1
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Huang Q, Gu Y, Qin A, Ma P, Xu H, Zhang S. FSO 2N 3-Mediated On-DNA Diazo-Transfer Chemistry. ACS Med Chem Lett 2024; 15:1591-1597. [PMID: 39291003 PMCID: PMC11403730 DOI: 10.1021/acsmedchemlett.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
DNA-encoded library (DEL) is a powerful hit selection technique in both basic science and innovative drug discovery. In this study, we report a robust and straightforward DNA-compatible diazo-transfer reaction utilizing FSO2N3 as the diazo-transfer reagent in solution. This reaction demonstrates high conversions and facile operation while being metal-free and maintaining high levels of DNA fidelity. It is also compatible with a wide range of substrates, allowing for convenient access to both aliphatic and aromatic amines. Consequently, it will further enrich the DEL chemistry toolbox.
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Affiliation(s)
- Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P.R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P.R. China
| | - An Qin
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P.R. China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
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2
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Huang Y, Hou R, Lam FS, Jia Y, Zhou Y, He X, Li G, Xiong F, Cao Y, Wang D, Li X. Agonist Discovery for Membrane Proteins on Live Cells by Using DNA-encoded Libraries. J Am Chem Soc 2024; 146:24638-24653. [PMID: 39171830 DOI: 10.1021/jacs.4c08624] [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: 08/23/2024]
Abstract
Identifying biologically active ligands for membrane proteins is an important task in chemical biology. We report an approach to directly identify small molecule agonists against membrane proteins by selecting DNA-encoded libraries (DELs) on live cells. This method connects extracellular ligand binding with intracellular biochemical transformation, thereby biasing the selection toward agonist identification. We have demonstrated the methodology with three membrane proteins: epidermal growth factor receptor (EGFR), thrombopoietin receptor (TPOR), and insulin receptor (INSR). A ∼30 million and a 1.033 billion-compound DEL were selected against these targets, and novel agonists with subnanomolar affinity and low micromolar cellular activities have been discovered. The INSR agonists activated the receptor by possibly binding to an allosteric site, exhibited clear synergistic effects with insulin, and activated the downstream signaling pathways. Notably, the agonists did not activate the insulin-like growth factor 1 receptor (IGF-1R), a highly homologous receptor whose activation may lead to tumor progression. Collectively, this work has developed an approach toward "functional" DEL selections on the cell surface and may provide a widely applicable method for agonist discovery for membrane proteins.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Rui Hou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Yunxuan Jia
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
| | - Xun He
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen 518110, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Feng Xiong
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen 518110, China
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Dongyao Wang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong SAR 999077, China
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3
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Wei Y, Wu B, Liu M, Cui CP. The Discovery of a Specific CKIP-1 Ligand for the Potential Treatment of Disuse Osteoporosis. Int J Mol Sci 2024; 25:8870. [PMID: 39201556 PMCID: PMC11354310 DOI: 10.3390/ijms25168870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/30/2024] [Accepted: 08/03/2024] [Indexed: 09/02/2024] Open
Abstract
Bone homeostasis relies on the delicate balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption. The casein kinase 2 interacting protein-1 (CKIP-1), a specific CK2α subunit-interacting protein, has been documented as one of the crucial negative regulators of bone formation. CKIP-1 siRNA therapy has constraints that limit its use in clinical applications. Therefore, it is necessary to explore effective targeting strategies for CKIP-1. In this study, we observed an upregulation of CKIP-1 protein expression in the microgravity environment, while its ubiquitination levels decreased. We further investigated the interaction between CKIP-1 and VHL and found that VHL enhanced CKIP-1 degradation through the ubiquitylation-proteasome system (UPS). Additionally, we discovered a small molecule ligand, named C77, through DNA-encoded library (DEL) screening, which binds to CKIP-1 both in vivo and in vitro, as confirmed by Surface Plasmon Resonance (SPR) and the Cellular Thermal shift assay (CETSA), respectively. Our findings demonstrated the potential of VHL and C77 as guiding factors in the development of CKIP-1-based Proteolysis-Targeting Chimeras (PROTACs), which could be future therapeutic interventions in disuse osteoporosis.
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Affiliation(s)
| | | | | | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China; (Y.W.); (B.W.); (M.L.)
