1
|
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
|
2
|
Hou R, Xie C, Gui Y, Li G, Li X. Machine-Learning-Based Data Analysis Method for Cell-Based Selection of DNA-Encoded Libraries. ACS OMEGA 2023; 8:19057-19071. [PMID: 37273617 PMCID: PMC10233830 DOI: 10.1021/acsomega.3c02152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is a powerful ligand discovery technology that has been widely adopted in the pharmaceutical industry. DEL selections are typically performed with a purified protein target immobilized on a matrix or in solution phase. Recently, DELs have also been used to interrogate the targets in the complex biological environment, such as membrane proteins on live cells. However, due to the complex landscape of the cell surface, the selection inevitably involves significant nonspecific interactions, and the selection data are much noisier than the ones with purified proteins, making reliable hit identification highly challenging. Researchers have developed several approaches to denoise DEL datasets, but it remains unclear whether they are suitable for cell-based DEL selections. Here, we report the proof-of-principle of a new machine-learning (ML)-based approach to process cell-based DEL selection datasets by using a Maximum A Posteriori (MAP) estimation loss function, a probabilistic framework that can account for and quantify uncertainties of noisy data. We applied the approach to a DEL selection dataset, where a library of 7,721,415 compounds was selected against a purified carbonic anhydrase 2 (CA-2) and a cell line expressing the membrane protein carbonic anhydrase 12 (CA-12). The extended-connectivity fingerprint (ECFP)-based regression model using the MAP loss function was able to identify true binders and also reliable structure-activity relationship (SAR) from the noisy cell-based selection datasets. In addition, the regularized enrichment metric (known as MAP enrichment) could also be calculated directly without involving the specific machine-learning model, effectively suppressing low-confidence outliers and enhancing the signal-to-noise ratio. Future applications of this method will focus on de novo ligand discovery from cell-based DEL selections.
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
|
3
|
Cai B, El Daibani A, Bai Y, Che T, Krusemark CJ. Direct Selection of DNA-Encoded Libraries for Biased Agonists of GPCRs on Live Cells. JACS AU 2023; 3:1076-1088. [PMID: 37124302 PMCID: PMC10131204 DOI: 10.1021/jacsau.2c00674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 05/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of human membrane target proteins for approved drugs. GPCR ligands can have a complex array of pharmacological activities. Among these activities, biased agonists have potential to serve as both chemical probes to understand specific aspects of receptor signaling and therapeutic leads with more specific, desired activity. Challenges exist, however, in the development of new biased activators due, in part, to the low throughput of traditional screening approaches. DNA-encoded chemical libraries (DELs) dramatically improve the throughput of drug discovery by allowing a collective selection, rather than discrete screening, of large compound libraries. The use of DELs has been largely limited to affinity-based selections against purified protein targets, which identify binders only. Herein, we report a split protein complementation approach that allows direct identification of DNA-linked molecules that induce the dimerization of two proteins. We used this selection with a DEL against opioid receptor GPCRs on living cells for the identification of small molecules that possess the specific function of activation of either β-arrestin or G protein signaling pathways. This approach was applied to δ-, μ-, and κ-opioid receptors and enabled the discovery of compound [66,66], a selective, G-protein-biased agonist of the κ-opioid receptor (EC50 = 100 nM, E max = 82%, Gi bias factor = 6.6). This approach should be generally applicable for the direct selection of chemical inducers of dimerization from DELs and expand the utility of DELs to enrich molecules with a specific and desired biochemical function.
