1
|
Hurd CA, Bush JT, Powell AJ, Walport LJ. mRNA Display in Cell Lysates Enables Identification of Cyclic Peptides Targeting the BRD3 Extraterminal Domain. Angew Chem Int Ed Engl 2024:e202406414. [PMID: 38899853 DOI: 10.1002/anie.202406414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/21/2024]
Abstract
mRNA display is a powerful technology to screen libraries of >1012 cyclic peptides against a protein target, enabling the rapid discovery of high affinity ligands. These cyclic peptides are particularly well suited to challenging protein targets that have been difficult to drug with small molecules. However, target choice can still be limited as screens are typically performed against purified proteins which often demands the use of isolated domains and precludes the use of aggregation-prone targets. Herein, we report a method to perform mRNA display selections in mammalian cell lysates without the need for prior target purification, vastly expanding the potential target scope of mRNA display. We have applied the methodology to identify low to sub-nanomolar peptide binders for two targets: a NanoLuc subunit (LgBiT) and full-length bromodomain-containing protein 3 (BRD3). Our cyclic peptides for BRD3 were found to bind to the extraterminal (ET) domain of BRD3 and the closely related BRD proteins, BRD2 and BRD4. While many chemical probes exist for the bromodomains of BRD proteins, the ET domain is relatively underexplored, making these peptides valuable additions to the BRD toolbox.
Collapse
Affiliation(s)
- Catherine A Hurd
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Crick-GSK Biomedical LinkLabs, The Francis Crick Institute, London, NW1 1AT
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Andrew J Powell
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Louise J Walport
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT
| |
Collapse
|
2
|
Dickson P. DNA-Encoded Library Technology─A Catalyst for Covalent Ligand Discovery. ACS Chem Biol 2024; 19:802-808. [PMID: 38527941 DOI: 10.1021/acschembio.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The identification of novel covalent ligands for therapeutic purposes has long depended on serendipity, with dedicated hit finding techniques emerging only in the early 2000s. Advances in chemoproteomics have enabled robust characterization of putative drugs to derisk the unique liabilities associated with covalent hit molecules, leading to a renewed interest in this targeting modality. DNA-encoded library (DEL) technology has similarly emerged over the past two decades as a highly efficient method to identify new chemical equity toward protein targets of interest. A number of commercial and academic groups have reported methods in covalent DEL synthesis and hit identification; however, it is evident that there is still much to be done to fully realize the power of this technology for covalent ligand discovery. This perspective will explore the current approaches in covalent DEL technology and reflect on the next steps to advance this field.
Collapse
Affiliation(s)
- Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| |
Collapse
|
3
|
Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
Collapse
Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
| |
Collapse
|
4
|
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
|
5
|
Schneider L, Sauter B, Dagher K, Gillingham D. Recording Binding Information Directly into DNA-Encoded Libraries Using Terminal Deoxynucleotidyl Transferase. J Am Chem Soc 2023; 145:20874-20882. [PMID: 37704585 PMCID: PMC10540198 DOI: 10.1021/jacs.3c05961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 09/15/2023]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is an unusual DNA polymerase that adds untemplated dNTPs to 3'-ends of DNA. If a target protein is expressed as a TdT fusion and incubated with a DNA-encoded library (DEL) in the presence of dATP, the binders of the target induce proximity between TdT and the DNA, promoting the synthesis of a poly-adenine (polyA) tail. The polyA tail length is proportional to the binding affinity, effectively serving as a stable molecular record of binding events. The polyA tail is also a convenient handle to enrich binders with magnetic poly(dT)25 beads before sequencing. In a benchmarking system, we show that ligands spanning nanomolar to double-digit micromolar binding can be cleanly identified by TdT extension, whereas only the tightest binding ligands are identified by classical affinity selection. The method is simple to implement and can function on any DEL that bears a free 3'-end.
Collapse
Affiliation(s)
| | - Basilius Sauter
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Koder Dagher
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| |
Collapse
|
6
|
Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
Collapse
Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
7
|
Torng W, Biancofiore I, Oehler S, Xu J, Xu J, Watson I, Masina B, Prati L, Favalli N, Bassi G, Neri D, Cazzamalli S, Feng JA. Deep Learning Approach for the Discovery of Tumor-Targeting Small Organic Ligands from DNA-Encoded Chemical Libraries. ACS OMEGA 2023; 8:25090-25100. [PMID: 37483198 PMCID: PMC10357458 DOI: 10.1021/acsomega.3c01775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
DNA-Encoded Chemical Libraries (DELs) have emerged as efficient and cost-effective ligand discovery tools, which enable the generation of protein-ligand interaction data of unprecedented size. In this article, we present an approach that combines DEL screening and instance-level deep learning modeling to identify tumor-targeting ligands against carbonic anhydrase IX (CAIX), a clinically validated marker of hypoxia and clear cell renal cell carcinoma. We present a new ligand identification and hit-to-lead strategy driven by machine learning models trained on DELs, which expand the scope of DEL-derived chemical motifs. CAIX-screening datasets obtained from three different DELs were used to train machine learning models for generating novel hits, dissimilar to elements present in the original DELs. Out of the 152 novel potential hits that were identified with our approach and screened in an in vitro enzymatic inhibition assay, 70% displayed submicromolar activities (IC50 < 1 μM). To generate lead compounds that are functionalized with anticancer payloads, analogues of top hits were prioritized for synthesis based on the predicted CAIX affinity and synthetic feasibility. Three lead candidates showed accumulation on the surface of CAIX-expressing tumor cells in cellular binding assays. The best compound displayed an in vitro KD of 5.7 nM and selectively targeted tumors in mice bearing human renal cell carcinoma lesions. Our results demonstrate the synergy between DEL and machine learning for the identification of novel hits and for the successful translation of lead candidates for in vivo targeting applications.