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4
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Chheda PR, Simmons N, Shi Z. Oxoammonium Salt-Mediated On-DNA Alcohol Oxidation for DEL Synthesis. Org Lett 2024; 26:6754-6759. [PMID: 39077878 DOI: 10.1021/acs.orglett.4c02474] [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: 07/31/2024]
Abstract
On-DNA carboxylic acids are important synthetic intermediates in the synthesis of DNA-encoded library (DEL) structures. Herein, we report an oxoammonium salt-mediated, room temperature, solution-phase oxidation of DNA-linked primary alcohols into carboxylic acids. This method exhibits a wide substrate scope, encompassing aliphatic, benzylic, and heterobenzylic alcohols, and is compatible with DEL encoding strategies. This advancement facilitates a DEL strategy to utilize unprotected alcohols as inert, masked carboxylic acids and enables access to noncommercial bifunctional carboxyl intermediates to enhance the accessible chemical diversity within DELs.
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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
| | - Zhicai Shi
- Discovery Chemistry, Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
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5
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Fan Y, Feng R, Zhang X, Wang ZL, Xiong F, Zhang S, Zhong ZF, Yu H, Zhang QW, Zhang Z, Wang Y, Li G. Encoding and display technologies for combinatorial libraries in drug discovery: The coming of age from biology to therapy. Acta Pharm Sin B 2024; 14:3362-3384. [PMID: 39220863 PMCID: PMC11365444 DOI: 10.1016/j.apsb.2024.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 09/04/2024] Open
Abstract
Drug discovery is a sophisticated process that incorporates scientific innovations and cutting-edge technologies. Compared to traditional bioactivity-based screening methods, encoding and display technologies for combinatorial libraries have recently advanced from proof-of-principle experiments to promising tools for pharmaceutical hit discovery due to their high screening efficiency, throughput, and resource minimization. This review systematically summarizes the development history, typology, and prospective applications of encoding and displayed technologies, including phage display, ribosomal display, mRNA display, yeast cell display, one-bead one-compound, DNA-encoded, peptide nucleic acid-encoded, and new peptide-encoded technologies, and examples of preclinical and clinical translation. We discuss the progress of novel targeted therapeutic agents, covering a spectrum from small-molecule inhibitors and nonpeptidic macrocycles to linear, monocyclic, and bicyclic peptides, in addition to antibodies. We also address the pending challenges and future prospects of drug discovery, including the size of screening libraries, advantages and disadvantages of the technology, clinical translational potential, and market space. This review is intended to establish a comprehensive high-throughput drug discovery strategy for scientific researchers and clinical drug developers.
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Affiliation(s)
- Yu Fan
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Ruibing Feng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Xinya Zhang
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Zhen-Liang Wang
- Geriatric Medicine, First People's Hospital of XinXiang and the Fifth Affiliated Hospital of Xinxiang Medical College, Xinxiang 453100, China
| | - Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518000, China
| | - Shuihua Zhang
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518000, China
| | - Zhang-Feng Zhong
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Hua Yu
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Qing-Wen Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, Guangzhou 510632, China
- Department of Pharmacy, Guangzhou Red Cross Hospital, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Yitao Wang
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Guodong Li
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
- Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
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6
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Puglioli S, Fabbri M, Comacchio C, Alvigini L, De Luca R, Oehler S, Gilardoni E, Bassi G, Cazzamalli S, Neri D, Favalli N. Permutational Encoding Strategy Accelerates HIT Validation from Single-Stranded DNA-Encoded Libraries. Bioconjug Chem 2024; 35:1033-1043. [PMID: 38963407 DOI: 10.1021/acs.bioconjchem.4c00233] [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: 07/05/2024]
Abstract
DNA-Encoded Libraries (DELs) allow the parallel screening of millions of compounds for various applications, including de novo discovery or affinity maturation campaigns. However, library construction and HIT resynthesis can be cumbersome, especially when library members present an unknown stereochemistry. We introduce a permutational encoding strategy suitable for the construction of highly pure single-stranded single-pharmacophore DELs, designed to distinguish isomers at the sequencing level (e.g., stereoisomers, regio-isomers, and peptide sequences). This approach was validated by synthesizing a mock 921,600-member 4-amino-proline single-stranded DEL ("DEL1"). While screening DEL1 against different targets, high-throughput sequencing results showed selective enrichment of the most potent stereoisomers, with enrichment factors that outperform conventional encoding strategies. The versatility of our methodology was additionally validated by encoding 24 scaffolds derived from different permutations of the amino acid sequence of a previously described cyclic peptide targeting Fibroblast Activation Protein (FAP-2286). The resulting library ("DEL2") was interrogated against human FAP, showing selective enrichment of five cyclic peptides. We observed a direct correlation between enrichment factors and on-DNA binding affinities. The presented encoding methodology accelerates drug discovery by facilitating library synthesis and streamlining HIT resynthesis while enhancing enrichment factors at the DEL sequencing level. This facilitates the identification of HIT candidates prior to medicinal chemistry and affinity maturation campaigns.
