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Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
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Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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2
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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.
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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.
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3
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Guo Q, Xue S, Feng J, Peng C, Zhou C, Qiao Y. AIE-Active Glycomimetics Triggered Bacterial Agglutination and Membrane-Intercalating toward Efficient Photodynamic Antiseptic. Adv Healthc Mater 2023; 12:e2300818. [PMID: 37246869 DOI: 10.1002/adhm.202300818] [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: 03/15/2023] [Revised: 05/12/2023] [Indexed: 05/30/2023]
Abstract
Opportunistic infections caused by Pseudomonas aeruginosa (P. aeruginosa) are particularly difficult to treat due to the altered membrane permeability and inherent resistance to conventional antibiotics. Here, a cationic glycomimetics is designed and synthesized with aggregation-induced emission (AIE) characteristics namely TPyGal, which self-assembles into the spherical aggregates with galactosylated surface. TPyGal aggregates can effectively cluster P. aeruginosa through multivalent carbohydrate-lectin interactions and auxiliary electrostatic interactions and subsequently trigger membrane-intercalating, which results in efficient photodynamic eradication of P. aeruginosa under white light irradiation by in situ singlet oxygen (1 O2 ) burst to disrupt bacterial membrane. Furthermore, the results demonstrate that TPyGal aggregates promote the healing of infected wounds, indicating the potential for clinical treatment of P. aeruginosa infections.
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Affiliation(s)
- Qiaoni Guo
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, China
| | - Shaobo Xue
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200435, China
| | - Jianguo Feng
- College of Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Chen Peng
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200435, China
| | - Chengcheng Zhou
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS) Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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4
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Imiołek M, Winssinger N. Two-Helix Supramolecular Proteomimetic Binders Assembled via PNA-Assisted Disulfide Crosslinking. Chembiochem 2023; 24:e202200561. [PMID: 36349499 DOI: 10.1002/cbic.202200561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Peptidic motifs folded in a defined conformation are able to inhibit protein-protein interactions (PPIs) covering large interfaces and as such they are biomedical molecules of interest. Mimicry of such natural structures with synthetically tractable constructs often requires complex scaffolding and extensive optimization to preserve the fidelity of binding to the target. Here, we present a novel proteomimetic strategy based on a 2-helix binding motif that is brought together by hybridization of peptide nucleic acids (PNA) and stabilized by a rationally positioned intermolecular disulfide crosslink. Using a solid phase synthesis approach (SPPS), the building blocks are easily accessible and such supramolecular peptide-PNA helical hybrids could be further coiled using precise templated chemistry. The elaboration of the structural design afforded high affinity SARS CoV-2 RBD (receptor binding domain) binders without interference with the underlying peptide sequence, creating a basis for a new architecture of supramolecular proteomimetics.
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Affiliation(s)
- Mateusz Imiołek
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
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5
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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6
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- 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
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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7
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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.
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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
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8
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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.
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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
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9
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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
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10
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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.
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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.
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11
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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.
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Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - 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
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12
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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: 13] [Impact Index Per Article: 4.3] [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.
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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
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13
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Luong P, Dube DH. Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans. Bioorg Med Chem 2021; 42:116268. [PMID: 34130219 DOI: 10.1016/j.bmc.2021.116268] [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: 04/18/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
The bacterial glycocalyx is a quintessential drug target comprised of structurally distinct glycans. Bacterial glycans bear unusual monosaccharide building blocks whose proper construction is critical for bacterial fitness, survival, and colonization in the human host. Despite their appeal as therapeutic targets, bacterial glycans are difficult to study due to the presence of rare bacterial monosaccharides that are linked and modified in atypical manners. Their structural complexity ultimately hampers their analytical characterization. This review highlights recent advances in bacterial chemical glycobiology and focuses on the development of chemical tools to probe, perturb, and image bacterial glycans and their biosynthesis. Current technologies have enabled the study of bacterial glycosylation machinery even in the absence of detailed structural information.
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Affiliation(s)
- Phuong Luong
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Danielle H Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA.
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14
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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15
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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.
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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
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16
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Angerani S, Winssinger N. Sense-and-Release Logic-Gated Molecular Network Responding to Dimeric Cell Surface Proteins. J Am Chem Soc 2020; 142:12333-12340. [PMID: 32539375 DOI: 10.1021/jacs.0c04469] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Dimeric proteins are prominent in biology, and receptor dimerization (homo- or heterodimerization) is central to signal transduction. Herein, we report a network that responds to a membrane-associated dimeric protein with the uncaging of a powerful cytotoxic. The network is based on two ligands functionalized with peptide nucleic acids (PNAs) (templating strand and catalyst-functionalized strand, respectively) and a substrate with the caged cytotoxic (monomethyl auristatin E: MMAE; a high-affinity tubulin ligand). In the presence of the dimeric protein, the network yields a cooperative supramolecular assembly with a hybridization architecture that enhances the templated reaction and enables the uncaging of a substrate. The network was tested on cells that express a cancer biomarker, carbonic anhydrase IX, in response to hypoxia. The output of the network correlates with the expression of carbonic anhydrase IX, and this biomarker was harnessed to uncage a potent cytotoxic agent.