Collapse
Affiliation(s)
- Wen Torng
- Google
Research, 1600 Amphitheatre
Parkway, Mountain View, California 94043, United States
| | | | - Sebastian Oehler
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
| | - Jin Xu
- Google
Research, 1600 Amphitheatre
Parkway, Mountain View, California 94043, United States
| | - Jessica Xu
- Google
Research, 1600 Amphitheatre
Parkway, Mountain View, California 94043, United States
| | - Ian Watson
- Google
Research, 1600 Amphitheatre
Parkway, Mountain View, California 94043, United States
| | - Brenno Masina
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
| | - Luca Prati
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
| | - Nicholas Favalli
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
| | - Gabriele Bassi
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
| | - Dario Neri
- R&D
Department, Philochem AG, Otelfingen, Zürich 8112, Switzerland
- Philogen
S.p.A., Siena 53100, Italy
- Department
of Chemistry and Applied Biosciences, Swiss
Federal Institute of Technology (ETH Zürich), Zürich 8092, Switzerland
| | | | - Jianwen A. Feng
- Google
Research, 1600 Amphitheatre
Parkway, Mountain View, California 94043, United States
| |
Collapse
|
8
|
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
|
9
|
Yu W, Weber DJ, MacKerell AD. Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation. J Chem Theory Comput 2023; 19:3007-3021. [PMID: 37115781 PMCID: PMC10205696 DOI: 10.1021/acs.jctc.3c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Covalent drug design is an important component in drug discovery. Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues and thus may offer a more effective therapeutic approach. To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivities, and to predict noncovalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: site identification by ligand competitive saturation) that intrinsically considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. Through docking of a library of representative warhead fragments using SILCS-Monte Carlo (SILCS-MC), reactive cysteines can be correctly identified for proteins being tested. Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. Based on these tools, an integrated SILCS-based workflow was developed, named SILCS-Covalent, which can both qualitatively and quantitatively inform covalent drug discovery.
Collapse
Affiliation(s)
- Wenbo Yu
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - David J. Weber
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, Maryland 20850, United States
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| |
Collapse
|
10
|
Yu L, Lee H, Rho SB, Park MK, Lee CH. Ethacrynic Acid: A Promising Candidate for Drug Repurposing as an Anticancer Agent. Int J Mol Sci 2023; 24:ijms24076712. [PMID: 37047688 PMCID: PMC10094867 DOI: 10.3390/ijms24076712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Ethacrynic acid (ECA) is a diuretic that inhibits Na-K-2Cl cotransporter (NKCC2) present in the thick ascending loop of Henle and muculo dens and is clinically used for the treatment of edema caused by excessive body fluid. However, its clinical use is limited due to its low bioavailability and side effects, such as liver damage and hearing loss at high doses. Despite this, ECA has recently emerged as a potential anticancer agent through the approach of drug repositioning, with a novel mechanism of action. ECA has been shown to regulate cancer hallmark processes such as proliferation, apoptosis, migration and invasion, angiogenesis, inflammation, energy metabolism, and the increase of inhibitory growth factors through various mechanisms. Additionally, ECA has been used as a scaffold for synthesizing a new material, and various derivatives have been synthesized. This review explores the potential of ECA and its derivatives as anticancer agents, both alone and in combination with adjuvants, by examining their effects on ten hallmarks of cancer and neuronal contribution to cancer. Furthermore, we investigated the trend of synthesis research of a series of ECA derivatives to improve the bioavailability of ECA. This review highlights the importance of ECA research and its potential to provide a cost-effective alternative to new drug discovery and development for cancer treatment.
Collapse
Affiliation(s)
- Lu Yu
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Ho Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy National Cancer Center, Goyang 10408, Republic of Korea
| | - Seung Bae Rho
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy National Cancer Center, Goyang 10408, Republic of Korea
| | - Mi Kyung Park
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy National Cancer Center, Goyang 10408, Republic of Korea
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| |
Collapse
|
11
|
Abstract
Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programmes and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
Collapse
Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
| |
Collapse
|
12
|
Blay V, Li X, Gerlach J, Urbina F, Ekins S. Combining DELs and machine learning for toxicology prediction. Drug Discov Today 2022; 27:103351. [PMID: 36096360 PMCID: PMC9995617 DOI: 10.1016/j.drudis.2022.103351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/31/2022] [Accepted: 09/06/2022] [Indexed: 01/12/2023]
Abstract
DNA-encoded libraries (DELs) allow starting chemical matter to be identified in drug discovery. The volume of experimental data generated also makes DELs an attractive resource for machine learning (ML). ML allows modeling complex relationships between compounds and numerical endpoints, such as the binding to a target measured by DELs. DELs could also empower other areas of drug discovery. Here, we propose that DELs and ML could be combined to model binding to off-targets, enabling better predictive toxicology. With enough data, ML models can make accurate predictions across a vast chemical space, and they can be reused and expanded across projects. Although there are limitations, more general toxicology models could be applied earlier during drug discovery, illuminating safety liabilities at a lower cost.