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Affiliation(s)
- Sara Puglioli
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Mosè Fabbri
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Claudia Comacchio
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Laura Alvigini
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Roberto De Luca
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Sebastian Oehler
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Ettore Gilardoni
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Gabriele Bassi
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Samuele Cazzamalli
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 1-5/10, Zürich CH-8093, Switzerland
- Philogen S.p.A., Via Bellaria, 35, Sovicille, SI IT-53018, Italy
| | - Nicholas Favalli
- R&D Department, Philochem AG, Libernstrasse 3, Otelfingen, ZH CH-8112, Switzerland
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7
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An Y, Lim J, Glavatskikh M, Wang X, Norris-Drouin J, Hardy PB, Leisner TM, Pearce KH, Kireev D. In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot. Nat Commun 2024; 15:5564. [PMID: 38956119 PMCID: PMC11219766 DOI: 10.1038/s41467-024-49892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
Chemical probes are an indispensable tool for translating biological discoveries into new therapies, though are increasingly difficult to identify since novel therapeutic targets are often hard-to-drug proteins. We introduce FRASE-based hit-finding robot (FRASE-bot), to expedite drug discovery for unconventional therapeutic targets. FRASE-bot mines available 3D structures of ligand-protein complexes to create a database of FRAgments in Structural Environments (FRASE). The FRASE database can be screened to identify structural environments similar to those in the target protein and seed the target structure with relevant ligand fragments. A neural network model is used to retain fragments with the highest likelihood of being native binders. The seeded fragments then inform ultra-large-scale virtual screening of commercially available compounds. We apply FRASE-bot to identify ligands for Calcium and Integrin Binding protein 1 (CIB1), a promising drug target implicated in triple negative breast cancer. FRASE-based virtual screening identifies a small-molecule CIB1 ligand (with binding confirmed in a TR-FRET assay) showing specific cell-killing activity in CIB1-dependent cancer cells, but not in CIB1-depletion-insensitive cells.
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Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Jiwoong Lim
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Xiaowen Wang
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - P Brian Hardy
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA.
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8
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Verma SK, Witkin KL, Sharman A, Smith MA. Targeting fusion oncoproteins in childhood cancers: challenges and future opportunities for developing therapeutics. J Natl Cancer Inst 2024; 116:1012-1018. [PMID: 38574391 PMCID: PMC11223828 DOI: 10.1093/jnci/djae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024] Open
Abstract
Fusion oncoproteins are associated with childhood cancers and have proven challenging to target, aside from those that include kinases. As part of its efforts for targeting childhood cancers, the National Cancer Institute recently conducted a series on Novel Chemical Approaches for Targeting Fusion Oncoproteins. Key learnings on leading platforms and technologies that can be used to advance the development of molecular therapeutics that target fusion oncoproteins in childhood cancers are described. Recent breakthroughs in medicinal chemistry and chemical biology provide new ground and creative strategies to exploit for the development of targeted agents for improving outcomes against these recalcitrant cancers.