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Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1205 Geneva, Switzerland
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17
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Sýkorová P, Novotná J, Demo G, Pompidor G, Dubská E, Komárek J, Fujdiarová E, Houser J, Hároníková L, Varrot A, Shilova N, Imberty A, Bovin N, Pokorná M, Wimmerová M. Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed β-propeller fold. Int J Biol Macromol 2020; 152:1113-1124. [DOI: 10.1016/j.ijbiomac.2019.10.200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/08/2023]
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18
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Chang D, Kim KT, Lindberg E, Winssinger N. Smartphone DNA or RNA Sensing Using Semisynthetic Luciferase-Based Logic Device. ACS Sens 2020; 5:807-813. [PMID: 32124606 DOI: 10.1021/acssensors.9b02454] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Detection of specific oligonucleotide sequences is central to numerous applications, and technologies amenable to point-of-care diagnostics or end users are needed. Here, we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conjugate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarkers, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.
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Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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19
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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).
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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.
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20
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Bachmann T, Rychlik M. Chemical glucosylation of pyridoxine. Carbohydr Res 2020; 489:107929. [DOI: 10.1016/j.carres.2020.107929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 11/28/2022]
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21
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Yeldell SB, Seitz O. Nucleic acid constructs for the interrogation of multivalent protein interactions. Chem Soc Rev 2020; 49:6848-6865. [DOI: 10.1039/d0cs00518e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-programmed self-assembly provides multivalent nucleic acid–ligand constructs used as tailor-made probes for unravelling and exploiting the mechanisms of multivalency-enhanced interactions on protein receptors.
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Affiliation(s)
- Sean B. Yeldell
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
| | - Oliver Seitz
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
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22
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Saarbach J, Sabale PM, Winssinger N. Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics. Curr Opin Chem Biol 2019; 52:112-124. [PMID: 31541865 DOI: 10.1016/j.cbpa.2019.06.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/07/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas.
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Affiliation(s)
- Jacques Saarbach
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Pramod M Sabale
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Faculty of Science, Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30 quai Ernest Ansermet, CH-1205 Geneva, Switzerland.
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23
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Purcell SC, Godula K. Synthetic glycoscapes: addressing the structural and functional complexity of the glycocalyx. Interface Focus 2019; 9:20180080. [PMID: 30842878 PMCID: PMC6388016 DOI: 10.1098/rsfs.2018.0080] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
The glycocalyx is an information-dense network of biomacromolecules extensively modified through glycosylation that populates the cellular boundary. The glycocalyx regulates biological events ranging from cellular protection and adhesion to signalling and differentiation. Owing to the characteristically weak interactions between individual glycans and their protein binding partners, multivalency of glycan presentation is required for the high-avidity interactions needed to trigger cellular responses. As such, biological recognition at the glycocalyx interface is determined by both the structure of glycans that are present as well as their spatial distribution. While genetic and biochemical approaches have proven powerful in controlling glycan composition, modulating the three-dimensional complexity of the cell-surface 'glycoscape' at the sub-micrometre scale remains a considerable challenge in the field. This focused review highlights recent advances in glycocalyx engineering using synthetic nanoscale glycomaterials, which allows for controlled de novo assembly of complexity with precision not accessible with traditional molecular biology tools. We discuss several exciting new studies in the field that demonstrate the power of precision glycocalyx editing in living cells in revealing and controlling the complex mechanisms by which the glycocalyx regulates biological processes.