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
| | - Amal El Daibani
- Center
for Clinical Pharmacology, Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Yuntian Bai
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for
Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tao Che
- Center
for Clinical Pharmacology, Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63110, 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
|
4
|
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: 47] [Impact Index Per Article: 23.5] [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
|
5
|
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
|
6
|
Daguer JP, Gonse A, Shchukin Y, Farrera-Soler L, Barluenga S, Winssinger N. Dual Bcl-X L /Bcl-2 inhibitors discovered from DNA-encoded libraries using a fragment pairing strategy. Bioorg Med Chem 2021; 44:116282. [PMID: 34216984 DOI: 10.1016/j.bmc.2021.116282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022]
Abstract
A dual Bcl-XL / Bcl-2 inhibitor was discovered from DNA-encoded libraries using a two steps process. In the first step, DNA was used to pair PNA-encoded fragments exploring > 250 000 combinations. In the second step, a focused library combining the selected fragments with linkers of different lengths and geometries led to the identification of tight binding adducts that were further investigated for their selective target engagement in pull-down assays, for their affinity by SPR, and their selectivity in a cytotoxicity assay. The best compound showed comparable cellular activity to venetoclax, the first-in-class therapeutic targeting Bcl-2.
Collapse
Affiliation(s)
- Jean-Pierre Daguer
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Arthur Gonse
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Yevhenii Shchukin
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Sciences, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
7
|
Oehler S, Catalano M, Scapozza I, Bigatti M, Bassi G, Favalli N, Mortensen MR, Samain F, Scheuermann J, Neri D. Affinity Selections of DNA-Encoded Chemical Libraries on Carbonic Anhydrase IX-Expressing Tumor Cells Reveal a Dependence on Ligand Valence. Chemistry 2021; 27:8985-8993. [PMID: 33905156 DOI: 10.1002/chem.202100816] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 12/19/2022]
Abstract
DNA-encoded chemical libraries are typically screened against purified protein targets. Recently, cell-based selections with encoded chemical libraries have been described, commonly revealing suboptimal performance due to insufficient recovery of binding molecules. We used carbonic anhydrase IX (CAIX)-expressing tumor cells as a model system to optimize selection procedures with code-specific quantitative polymerase chain reaction (qPCR) as selection readout. Salt concentration and performing PCR on cell suspension had the biggest impact on selection performance, leading to 15-fold enrichment factors for high-affinity monovalent CAIX binders (acetazolamide; KD =8.7 nM). Surprisingly, the homobivalent display of acetazolamide at the extremities of both complementary DNA strands led to a substantial improvement of both ligand recovery and enrichment factors (above 100-fold). The optimized procedures were used for selections with a DNA-encoded chemical library comprising 1 million members against tumor cell lines expressing CAIX, leading to a preferential recovery of known and new ligands against this validated tumor-associated target. This work may facilitate future affinity selections on cells against target proteins which might be difficult to express otherwise.
Collapse
Affiliation(s)
- Sebastian Oehler
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Ilario Scapozza
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Martina Bigatti
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Michael R Mortensen
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Dario Neri
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| |
Collapse
|
8
|
Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [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
|
9
|
Saarbach J, Barluenga S, Winssinger N. PNA-Encoded Synthesis (PES) and DNA Display of Small Molecule Libraries. Methods Mol Biol 2021; 2105:119-139. [PMID: 32088867 DOI: 10.1007/978-1-0716-0243-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DNA-encoded library technologies have emerged as a powerful platform to rapidly screen for binders to a protein of interest. These technologies are underpinned by the ability to encode a rich diversity of small molecules. While large libraries are accessible by cycles of mix and split synthesis, libraries based on single chemistries tend to be redundant. Furthermore, the quality of libraries generally decreases with the number of synthetic transformations performed in its synthesis. An alternative approach is to use hybridization to program the combinatorial assembly of fragment pairs onto a library of DNA templates. A broad molecular diversity is more easily sampled since it arises from the pairing of diverse fragments. Upon identification of productive fragment pairs, a focused library covalently linking the fragments is prepared. This focused library includes linker of different length and geometry and offers the opportunity to enrich the selected fragment set with close neighbors. Herein we describe detailed protocols to covalently link diverse fragments and screen fragment-based libraries using commercially available microarray platform.