Collapse
Affiliation(s)
- Vincent Blay
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jacob Gerlach
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Fabio Urbina
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA.
| |
Collapse
|
13
|
Li L, Su M, Lu W, Song H, Liu J, Wen X, Suo Y, Qi J, Luo X, Zhou YB, Liao XH, Li J, Lu X. Triazine-Based Covalent DNA-Encoded Libraries for Discovery of Covalent Inhibitors of Target Proteins. ACS Med Chem Lett 2022; 13:1574-1581. [PMID: 36262386 PMCID: PMC9575176 DOI: 10.1021/acsmedchemlett.2c00127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/10/2022] [Indexed: 11/28/2022] Open
Abstract
Since ibrutinib was approved by the FDA as an effective monotherapy for chronic lymphocytic leukemia (CLL) and multilymphoma, more and more FDA-approved covalent drugs are coming back into the market. On this occasion, the resurgence of interest in covalent drugs calls for more hit discovery techniques. However, the limited numbers of covalent libraries prevent the development of this area. Herein, we report the design of covalent DNA-encoded library (DEL) and its selection method for the discovery of covalent inhibitors for target proteins. These triazine-based covalent DELs yielded potent compounds after covalent selection against target proteins, including Bruton's Tyrosine Kinase (BTK), Janus kinase 3 (JAK3), and peptidyl-prolyl cis/trans isomerase NIMA-interacting-1 (Pin1).
Collapse
Affiliation(s)
- Linjie Li
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Mingbo Su
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Weiwei Lu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Hongzhi Song
- School
of Medicine, Shanghai University, Shanghai 200444, P. R. China
| | - Jiaxiang Liu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Xin Wen
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
| | - Yanrui Suo
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
| | - Jingjing Qi
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Xiaomin Luo
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Yu-Bo Zhou
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400,P. R. China
| | - Xin-Hua Liao
- School of
Life Sciences, Shanghai University, Shanghai200444, P. R. China
| | - Jia Li
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400,P. R. China
| | - Xiaojie Lu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R.
China
| |
Collapse
|
14
|
Sunkari YK, Meijer L, Flajolet M. The protein kinase CK1: Inhibition, activation, and possible allosteric modulation. Front Mol Biosci 2022; 9:916232. [PMID: 36090057 PMCID: PMC9449355 DOI: 10.3389/fmolb.2022.916232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
Protein kinases play a vital role in biology and deregulation of kinases is implicated in numerous diseases ranging from cancer to neurodegenerative diseases, making them a major target class for the pharmaceutical industry. However, the high degree of conservation that exists between ATP-binding sites among kinases makes it difficult for current inhibitors to be highly specific. In the context of neurodegeneration, several groups including ours, have linked different kinases such as CK1 and Alzheimer’s disease for example. Strictly CK1-isoform specific regulators do not exist and known CK1 inhibitors are inhibiting the enzymatic activity, targeting the ATP-binding site. Here we review compounds known to target CK1, as well as other inhibitory types that could benefit CK1. We introduce the DNA-encoded library (DEL) technology that might represent an interesting approach to uncover allosteric modulators instead of ATP competitors. Such a strategy, taking into account known allosteric inhibitors and mechanisms, might help designing modulators that are more specific towards a specific kinase, and in the case of CK1, toward specific isoforms.
Collapse
Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States
| | - Laurent Meijer
- Perha Pharmaceuticals, Hôtel de Recherche, Roscoff, France
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States
- *Correspondence: Marc Flajolet, ,
| |
Collapse
|
15
|
Chheda PR, Simmons N, Schuman DP, Shi Z. Palladium-Mediated Carbonylative Suzuki Coupling for DNA-Encoded Library Synthesis. Org Lett 2022; 24:5214-5219. [PMID: 35830624 DOI: 10.1021/acs.orglett.2c02113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing new DNA-compatible reactions is key to expanding the accessible chemical space of DNA-encoded library (DEL) technology. Here we disclose the first report of a DNA-compatible carbonylative Suzuki coupling of DNA-conjugated (hetero)aryl iodides with (hetero)aryl boronic acids to access di(hetero)aryl ketones, a valuable structural motif present within several approved or clinically advanced small molecules. The reported DNA-compatible, Pd(OAc)2-mediated system is mild, uses a robust protocol, has a wide substrate scope for both coupling partners, is suitable for large-scale DEL productions, and provides a source of previously unexplored chemical matter for DEL screens.
Collapse
Affiliation(s)
- Pratik R Chheda
- Discovery Chemistry, Janssen Research & Development, LLC, San Diego, California 92121, United States
| | - Nicholas Simmons
- Discovery Chemistry, Janssen Research & Development, LLC, San Diego, California 92121, United States
| | - David P Schuman
- Discovery Chemistry, Janssen Research & Development, LLC, San Diego, California 92121, United States
| | - Zhicai Shi
- Discovery Chemistry, Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
16
|
Gui Y, Wong CS, Zhao G, Xie C, Hou R, Li Y, Li G, Li X. Converting Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded Libraries for More Versatile Selections. ACS OMEGA 2022; 7:11491-11500. [PMID: 35415338 PMCID: PMC8992267 DOI: 10.1021/acsomega.2c01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is an efficient high-throughput screening technology platform in drug discovery and is also gaining momentum in academic research. Today, the majority of DELs are assembled and encoded with double-stranded DNA tags (dsDELs) and has been selected against numerous biological targets; however, dsDELs are not amendable to some of the recently developed selection methods, such as the cross-linking-based selection against immobilized targets and live-cell-based selections, which require DELs encoded with single-stranded DNAs (ssDELs). Herein, we present a simple method to convert dsDELs to ssDELs using exonuclease digestion without library redesign and resynthesis. We show that dsDELs could be efficiently converted to ssDELs and used for affinity-based selections either with purified proteins or on live cells.
