerations for this, and outlines some applications of the technology that academia could contribute to the field.
Collapse
Affiliation(s)
- Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London, W12 0BZ, UK
| | - James H Hunter
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural & Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural & Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| |
Collapse
|
21
|
Huang Y, Meng L, Nie Q, Zhou Y, Chen L, Yang S, Fung YME, Li X, Huang C, Cao Y, Li Y, Li X. Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. Nat Chem 2020; 13:77-88. [PMID: 33349694 DOI: 10.1038/s41557-020-00605-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Membrane proteins on the cell surface perform a myriad of biological functions; however, ligand discovery for membrane proteins is highly challenging, because a natural cellular environment is often necessary to maintain protein structure and function. DNA-encoded chemical libraries (DELs) have emerged as a powerful technology for ligand discovery, but they are mainly limited to purified proteins. Here we report a method that can specifically label membrane proteins with a DNA tag, and thereby enable target-specific DEL selections against endogenous membrane proteins on live cells without overexpression or any other genetic manipulation. We demonstrate the generality and performance of this method by screening a 30.42-million-compound DEL against the folate receptor, carbonic anhydrase 12 and the epidermal growth factor receptor on live cells, and identify and validate a series of novel ligands for these targets. Given the high therapeutic significance of membrane proteins and their intractability to traditional high-throughput screening approaches, this method has the potential to facilitate membrane-protein-based drug discovery by harnessing the power of DEL.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Langdong Chen
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yi Man Eva Fung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaomeng Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Cen Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK, Hong Kong SAR, China.
| |
Collapse
|
22
|
Cai B, Kim D, Akhand S, Sun Y, Cassell RJ, Alpsoy A, Dykhuizen EC, Van Rijn RM, Wendt MK, Krusemark CJ. Selection of DNA-Encoded Libraries to Protein Targets within and on Living Cells. J Am Chem Soc 2019; 141:17057-17061. [PMID: 31613623 DOI: 10.1021/jacs.9b08085] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the selection of DNA-encoded small molecule libraries against protein targets within the cytosol and on the surface of live cells. The approach relies on generation of a covalent linkage of the DNA to protein targets by affinity labeling. This cross-linking event enables subsequent copurification by a tag on the recombinant protein. To access targets within cells, a cyclic cell-penetrating peptide is appended to DNA-encoded libraries for delivery across the cell membrane. As this approach assesses binding of DELs to targets in live cells, it provides a strategy for selection of DELs against challenging targets that cannot be expressed and purified as active.
Collapse
Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Dongwook Kim
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Saeed Akhand
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Yixing Sun
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Robert J Cassell
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Richard M Van Rijn
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| |
Collapse
|
23
|
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
|
24
|
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: 14] [Impact Index Per Article: 2.8] [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
|
25
|
Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
Collapse
Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| |
Collapse
|
26
|
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
|
27
|
Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries. Chembiochem 2019; 20:955-962. [DOI: 10.1002/cbic.201800766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Elena Gabriele
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | | | - Sara Mulatto
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jacopo Piazzi
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| |
Collapse
|
28
|
Vinals DF, Kitov PI, Tu Z, Zou C, Cairo CW, Lin HCH, Derda R. Selection of galectin-3 ligands derived from genetically encoded glycopeptide libraries. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Pavel I. Kitov
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica; Taipei Taiwan
| | - Chunxia Zou
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| | | | | | - Ratmir Derda
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada
| |
Collapse
|
29
|
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: 260] [Impact Index Per Article: 43.3] [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
|
30
|
Goodnow RA, Davie CP. DNA-Encoded Library Technology: A Brief Guide to Its Evolution and Impact on Drug Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|