Collapse
Affiliation(s)
- Jacques Saarbach
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland.
| |
Collapse
|
10
|
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
|
11
|
Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
Collapse
|
12
|
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
|
13
|
Favalli N, Bassi G, Scheuermann J, Neri D. DNA-encoded chemical libraries - achievements and remaining challenges. FEBS Lett 2018; 592:2168-2180. [PMID: 29683493 PMCID: PMC6126621 DOI: 10.1002/1873-3468.13068] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 11/10/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
Collapse
Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| |
Collapse
|
14
|
Wang F, Li L, Sun W, Li L, Liu Y, Huang Y, Zhou Z. A novel α Vβ 3 ligand-modified HPMA copolymers for anticancer drug delivery. J Drug Target 2017; 26:231-241. [PMID: 28792244 DOI: 10.1080/1061186x.2017.1365872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The integrin αVβ3 receptor emerged as one of the most promising targets owing to its high expression on the surface of various malignant tumour cells and tumour angiogenesis endothelial cells, but with little expression in mature endothelial cells and the majority of normal cells. Here, we report a new targeting ligand FQSIYPpIK (FQS) with high affinity to integrin αVβ3 receptor. To take the advantage of the particular interaction between FQS and integrin αVβ3 receptor, FQS was linked to N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers. A model drug doxorubicin (DOX) was simultaneously conjugated to the same HPMA copolymers via pH-sensitive hydrazone linkages (FQS-HPMA-DOX). In in vitro study, FQS-HPMA-DOX could be internalised into αVβ3 receptor-overexpressed B16F10 cells via a highly specific ligand - receptor pathway (5.0 times and 4.5 times higher cellular internalisation than HPMA-DOX and a scrambled peptide (s)-FQS (sequence: SYFIPKQIp)-modified copolymers ((s)-FQS-HPMA-DOX)). It is worth noting that compared with the classical αVβ3 ligand cRGDfK-modified HPMA copolymers (cRGDfK-HPMA-DOX), FQS-HPMA-DOX also showed superior targeting efficiency. In in vivo study in the B16F10 melanoma bearing mice model showed the antitumour efficiency of FQS-HPMA-DOX (83.9%) were significantly higher than HPMA-DOX (44.9%) and cRGDfK-HPMA-DOX (77.5%). These results suggest that FQS peptide can act as an effective targeting ligand for the delivery of therapeutic agents.
Collapse
Affiliation(s)
- Fengling Wang
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Lian Li
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Wei Sun
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Lijia Li
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Yuanyuan Liu
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Yuan Huang
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| | - Zhou Zhou
- a Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education , West China School of Pharmacy, Sichuan University , Chengdu , China
| |
Collapse
|
15
|
Shi B, Deng Y, Zhao P, Li X. Selecting a DNA-Encoded Chemical Library against Non-immobilized Proteins Using a “Ligate–Cross-Link–Purify” Strategy. Bioconjug Chem 2017; 28:2293-2301. [PMID: 28742329 DOI: 10.1021/acs.bioconjchem.7b00343] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bingbing Shi
- Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 2199 Lishui Road West, Shenzhen 518055, China
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yuqing Deng
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Peng Zhao
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Institute
of Nuclear Physics and Chemistry, China Academy of Engineering Physics, 64 Mianshan Road, Mianyang, Sichuan 621900, China
| | - Xiaoyu Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
16
|
Liu R, Li X, Xiao W, Lam KS. Tumor-targeting peptides from combinatorial libraries. Adv Drug Deliv Rev 2017; 110-111:13-37. [PMID: 27210583 DOI: 10.1016/j.addr.2016.05.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 02/07/2023]
Abstract
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.