Collapse
Affiliation(s)
- Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Clara Shania Wong
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
| |
Collapse
|
17
|
Ge R, Shen Z, Yin J, Chen W, Zhang Q, An Y, Tang D, Satz AL, Su W, Kuai L. Discovery of SARS-CoV-2 main protease covalent inhibitors from a DNA-encoded library selection. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:79-85. [PMID: 35063690 PMCID: PMC8767972 DOI: 10.1016/j.slasd.2022.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent inhibitors targeting the main protease (Mpro, or 3CLpro) of SARS-CoV-2 have shown promise in preclinical investigations. Herein, we report the discovery of two new series of molecules that irreversibly bind to SARS-CoV-2 Mpro. These acrylamide containing molecules were discovered using our covalent DNA-encoded library (DEL) screening platform. Following selection against SARS-CoV-2 Mpro, off-DNA compounds were synthesized and investigated to determine their inhibitory effects, the nature of their binding, and to generate preliminary structure-activity relationships. LC-MS analysis indicates a 1:1 (covalent) binding stoichiometry between our hit molecules and SARS-CoV-2 Mpro. Fluorescent staining assay for covalent binding in the presence of cell lysate suggests reasonable selectivity for SARS-CoV-2 Mpro. And lastly, inhibition of enzymatic activity was also observed against a panel of 3CLpro enzymes from different coronavirus strains, with IC50 values ranging from inactive to single digit micromolar. Our results indicate that DEL selection is a useful approach for identifying covalent inhibitors of cysteine proteases.
Collapse
Affiliation(s)
- Rui Ge
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zuyuan Shen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Yin
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenhua Chen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Dewei Tang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Letian Kuai
- WuXi AppTec(,) 55 Cambridge Parkway, 8th Floor(,) Cambridge, MA 02142, USA.
| |
Collapse
|
18
|
Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double‐ and Single‐Stranded DNA‐Encoded Chemical Libraries. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University 400044 Chongqing P. R. China
| |
Collapse
|
19
|
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
|
20
|
Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
Collapse
Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
| |
Collapse
|
21
|
Gao Y, Zhao G, He P, Zhang G, Li Y, Li Y. DNA-Compatible Synthesis of α,β-Epoxyketones for DNA-Encoded Chemical Libraries. Bioconjug Chem 2022; 33:105-110. [PMID: 34927428 DOI: 10.1021/acs.bioconjchem.1c00567] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As a powerful platform in drug discovery, the DNA-encoded chemical library technique enables the generation of numerous chemical members with high structural diversity. Epoxides widely exist in a variety of approved drugs and clinical candidates, eliciting multiple pharmaceutical activities. Herein, we report a non-oxidative DNA-compatible synthesis of di-/trisubstituted α,β-epoxyketones by implementing aldehydes and α-chlorinated ketones as abundant building blocks. This methodology was demonstrated to cover a broad substrate scope with medium-to-excellent conversions. Further structural diversification and transformation were also successfully explored to fully leverage α,β-epoxyketone moiety.
Collapse
Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Pengyang He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044, Chongqing, P. R. China
| |
Collapse
|
22
|
Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double- and Single-Stranded DNA-Encoded Chemical Libraries. Angew Chem Int Ed Engl 2021; 61:e202115157. [PMID: 34904335 DOI: 10.1002/anie.202115157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The use of a proper encoding methodology is one of the most important aspects when practicing DEL technology. A "headpiece"-based double-stranded DEL encoding method is currently the most widely used for productive DEL. However, the robustness of double-stranded DEL construction conflicts with the versatility presented by single-stranded DEL applications. We here report a novel encoding method, which is based on a "reversible covalent headpiece (RCHP)". The RCHP allows reversible interconversion between double- and single-stranded DNA formats, providing an avenue to robust synthesis and allowing for the applications in distinct setups. We have validated the versatility of this encoding method with encoded self-assembled chemical library and DNA-encoded dynamic library technology. Notably, based on the RCHP-settled library construction, a unique "ternary covalent complex" mediating ligand isolation methodology against non-immobilized targets was developed.
Collapse
Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044, Chongqing, P. R. China
| |
Collapse
|
23
|
Sunkari YK, Siripuram VK, Nguyen TL, Flajolet M. High-power screening (HPS) empowered by DNA-encoded libraries. Trends Pharmacol Sci 2021; 43:4-15. [PMID: 34782164 DOI: 10.1016/j.tips.2021.10.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023]
Abstract
The world is totally dependent on medications. As science progresses, new, better, and cheaper drugs are needed more than ever. The pharmaceutical industry has been predominantly dependent on high-throughput screening (HTS) for the past three decades. Considering that the discovery rate has been relatively constant, can one hope for a much-needed sudden trend uptick? DNA-encoded libraries (DELs) and similar technologies, that have several orders of magnitude more screening power than HTS, and that we propose to group together under the umbrella term of high-power screening (HPS), are very well positioned to do exactly that. HPS also offers novel screening options such as parallel screening, ex vivo and in vivo screening, as well as a new path to druggable alternatives such as proteolysis targeting chimeras (PROTACs). Altogether, HPS unlocks novel powerful drug discovery avenues.