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Affiliation(s)
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358, USA
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24
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Ramberg KO, Antonik PM, Cheung DL, Crowley PB. Measuring the Impact of PEGylation on a Protein-Polysaccharide Interaction. Bioconjug Chem 2019; 30:1162-1168. [PMID: 30869874 DOI: 10.1021/acs.bioconjchem.9b00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PEGylation is the most widely used half-life extension strategy for protein therapeutics. While it imparts a range of attractive attributes PEGylation can impede protein binding and reduce efficacy. A model system to probe the effects of PEGylation on protein binding has practical applications. Here, we present a system based on complex formation between a hexavalent lectin (RSL) and the globular polysaccharide Ficoll PM70 (a type of glycocluster). Mutants of the lectin were used to generate conjugates with 3, 6, or 12 PEG (1 kDa) chains. Using NMR spectroscopy we monitored how the degree of PEGylation impacted the lectin-Ficoll interaction. The binding propensity was observed to decrease with increasing polymer density. Apparently, the extended PEG chains sterically impede the lectin-Ficoll binding. This deduction was supported by molecular dynamics simulations of the protein-polymer conjugates. The implications for protein-surface interactions are discussed.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Paweł M Antonik
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - David L Cheung
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
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25
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Bonnardel F, Kumar A, Wimmerova M, Lahmann M, Perez S, Varrot A, Lisacek F, Imberty A. Architecture and Evolution of Blade Assembly in β-propeller Lectins. Structure 2019; 27:764-775.e3. [PMID: 30853410 DOI: 10.1016/j.str.2019.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/10/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022]
Abstract
Lectins with a β-propeller fold bind glycans on the cell surface through multivalent binding sites and appropriate directionality. These proteins are formed by repeats of short domains, raising questions about evolutionary duplication. However, these repeats are difficult to detect in translated genomes and seldom correctly annotated in sequence databases. To address these issues, we defined the blade signature of the five types of β-propellers using 3D-structural data. With these templates, we predicted 3,887 β-propeller lectins in 1,889 species and organized this information in a searchable online database. The data reveal a widespread distribution of β-propeller lectins across species. Prediction also emphasizes multiple architectures and led to the discovery of a β-propeller assembly scenario. This was confirmed by producing and characterizing a predicted protein coded in the genome of Kordia zhangzhouensis. The crystal structure uncovers an intermediate in the evolution of β-propeller assembly and demonstrates the power of our tools.
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Affiliation(s)
- François Bonnardel
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France; Swiss Institute of Bioinformatics, 1227 Geneva, Switzerland; Computer Science Department, UniGe, 1227 Geneva, Switzerland
| | - Atul Kumar
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France; CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Michaela Wimmerova
- CEITEC, Masaryk University, 625 00 Brno, Czech Republic; NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Martina Lahmann
- School of Chemistry, University of Bangor, LL57 2UW Bangor, UK
| | - Serge Perez
- University of Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Annabelle Varrot
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, 1227 Geneva, Switzerland; Computer Science Department, UniGe, 1227 Geneva, Switzerland; Section of Biology, UniGe, 1205 Geneva, Switzerland.
| | - Anne Imberty
- University of Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
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26
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Binding inhibition of various influenza viruses by sialyllactose-modified trimer DNAs. Bioorg Med Chem Lett 2019; 29:744-748. [DOI: 10.1016/j.bmcl.2018.12.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/30/2018] [Accepted: 12/31/2018] [Indexed: 11/19/2022]
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27
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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
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28
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Choi H, Jung Y. Applying Multivalent Biomolecular Interactions for Biosensors. Chemistry 2018; 24:19103-19109. [DOI: 10.1002/chem.201801408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/27/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Hyeongjoo Choi
- Department of ChemistryKorea Advanced Institute of Science and Technology Daejeon 34141 Korea
| | - Yongwon Jung
- Department of ChemistryKorea Advanced Institute of Science and Technology Daejeon 34141 Korea
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29
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Yu Z, Guo C, Wei Y, Hashiya K, Bando T, Sugiyama H. Pip-HoGu: An Artificial Assembly with Cooperative DNA Recognition Capable of Mimicking Transcription Factor Pairs. J Am Chem Soc 2018; 140:2426-2429. [DOI: 10.1021/jacs.7b13275] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zutao Yu
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Chuanxin Guo
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yulei Wei
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences
(WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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30
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Hsieh WC, Bahal R, Thadke SA, Bhatt K, Sobczak K, Thornton C, Ly DH. Design of a "Mini" Nucleic Acid Probe for Cooperative Binding of an RNA-Repeated Transcript Associated with Myotonic Dystrophy Type 1. Biochemistry 2018; 57:907-911. [PMID: 29334465 DOI: 10.1021/acs.biochem.7b01239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Toxic RNAs containing expanded trinucleotide repeats are the cause of many neuromuscular disorders, one being myotonic dystrophy type 1 (DM1). DM1 is triggered by CTG-repeat expansion in the 3'-untranslated region of the DMPK gene, resulting in a toxic gain of RNA function through sequestration of MBNL1 protein, among others. Herein, we report the development of a relatively short miniPEG-γ peptide nucleic acid probe, two triplet repeats in length, containing terminal pyrene moieties, that is capable of binding rCUG repeats in a sequence-specific and selective manner. The newly designed probe can discriminate the pathogenic rCUGexp from the wild-type transcript and disrupt the rCUGexp-MBNL1 complex. The work provides a proof of concept for the development of relatively short nucleic acid probes for targeting RNA-repeat expansions associated with DM1 and other related neuromuscular disorders.