Collapse
Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA
| |
Collapse
|
17
|
Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| |
Collapse
|
18
|
Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
Collapse
|
19
|
Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
Collapse
|
20
|
Abstract
DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
Collapse
Affiliation(s)
- Marie L. Malone
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| |
Collapse
|
21
|
Affiliation(s)
- Raphael M. Franzini
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Cassie Randolph
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| |
Collapse
|
22
|
The transport mechanism of integrin αvβ3 receptor targeting nanoparticles in Caco-2 cells. Int J Pharm 2016; 500:42-53. [PMID: 26784984 DOI: 10.1016/j.ijpharm.2016.01.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/23/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
Abstract
As for the existence of epithelium barrier, accelerating the transport remains huge challenges for orally delivered protein and peptide drugs into blood circulation. Modifying nanopaticles (NPs) with targeting peptides can enhance the intestinal absorption of loaded macromolecular drugs. However, the transport process, which mainly means how the NPs pass through the apical membrane and the basolateral side and then enter into blood circulation, is needed comprehensive investigation. In this study, we systemically studied the transport mechanisms in Caco-2 cell model of trimethyl chitosan based NPs (TMC NPs) before and after modification of FQS, an integrin αvβ3 receptor targeting peptide. Our results showed FQS peptide mediated multiple endocytosis pathways and could activate integrin αvβ3 receptor by interacting with FAK and Src-family kinases to induce receptor-mediated endocytosis of the NPs. Then, both endocytosed NPs could transport from early endosome to lysososmes via late endosomes/lysosome pathway, as well as to recycling endosomes and Golgi apparatus through early endosome/recycling endosomes and Golgi apparatus/recycling endosomes/plasma membrane pathways, respectively. After FQS peptide modification, the endocytosis subpathways of NPs have been changed, and more pathways are involved in exocytosis process for FQS-modified NPs compared with non-modified NPs. Our study indicated the ligand modification could enhance the uptake and transport by altering some pathways in whole transport process of NPs.
Collapse
|
23
|
Zambaldo C, Daguer JP, Saarbach J, Barluenga S, Winssinger N. Screening for covalent inhibitors using DNA-display of small molecule libraries functionalized with cysteine reactive moieties. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00242k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Discriminating between non-covalent and covalent inhibitors with SDS wash in microarray-based screen.
Collapse
Affiliation(s)
- C. Zambaldo
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J.-P. Daguer
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J. Saarbach
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - S. Barluenga
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - N. Winssinger
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| |
Collapse
|
24
|
Liu M, Wu L, Zhu X, Shan W, Li L, Cui Y, Huang Y. Core–shell stability of nanoparticles plays an important role for overcoming the intestinal mucus and epithelium barrier. J Mater Chem B 2016; 4:5831-5841. [PMID: 32263756 DOI: 10.1039/c6tb01199c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stability of the core–shell structure plays an important role in the nanoparticles ability to overcome both the mucus and epithelium absorption barrier.
Collapse
Affiliation(s)
- Min Liu
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Lei Wu
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Xi Zhu
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Wei Shan
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Lian Li
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Yi Cui
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Yuan Huang
- Key laboratory of Drug Targeting and Drug Delivery System (Ministry of Education)
- West China School of Pharmacy
- Sichuan University
- Chengdu 610041
- P. R. China
| |
Collapse
|
25
|
Wu Z, Graybill TL, Zeng X, Platchek M, Zhang J, Bodmer VQ, Wisnoski DD, Deng J, Coppo FT, Yao G, Tamburino A, Scavello G, Franklin GJ, Mataruse S, Bedard KL, Ding Y, Chai J, Summerfield J, Centrella PA, Messer JA, Pope AJ, Israel DI. Cell-Based Selection Expands the Utility of DNA-Encoded Small-Molecule Library Technology to Cell Surface Drug Targets: Identification of Novel Antagonists of the NK3 Tachykinin Receptor. ACS COMBINATORIAL SCIENCE 2015; 17:722-31. [PMID: 26562224 DOI: 10.1021/acscombsci.5b00124] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded small-molecule library technology has recently emerged as a new paradigm for identifying ligands against drug targets. To date, this technology has been used with soluble protein targets that are produced and used in a purified state. Here, we describe a cell-based method for identifying small-molecule ligands from DNA-encoded libraries against integral membrane protein targets. We use this method to identify novel, potent, and specific inhibitors of NK3, a member of the tachykinin family of G-protein coupled receptors (GPCRs). The method is simple and broadly applicable to other GPCRs and integral membrane proteins. We have extended the application of DNA-encoded library technology to membrane-associated targets and demonstrate the feasibility of selecting DNA-tagged, small-molecule ligands from complex combinatorial libraries against targets in a heterogeneous milieu, such as the surface of a cell.