Collapse
Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
24
|
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
|
25
|
Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
Collapse
Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
26
|
Gironda-Martínez A, Donckele EJ, Samain F, Neri D. DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges. ACS Pharmacol Transl Sci 2021; 4:1265-1279. [PMID: 34423264 PMCID: PMC8369695 DOI: 10.1021/acsptsci.1c00118] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) represent a versatile and powerful technology platform for the discovery of small-molecule ligands to protein targets of biological and pharmaceutical interest. DELs are collections of molecules, individually coupled to distinctive DNA tags serving as amplifiable identification barcodes. Thanks to advances in DNA-compatible reactions, selection methodologies, next-generation sequencing, and data analysis, DEL technology allows the construction and screening of libraries of unprecedented size, which has led to the discovery of highly potent ligands, some of which have progressed to clinical trials. In this Review, we present an overview of diverse approaches for the generation and screening of DEL molecular repertoires. Recent success stories are described, detailing how novel ligands were isolated from DEL screening campaigns and were further optimized by medicinal chemistry. The goal of the Review is to capture some of the most recent developments in the field, while also elaborating on future challenges to further improve DEL technology as a therapeutic discovery platform.
Collapse
Affiliation(s)
| | | | - Florent Samain
- Philochem
AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss
Federal Institute of Technology, CH-8093 Zürich, Switzerland
- Philogen
S.p.A, 53100 Siena, Italy
| |
Collapse
|
27
|
Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
| |
Collapse
|
28
|
Guilinger JP, Archna A, Augustin M, Bergmann A, Centrella PA, Clark MA, Cuozzo JW, Däther M, Guié MA, Habeshian S, Kiefersauer R, Krapp S, Lammens A, Lercher L, Liu J, Liu Y, Maskos K, Mrosek M, Pflügler K, Siegert M, Thomson HA, Tian X, Zhang Y, Konz Makino DL, Keefe AD. Novel irreversible covalent BTK inhibitors discovered using DNA-encoded chemistry. Bioorg Med Chem 2021; 42:116223. [PMID: 34091303 DOI: 10.1016/j.bmc.2021.116223] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Libraries of DNA-Encoded small molecules created using combinatorial chemistry and synthetic oligonucleotides are being applied to drug discovery projects across the pharmaceutical industry. The majority of reported projects describe the discovery of reversible, i.e. non-covalent, target modulators. We synthesized multiple DNA-encoded chemical libraries terminated in electrophiles and then used them to discover covalent irreversible inhibitors and report the successful discovery of acrylamide- and epoxide-terminated Bruton's Tyrosine Kinase (BTK) inhibitors. We also demonstrate their selectivity, potency and covalent cysteine engagement using a range of techniques including X-ray crystallography, thermal transition shift assay, reporter displacement assay and intact protein complex mass spectrometry. The epoxide BTK inhibitors described here are the first ever reported to utilize this electrophile for this target.
Collapse
Affiliation(s)
| | - Archna Archna
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Martin Augustin
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Andreas Bergmann
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | | | - John W Cuozzo
- ZebiAI Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | - Maike Däther
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Sevan Habeshian
- Laboratory of Therapeutic Proteins and Peptides École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Reiner Kiefersauer
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Stephan Krapp
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Alfred Lammens
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Lukas Lercher
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Julie Liu
- Accent Therapeutics Inc., 65 Hayden Avenue, Lexington, MA 02421, USA
| | - Yanbin Liu
- Cyteir Therapeutics, 128 Spring St, Lexington, MA 02421, USA
| | - Klaus Maskos
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Klaus Pflügler
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | - Markus Siegert
- Proteros biostructures GmbH, Bunsenstr. 7a, 82152 Planegg-Martinsried, Germany
| | | | - Xia Tian
- Nurix Therapeutics Inc., 1700 Owens Street, Suite 205 San Francisco, CA 94158, USA
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | | | | |
Collapse
|
29
|
Fukunaga K, Yokobayashi Y. Directed evolution of orthogonal RNA-RBP pairs through library-vs-library in vitro selection. Nucleic Acids Res 2021; 50:601-616. [PMID: 34219162 PMCID: PMC8789040 DOI: 10.1093/nar/gkab527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022] Open
Abstract
RNA-binding proteins (RBPs) and their RNA ligands play many critical roles in gene regulation and RNA processing in cells. They are also useful for various applications in cell biology and synthetic biology. However, re-engineering novel and orthogonal RNA-RBP pairs from natural components remains challenging while such synthetic RNA-RBP pairs could significantly expand the RNA-RBP toolbox for various applications. Here, we report a novel library-vs-library in vitro selection strategy based on Phage Display coupled with Systematic Evolution of Ligands by EXponential enrichment (PD-SELEX). Starting with pools of 1.1 × 1012 unique RNA sequences and 4.0 × 108 unique phage-displayed L7Ae-scaffold (LS) proteins, we selected RNA-RBP complexes through a two-step affinity purification process. After six rounds of library-vs-library selection, the selected RNAs and LS proteins were analyzed by next-generation sequencing (NGS). Further deconvolution of the enriched RNA and LS protein sequences revealed two synthetic and orthogonal RNA-RBP pairs that exhibit picomolar affinity and >4000-fold selectivity.