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Affiliation(s)
- Wei-Che Hsieh
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Raman Bahal
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Shivaji A Thadke
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Kirti Bhatt
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Krzysztof Sobczak
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Charles Thornton
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Danith H Ly
- Department of Chemistry, ‡Institute for Biomolecular Design and Discovery (IBD), and §CNAST, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States.,Department of Neurology, Box 645, University of Rochester Medical Center , 601 Elmwood Avenue, Rochester, New York 14642, United States
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31
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Probst N, Lartia R, Théry O, Alami M, Defrancq E, Messaoudi S. Efficient Buchwald-Hartwig-Migita Cross-Coupling for DNA Thioglycoconjugation. Chemistry 2018; 24:1795-1800. [PMID: 29205564 DOI: 10.1002/chem.201705371] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 11/11/2022]
Abstract
An efficient method for the thioglycoconjugation of iodinated oligonucleotides by Buchwald-Hartwig-Migita cross-coupling under mild conditions is reported. The method enables divergent synthesis of many different functionalized thioglycosylated ODNs in good yields, without affecting the integrity of the other A, C, and G nucleobases.
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Affiliation(s)
- Nicolas Probst
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Rémy Lartia
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Océane Théry
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Mouâd Alami
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Eric Defrancq
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Samir Messaoudi
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
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32
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Goyard D, Baldoneschi V, Varrot A, Fiore M, Imberty A, Richichi B, Renaudet O, Nativi C. Multivalent Glycomimetics with Affinity and Selectivity toward Fucose-Binding Receptors from Emerging Pathogens. Bioconjug Chem 2017; 29:83-88. [DOI: 10.1021/acs.bioconjchem.7b00616] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Veronica Baldoneschi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
| | | | - Michele Fiore
- ICBMS, University of Lyon, 43 Blvd. du 11 novembre 1918, 69622, Villeubanne Cedex, France
| | | | - Barbara Richichi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
| | | | - Cristina Nativi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
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33
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Lee JM, Hwang A, Choi H, Jo Y, Kim B, Kang T, Jung Y. A Multivalent Structure-Specific RNA Binder with Extremely Stable Target Binding but Reduced Interaction with Nonspecific RNAs. Angew Chem Int Ed Engl 2017; 56:15998-16002. [DOI: 10.1002/anie.201709153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/01/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Jeong Min Lee
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Ahreum Hwang
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Hazards Monitoring Bionano Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
| | - Hyeongjoo Choi
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Yongsang Jo
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Bongsoo Kim
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Taejoon Kang
- Hazards Monitoring Bionano Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
- BioNano Health Guard Research Center, KRIBB, Daejeon 34141 (Korea); Department of Nanobiotechnology; KRIBB School of Biotechnology, UST; Daejeon 34113 Korea
| | - Yongwon Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
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Lee JM, Hwang A, Choi H, Jo Y, Kim B, Kang T, Jung Y. A Multivalent Structure-Specific RNA Binder with Extremely Stable Target Binding but Reduced Interaction with Nonspecific RNAs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jeong Min Lee
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Ahreum Hwang
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Hazards Monitoring Bionano Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
| | - Hyeongjoo Choi
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Yongsang Jo
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Bongsoo Kim
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
| | - Taejoon Kang
- Hazards Monitoring Bionano Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
- BioNano Health Guard Research Center, KRIBB, Daejeon 34141 (Korea); Department of Nanobiotechnology; KRIBB School of Biotechnology, UST; Daejeon 34113 Korea
| | - Yongwon Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
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Bandlow V, Liese S, Lauster D, Ludwig K, Netz RR, Herrmann A, Seitz O. Spatial Screening of Hemagglutinin on Influenza A Virus Particles: Sialyl-LacNAc Displays on DNA and PEG Scaffolds Reveal the Requirements for Bivalency Enhanced Interactions with Weak Monovalent Binders. J Am Chem Soc 2017; 139:16389-16397. [DOI: 10.1021/jacs.7b09967] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Victor Bandlow
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Susanne Liese
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Daniel Lauster
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Kai Ludwig
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Roland R. Netz
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Andreas Herrmann
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Oliver Seitz
- Institute
of Chemistry, and ‡Institute of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
- Institute of Theoretical Physics, and ∥Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
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