Collapse
Affiliation(s)
- Zining Wu
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Todd L. Graybill
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xin Zeng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Platchek
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jean Zhang
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Vera Q. Bodmer
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David D. Wisnoski
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jianghe Deng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Frank T. Coppo
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Gang Yao
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Alex Tamburino
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Genaro Scavello
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - G. Joseph Franklin
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Katie L. Bedard
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jing Chai
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jennifer Summerfield
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jeffrey A. Messer
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Andrew J. Pope
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David I. Israel
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| |
Collapse
|
26
|
Novel PTP1B inhibitors identified by DNA display of fragment pairs. Bioorg Med Chem Lett 2015; 26:1080-1085. [PMID: 26691757 DOI: 10.1016/j.bmcl.2015.11.102] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 12/15/2022]
Abstract
DNA display of PNA-encoded libraries was used to pair fragments containing different phosphotyrosine surrogates with diverse triazoles. Microarray-based screening of the combinatorially paired fragment sets (62,500 combinations) against a prototypical phosphatase, PTP1B, was used to identify the fittest fragments. A focused library (10,000 members) covalently pairing identified fragments with linkers of different length and geometry was synthesized. Screening of the focused library against PTP1B and closely related TCPTP revealed orthogonal inhibitors. The selectivity of the identified inhibitors for PTP1B versus TCPT was confirmed by enzymatic inhibition assay.
Collapse
|
27
|
Liu C, Shan W, Liu M, Zhu X, Xu J, Xu Y, Huang Y. A novel ligand conjugated nanoparticles for oral insulin delivery. Drug Deliv 2015. [PMID: 26203690 DOI: 10.3109/10717544.2015.1058433] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to enhance the interaction between nanocarrier and gastrointestinal epithelial cells, we developed nanoparticles (NPs) modified with targeting ligand FQSIYPpIK (FQS), which specifically interact with integrin αvβ3 receptor expressing on the intestinal epithelium. The targeting NPs were prepared by coating the insulin-loaded poly(lactide-co-glycolide)-monomethoxy-poly(polyethylene glycol) micelle cores with FQS modified trimethyl chitosan chloride. In in vitro study, the fabricated NPs showed ameliorated drug release profile and improved enzymatic stability compared with micelles alone. In the integrin αvβ3 receptor over-expressed Caco-2 cells model, FQS modified NPs exhibited significantly accelerated intracellular uptake due to the active ligand-receptor mediation. Meanwhile, the targeting NPs also showed enhanced transport across the Caco-2 monolayer cells via both transcellular and paracellular pathways. Besides, orally administered FQS modified NPs produced a prominent hypoglycemic response and an increase of the serum insulin concentration in diabetic rats. Both in vitro and in vivo results demonstrated the FQS peptide modified NPs as promising intestinal cell-targeting nanocarriers for efficient oral delivery of insulin.
Collapse
Affiliation(s)
- Chong Liu
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Wei Shan
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Min Liu
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Xi Zhu
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Juan Xu
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Yining Xu
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| | - Yuan Huang
- a Key Laboratory of Drug Targeting and Drug Delivery System , Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu , P.R. China
| |
Collapse
|
28
|
Li G, Zheng W, Liu Y, Li X. Novel encoding methods for DNA-templated chemical libraries. Curr Opin Chem Biol 2015; 26:25-33. [PMID: 25635927 DOI: 10.1016/j.cbpa.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 12/12/2022]
Abstract
Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.