Collapse
Affiliation(s)
- Keisuke Fukunaga
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| |
Collapse
|
30
|
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
|
31
|
Liang Q, He J, Zhao X, Xue Y, Zuo H, Xu R, Jin Y, Wang J, Li Q, Zhao X. Selective Discovery of GPCR Ligands within DNA-Encoded Chemical Libraries Derived from Natural Products: A Case Study on Antagonists of Angiotensin II Type I Receptor. J Med Chem 2021; 64:4196-4205. [PMID: 33784102 DOI: 10.1021/acs.jmedchem.1c00123] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Natural products have failed to meet the urgent need for drug discovery in recent decades due to limited resources, necessitating new strategies for re-establishing the key role of natural products in hit screening. This work introduced DNA-encoding techniques into the synthesis of phenolic acid-focused libraries containing 32 000 diverse compounds. Online selection of the library using immobilized angiotensin II type I receptor (AT1R) resulted in seven phenolic acid derivatives. The half-maximal concentration (IC50) of hit 1 for the right shift of the [125I]-Sar1-AngII competition curve was 19.6 nM. Pharmacological examination of renovascular hypertensive rats demonstrated that hit 1 significantly lowered the blood pressure of the animals without changing their heart rates. These results were used to create a general strategy for rapid and unbiased discovery of hits derived from natural products with high throughput and efficiency.
Collapse
Affiliation(s)
- Qi Liang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jianyu He
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xue Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Xue
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haiyue Zuo
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ru Xu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Jin
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qian Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| |
Collapse
|
32
|
Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
Collapse
Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| |
Collapse
|
33
|
Petersen LK, Christensen AB, Andersen J, Folkesson CG, Kristensen O, Andersen C, Alzu A, Sløk FA, Blakskjær P, Madsen D, Azevedo C, Micco I, Hansen NJV. Screening of DNA-Encoded Small Molecule Libraries inside a Living Cell. J Am Chem Soc 2021; 143:2751-2756. [DOI: 10.1021/jacs.0c09213] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lars K. Petersen
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | | | - Jacob Andersen
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | | | - Ole Kristensen
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | | | - Amaya Alzu
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Frank A. Sløk
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Peter Blakskjær
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Daniel Madsen
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Carlos Azevedo
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Iolanda Micco
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | | |
Collapse
|
34
|
Shi Y, Wu YR, Yu JQ, Zhang WN, Zhuang CL. DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output. RSC Adv 2021; 11:2359-2376. [PMID: 35424149 PMCID: PMC8693808 DOI: 10.1039/d0ra09889b] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
A DNA-encoded library is a collection of small molecules covalently linked to DNA that has unique information about the identity and the structure of each library member. A DNA-encoded chemical library (DEL) is broadly adopted by major pharmaceutical companies and used in numerous drug discovery programs. The application of the DEL technology is advantageous at the initial period of drug discovery because of reduced cost, time, and storage space for the identification of target compounds. The key points for the construction of DELs comprise the development and the selection of the encoding methods, transfer of routine chemical reaction from off-DNA to on-DNA, and exploration of new chemical reactions on DNA. The limitations in the chemical space and the diversity of DEL were reduced gradually by using novel DNA-compatible reactions based on the formation and the cleavage of various bonds. Here, we summarized a series of novel DNA-compatible chemistry reactions for DEL building blocks and analysed the druggability of screened hit molecules via DELs in the past five years.
Collapse
Affiliation(s)
- Ying Shi
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Yan-Ran Wu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Jian-Qiang Yu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Wan-Nian Zhang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| | - Chun-Lin Zhuang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| |
Collapse
|
35
|
McEnaney P, Balzarini M, Park H, Kodadek T. Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin. Chem Commun (Camb) 2020; 56:10560-10563. [PMID: 32785302 DOI: 10.1039/d0cc02588g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A high affinity Streptavidin ligand was mined from a DNA-encoded library of non-peptidic oligimers and characterized structurally.
Collapse
Affiliation(s)
- Patrick McEnaney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 3345, USA.
| | | | | | | |
Collapse
|
36
|
Kwong AJ, Scheidt KA. Non-'classical' MEKs: A review of MEK3-7 inhibitors. Bioorg Med Chem Lett 2020; 30:127203. [PMID: 32389527 PMCID: PMC7299838 DOI: 10.1016/j.bmcl.2020.127203] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
The MAPK pathways are an enduring area of interest due to their essential roles in cell processes. Increased expression and activity can lead to a multitude of diseases, sparking research efforts in developing inhibitors against these kinases. Though great strides have been made in developing MEK1/2 inhibitors, there is a notable lack of chemical probes for MEK3-7, given their central role in stimuli response, cell growth, and development. This review summarizes the progress that has been made on developing small molecule probes for MEK3-7, the specific disease states in which they have been studied, and their potential to become novel therapeutics.