Collapse
Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| |
Collapse
|
29
|
Zambaldo C, Barluenga S, Winssinger N. PNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:8-15. [PMID: 25621730 DOI: 10.1016/j.cbpa.2015.01.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
Abstract
Peptide nucleic acid (PNA)-encoded chemical libraries along with DNA-encoded libraries have provided a powerful new paradigm for library synthesis and ligand discovery. PNA-encoding stands out for its compatibility with standard solid phase synthesis and the technology has been used to prepare libraries of peptides, heterocycles and glycoconjugates. Different screening formats have now been reported including selection-based and microarray-based methods that have yielded specific ligands against diverse target classes including membrane receptors, lectins and challenging targets such as Hsp70.
Collapse
Affiliation(s)
- Claudio Zambaldo
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland.
| |
Collapse
|
30
|
Franzini RM, Nauer A, Scheuermann J, Neri D. Interrogating target-specificity by parallel screening of a DNA-encoded chemical library against closely related proteins. Chem Commun (Camb) 2015; 51:8014-6. [DOI: 10.1039/c5cc01230a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Screening a DNA-encoded chemical library against closely related proteins enabled us to predict target specificity as illustrated for serum albumins from different species.
Collapse
Affiliation(s)
| | - Angela Nauer
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| |
Collapse
|
31
|
Shi H, Yang F, Li W, Zhao W, Nie K, Dong B, Liu Z. A review: fabrications, detections and applications of peptide nucleic acids (PNAs) microarray. Biosens Bioelectron 2014; 66:481-9. [PMID: 25499661 DOI: 10.1016/j.bios.2014.12.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/25/2014] [Accepted: 12/02/2014] [Indexed: 01/24/2023]
Abstract
Peptide nucleic acid (PNA) is a mimic of DNA that shows a high chemical stability and can survive the enzymatic degradation of nucleases and proteases. The superior binding properties of PNA enable the formation of PNA/DNA or PNA/RNA duplex with excellent thermal stability and unique ionic strength effect. The introduction of microarray makes it possible to achieve accurate, high throughput parallel analysis of DNA or RNA with a highly integrated and low reagents consuming device. This powerful tool expands the applications of PNA in genotyping based on single nucleotide polymorphism (SNP) detection, the monitoring of disease-related miRNA expression and pathogen detection. This review paper discusses the fabrications of PNA microarrays through in situ synthesis strategy or spotting method by automatic devices, the various detection methods for the microarray-based hybridization and the current applications of PNA microarrays.
Collapse
Affiliation(s)
- Huanhuan Shi
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Feipeng Yang
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Wenjia Li
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Weiwei Zhao
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Kaixuan Nie
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Bo Dong
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China
| | - Zhengchun Liu
- Institute of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University, Changsha 410083, China.
| |
Collapse
|
32
|
Gholami Z, Hanley Q. Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer. Bioconjug Chem 2014; 25:1820-8. [PMID: 25191824 DOI: 10.1021/bc500319p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks, forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O(6)-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA-directed assembly of homo- and heterodimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template-directed assembly of PNA-modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels, which may find use in the study of assembly processes in cells.
Collapse
Affiliation(s)
- Zahra Gholami
- School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | | |
Collapse
|
33
|
Huang YC, Cao C, Tan XL, Li X, Liu L. Facile solid-phase synthesis of PNA–peptide conjugates using pNZ-protected PNA monomers. Org Chem Front 2014. [DOI: 10.1039/c4qo00217b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014; 53:10056-9. [DOI: 10.1002/anie.201404830] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/07/2022]
|
35
|
Zhao P, Chen Z, Li Y, Sun D, Gao Y, Huang Y, Li X. Selection of DNA-Encoded Small Molecule Libraries Against Unmodified and Non-Immobilized Protein Targets. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404830] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
36
|
Franzini RM, Neri D, Scheuermann J. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries. Acc Chem Res 2014; 47:1247-55. [PMID: 24673190 DOI: 10.1021/ar400284t] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target proteins and is likely to become a standard tool for pharmaceutical hit discovery, lead expansion, and Chemical Biology research. The introduction of new methodologies for library encoding and for compound synthesis in the presence of DNA is an exciting research field and will crucially contribute to the performance and the propagation of the technology.