Collapse
Affiliation(s)
- Ada J Kwong
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, United States
| | - Karl A Scheidt
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, United States.
| |
Collapse
|
37
|
USP1 inhibitor ML323 enhances osteogenic potential of human dental pulp stem cells. Biochem Biophys Res Commun 2020; 530:418-424. [PMID: 32546349 DOI: 10.1016/j.bbrc.2020.05.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/14/2020] [Indexed: 12/17/2022]
Abstract
LIM homeobox 8 (LHX8) is expressed during embryonic development of craniofacial tissues, including bone and teeth. In a previous study, the overexpression of LHX8 inhibited osteodifferentiation of human dental pulp stem cells (DPSCs). In this study, a cDNA microarray analysis was performed to reveal the molecular changes which occur in response to LHX8 overexpression in DPSCs and discover possible targets for an osteoinductive agent. There were 345 differentially expressed genes (DEGs) in response to osteoinductive signaling and 53 DEGs in response to LHX8 overexpression and osteoinductive signaling, respectively. Thirty-eight genes were common in both conditions, and among these, genes upregulated in LHX8 DPSCs but downregulated in osteodifferentiated DPSCs were chosen. Five of them had commercial inhibitors available. Among the tested inhibitors, ML323, which target DNA-binding protein inhibitor ID-1, promoted osteodifferentiation of DPSCs. In conclusion, inhibition of ID-1 led to increased osteogenesis of human DPSCs.
Collapse
|
38
|
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
|
39
|
Terai T, Koike T, Nemoto N. Photocrosslinking of cDNA Display Molecules with Their Target Proteins as a New Strategy for Peptide Selection. Molecules 2020; 25:molecules25061472. [PMID: 32214008 PMCID: PMC7146492 DOI: 10.3390/molecules25061472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 12/29/2022] Open
Abstract
Binding peptides for given target molecules are often selected in vitro during drug discovery and chemical biology research. Among several display technologies for this purpose, complementary DNA (cDNA) display (a covalent complex of a peptide and its encoding cDNA linked via a specially designed puromycin-conjugated DNA) is unique in terms of library size, chemical stability, and flexibility of modification. However, selection of cDNA display libraries often suffers from false positives derived from non-specific binding. Although rigorous washing is a straightforward solution, this also leads to the loss of specific binders with moderate affinity because the interaction is non-covalent. To address this issue, herein, we propose a method to covalently link cDNA display molecules with their target proteins using light irradiation. We designed a new puromycin DNA linker that contains a photocrosslinking nucleic acid and prepared cDNA display molecules using the linker. Target proteins were also labeled with a short single-stranded DNA that should transiently hybridize with the linker. Upon ultraviolet (UV) light irradiation, cDNA display molecules encoding correct peptide aptamers made stable crosslinked products with the target proteins in solution, while display molecules encoding control peptides did not. Although further optimization and improvement is necessary, the results pave the way for efficient selection of peptide aptamers in multimolecular crowding biosystems.
Collapse
Affiliation(s)
- Takuya Terai
- Correspondence: (T.T.); or (N.N); Tel.: +81-48-858-3534 (T.T.); +81-48-858-3531 (N.N.)
| | | | - Naoto Nemoto
- Correspondence: (T.T.); or (N.N); Tel.: +81-48-858-3534 (T.T.); +81-48-858-3531 (N.N.)
| |
Collapse
|
40
|
Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
Collapse
Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
41
|
Song J, Zheng Y, Huang M, Wu L, Wang W, Zhu Z, Song Y, Yang C. A Sequential Multidimensional Analysis Algorithm for Aptamer Identification based on Structure Analysis and Machine Learning. Anal Chem 2020; 92:3307-3314. [PMID: 31876151 DOI: 10.1021/acs.analchem.9b05203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular recognition ligands are of great significance in many fields, but our ability to develop new recognition molecules remains to be expanded. Here, we developed a Sequential Multidimensional Analysis algoRiThm for aptamer discovery (SMART-Aptamer) from high-throughput sequencing (HTS) data of SELEX libraries based on multilevel structure analysis and unsupervised machine learning to discover nucleic acid recognition ligands with high accuracy and efficiency. We validated SMART-Aptamer with three sets of HTS data from screening pools against hESCs, EpCAM, and CSV. High affinity aptamers for all three targets were successfully obtained, and the results revealed that SMART-Aptamer is able to pick out high affinity aptamers with low false positive and negative rates. With the advantages of accuracy, efficiency, and robustness, SMART-Aptamer represents a paradigm-shift strategy for the discovery of binding ligands for a variety of biomedical applications.
Collapse
Affiliation(s)
- Jia Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yuan Zheng
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Mengjiao Huang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Zhi Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , People's Republic of China
| |
Collapse
|
42
|
Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
Collapse
Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| |
Collapse
|
43
|
Johnson EO, Hung DT. A Point of Inflection and Reflection on Systems Chemical Biology. ACS Chem Biol 2019; 14:2497-2511. [PMID: 31613592 DOI: 10.1021/acschembio.9b00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the past several decades, chemical biologists have been leveraging chemical principles for understanding biology, tackling disease, and biomanufacturing, while systems biologists have holistically applied computation and genome-scale experimental tools to the same problems. About a decade ago, the benefit of combining the philosophies of chemical biology with systems biology into systems chemical biology was advocated, with the potential to systematically understand the way small molecules affect biological systems. Recently, there has been an explosion in new technologies that permit massive expansion in the scale of biological experimentation, increase access to more diverse chemical space, and enable powerful computational interpretation of large datasets. Fueled by these rapidly increasing capabilities, systems chemical biology is now at an inflection point, poised to enter a new era of more holistic and integrated scientific discovery. Systems chemical biology is primed to reveal an integrated understanding of fundamental biology and to discover new chemical probes to comprehensively dissect and systematically understand that biology, thereby providing a path to novel strategies for discovering therapeutics, designing drug combinations, avoiding toxicity, and harnessing beneficial polypharmacology. In this Review, we examine the emergence of new capabilities driving us to this inflection point in systems chemical biology, and highlight holistic approaches and opportunities that are arising from integrating chemical biology with a systems-level understanding of the intersection of biology and chemistry.