Collapse
Affiliation(s)
- Raphael M. Franzini
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| |
Collapse
|
37
|
Groen N, van de Peppel J, Yuan H, van Leeuwen JP, van Blitterswijk CA, de Boer J. Bioinformatics-based selection of a model cell type for in vitro biomaterial testing. Biomaterials 2013; 34:5552-61. [DOI: 10.1016/j.biomaterials.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 04/01/2013] [Indexed: 12/21/2022]
|
38
|
Chouikhi D, Ciobanu M, Zambaldo C, Duplan V, Barluenga S, Winssinger N. Expanding the scope of PNA-encoded synthesis (PES): Mtt-protected PNA fully orthogonal to fmoc chemistry and a broad array of robust diversity-generating reactions. Chemistry 2012; 18:12698-704. [PMID: 22915361 DOI: 10.1002/chem.201201337] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/15/2012] [Indexed: 01/11/2023]
Abstract
Nucleic acid-encoded libraries are emerging as an attractive and highly miniaturized format for the rapid identification of protein ligands. An important criterion in the synthesis of nucleic acid encoded libraries is the scope of reactions that can be used to introduce molecular diversity and devise divergent pathways for diversity-oriented synthesis (DOS). To date, the protecting group strategies that have been used in peptide nucleic acid (PNA) encoded synthesis (PES) have limited the choice of reactions used in the library synthesis to just a few prototypes. Herein, we describe the preparation of PNA monomers with a protecting group combination (Mtt/Boc) that is orthogonal to Fmoc-based synthesis and compatible with a large palette of reactions that have been productively used in DOS (palladium cross-couplings, metathesis, reductive amination, amidation, heterocycle formation, nucleophilic addition, conjugate additions, Pictet-Spengler cyclization). We incorporate γ-modifications in the PNA backbone that are known to enhance hybridization and solubility. We demonstrate the robustness of this strategy with a library synthesis that is characterized by MALDI MS analysis at every step.
Collapse
Affiliation(s)
- Dalila Chouikhi
- Institut de Science et Ingénierie Supramoléculaires, ISIS - UMR, Université de Strasbourg - CNRS, France
| | | | | | | | | | | |
Collapse
|
39
|
Winssinger N. DNA display of PNA-tagged ligands: a versatile strategy to screen libraries and control geometry of multidentate ligands. ARTIFICIAL DNA, PNA & XNA 2012; 3:105-8. [PMID: 22871882 PMCID: PMC3581508 DOI: 10.4161/adna.21108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past decade, several technologies have emerged to access nucleic acid-tagged libraries and select the fittest compound within such libraries. This perspective focuses on recent development with PNA-tagged small molecules displayed on DNA templates for screening purposes and to probe the optimal geometry in multivalent interactions.
Collapse
Affiliation(s)
- Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires, Université de Strasbourg, CNRS, Strasbourg, France.
| |
Collapse
|
40
|
Galloway WRJD, Spring DR. PNA to DNA to microarray decoding facilitates ligand discovery. ACTA ACUST UNITED AC 2012; 18:1209-10. [PMID: 22035789 DOI: 10.1016/j.chembiol.2011.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of a method for the amplification of PNA tags (Svensen et al., in this issue of Chemistry & Biology) should expand the range of biological targets amenable to screening using PNA-encoded combinatorial libraries and thus facilitate the discovery of new biologically useful agents.
Collapse
|
41
|
Svensen N, Walton JG, Bradley M. Peptides for cell-selective drug delivery. Trends Pharmacol Sci 2012; 33:186-92. [DOI: 10.1016/j.tips.2012.02.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
|
42
|
Daguer JP, Ciobanu M, Barluenga S, Winssinger N. Discovery of an entropically-driven small molecule streptavidin binder from nucleic acid-encoded libraries. Org Biomol Chem 2012; 10:1502-5. [DOI: 10.1039/c2ob06880j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|