Collapse
Affiliation(s)
- Eachan O. Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
44
|
Cai B, Kim D, Akhand S, Sun Y, Cassell RJ, Alpsoy A, Dykhuizen EC, Van Rijn RM, Wendt MK, Krusemark CJ. Selection of DNA-Encoded Libraries to Protein Targets within and on Living Cells. J Am Chem Soc 2019; 141:17057-17061. [PMID: 31613623 DOI: 10.1021/jacs.9b08085] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the selection of DNA-encoded small molecule libraries against protein targets within the cytosol and on the surface of live cells. The approach relies on generation of a covalent linkage of the DNA to protein targets by affinity labeling. This cross-linking event enables subsequent copurification by a tag on the recombinant protein. To access targets within cells, a cyclic cell-penetrating peptide is appended to DNA-encoded libraries for delivery across the cell membrane. As this approach assesses binding of DELs to targets in live cells, it provides a strategy for selection of DELs against challenging targets that cannot be expressed and purified as active.
Collapse
Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Dongwook Kim
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Saeed Akhand
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Yixing Sun
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Robert J Cassell
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Richard M Van Rijn
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology , Purdue Center for Cancer Research, Purdue University , West Lafayette , Indiana 47907 , United States
| |
Collapse
|
45
|
Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
Collapse
|
46
|
Yan M, Zhu Y, Liu X, Lasanajak Y, Xiong J, Lu J, Lin X, Ashline D, Reinhold V, Smith DF, Song X. Next-Generation Glycan Microarray Enabled by DNA-Coded Glycan Library and Next-Generation Sequencing Technology. Anal Chem 2019; 91:9221-9228. [PMID: 31187982 DOI: 10.1021/acs.analchem.9b01988] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interactions of glycans with proteins, cells, and microorganisms play important roles in cell-cell adhesion and host-pathogen interaction. Glycan microarray technology, in which multiple glycan structures are immobilized on a single glass slide and interrogated with glycan-binding proteins (GBPs), has become an indispensable tool in the study of protein-glycan interactions. Despite its great success, the current format of the glycan microarray requires expensive, specialized instrumentation and labor-intensive assay and image processing procedures, which limit automation and possibilities for high-throughput analyses. Furthermore, the current microarray is not suitable for assaying interaction with intact cells due to their large size compared to the two-dimensional microarray surface. To address these limitations, we developed the next-generation glycan microarray (NGGM) based on artificial DNA coding of glycan structures. In this novel approach, a glycan library is presented as a mixture of glycans and glycoconjugates, each of which is coded with a unique oligonucleotide sequence (code). The glycan mixture is interrogated by GBPs followed by the separation of unbound coded glycans. The DNA sequences that identify individual bound glycans are quantitatively sequenced (decoded) by powerful next-generation sequencing (NGS) technology, and copied numbers of the DNA codes represent relative binding specificities of corresponding glycan structures to GBPs. We demonstrate that NGGM generates glycan-GBP binding data that are consistent with that generated in a slide-based glycan microarray. More importantly, the solution phase binding assay is directly applicable to identifying glycan binding to intact cells, which is often challenging using glass slide-based glycan microarrays.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - David Ashline
- College of Life Sciences and Agriculture , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | - Vernon Reinhold
- College of Life Sciences and Agriculture , University of New Hampshire , Durham , New Hampshire 03824 , United States
| | | | | |
Collapse
|
47
|
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
|
48
|
Shi B, Deng Y, Li X. Polymerase-Extension-Based Selection Method for DNA-Encoded Chemical Libraries against Nonimmobilized Protein Targets. ACS COMBINATORIAL SCIENCE 2019; 21:345-349. [PMID: 30920794 DOI: 10.1021/acscombsci.9b00011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) have become an important ligand discovery technology in biomedical research and drug discovery. DELs can be comprised of hundreds of millions to billions of candidate molecules and provide outstanding chemical diversity for discovering novel ligands and inhibitors for a large variety of biological targets. However, in most cases, DELs are selected against purified and immobilized proteins based on binding affinity. The development and application of DELs to more complex biological targets requires selection methods compatible with nonimmobilized and unpurified proteins. Here, we describe an approach using polymerase-based extension and target-directed photo-cross-linking and its application to the interrogation of a solution-phase protein target, carbonic anhydrase II.
Collapse
Affiliation(s)
- Bingbing Shi
- Department of Food Science, Tibet Agriculture and Animal Husbandry University, 100 Yucai Road West, Nyingchi, China 860000
| | - Yuqing Deng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
49
|
Liszczak G, Muir TW. Barcoding mit Nukleinsäuren: Anwendung der DNA‐Sequenzierung als molekulares Zählwerk. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201808956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Glen Liszczak
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Aktuelle Adresse: Department of BiochemistryUT Southwestern Medical Center Dallas TX 75390 USA
| | - Tom W. Muir
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
| |
Collapse
|
50
|
Liszczak G, Muir TW. Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. Angew Chem Int Ed Engl 2019; 58:4144-4162. [PMID: 30153374 DOI: 10.1002/anie.201808956] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 12/17/2022]
Abstract
The emergence of high-throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.
Collapse
Affiliation(s)
- Glen Liszczak
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| |
Collapse
|