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Affiliation(s)
- Sharad K Verma
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keren L Witkin
- Division of Cancer Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anu Sharman
- Division of Cancer Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malcolm A Smith
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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9
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Zhang YN, Wan XC, Tang Y, Chen Y, Zheng FH, Cui ZH, Zhang H, Zhou Z, Fang GM. Employing unnatural promiscuity of sortase to construct peptide macrocycle libraries for ligand discovery. Chem Sci 2024; 15:9649-9656. [PMID: 38939140 PMCID: PMC11206207 DOI: 10.1039/d4sc01992j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/11/2024] [Indexed: 06/29/2024] Open
Abstract
With the increasing attention paid to macrocyclic scaffolds in peptide drug development, genetically encoded peptide macrocycle libraries have become invaluable sources for the discovery of high-affinity peptide ligands targeting disease-associated proteins. The traditional phage display technique of constructing disulfide-tethered macrocycles by cysteine oxidation has the inherent drawback of reduction instability of the disulfide bond. Chemical macrocyclization solves the problem of disulfide bond instability, but the involved highly electrophilic reagents are usually toxic to phages and may bring undesirable side reactions. Here, we report a unique Sortase-mediated Peptide Ligation and One-pot Cyclization strategy (SPLOC) to generate peptide macrocycle libraries, avoiding the undesired reactions of electrophiles with phages. The key to this platform is to mine the unnatural promiscuity of sortase on the X residue of the pentapeptide recognition sequence (LPXTG). Low reactive electrophiles are incorporated into the X-residue side chain, enabling intramolecular cyclization with the cysteine residue of the phage-displayed peptide library. Utilizing the genetically encoded peptide macrocycle library constructed by the SPLOC platform, we found a high-affinity bicyclic peptide binding TEAD4 with a nanomolar KD value (63.9 nM). Importantly, the binding affinity of the bicyclic peptide ligand is 102-fold lower than that of the acyclic analogue. To our knowledge, this is the first time to mine the unnatural promiscuity of ligases to generate peptide macrocycles, providing a new avenue for the construction of genetically encoded cyclic peptide libraries.
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Affiliation(s)
- Yan-Ni Zhang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Xiao-Cui Wan
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Yang Tang
- Department of Medical Ultrasound, Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine Shanghai 200072 P. R. China
| | - Ying Chen
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Feng-Hao Zheng
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhi-Hui Cui
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Hua Zhang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University Shanghai 200438 P. R. China
| | - Ge-Min Fang
- School of Life Sciences, Institutes of Physical Science and Information Technology, Anhui University Hefei 230601 P. R. China
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10
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Keller M, Petrov D, Gloger A, Dietschi B, Jobin K, Gradinger T, Martinelli A, Plais L, Onda Y, Neri D, Scheuermann J. Highly pure DNA-encoded chemical libraries by dual-linker solid-phase synthesis. Science 2024; 384:1259-1265. [PMID: 38870307 DOI: 10.1126/science.adn3412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
The first drugs discovered using DNA-encoded chemical library (DEL) screens have entered late-stage clinical development. However, DEL technology as a whole still suffers from poor chemical purity resulting in suboptimal performance. In this work, we report a technique to overcome this issue through self-purifying release of the DEL after magnetic bead-based synthesis. Both the first and last building blocks of each assembled library member were linked to the beads by tethers that could be cleaved by mutually orthogonal chemistry. Sequential cleavage of the first and last tether, with washing in between, ensured that the final library comprises only the fully complete compounds. The outstanding purity attained by this approach enables a direct correlation of chemical display and encoding, allows for an increased chemical reaction scope, and facilitates the use of more diversity elements while achieving greatly improved signal-to-noise ratios in selections.
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Affiliation(s)
- Michelle Keller
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dimitar Petrov
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Gloger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Bastien Dietschi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Kilian Jobin
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Timon Gradinger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Yuichi Onda
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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11
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Nishihara T, Motohashi Y, Mio R, Sugawara M, Tanabe K. A detection system using sensing motif-tethered oligodeoxynucleotides for multiplex biomolecular analysis. Chem Commun (Camb) 2024; 60:6059-6062. [PMID: 38780054 DOI: 10.1039/d4cc01470g] [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: 05/25/2024]
Abstract
We developed a system to detect multiple target biomolecules through sensing motif-tethered oligodeoxynucleotides. DNA-based molecular probes gave the primary amine motif upon reaction with the target biomolecules, glutathione (GSH) and H2O2. After labelling with biotin, the product DNAs were selectively collected to be quantified by qPCR.
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Affiliation(s)
- Tatsuya Nishihara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Yuto Motohashi
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Reoto Mio
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Masato Sugawara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
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12
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Chheda PR, Simmons N, Shi Z. Hydrophobic Surfactant-DNA Complex (Surf-DNA) Enables DNA-Encoded-Library-Compatible Decarboxylative Arylation under Anhydrous Conditions. Org Lett 2024; 26:4365-4370. [PMID: 38743933 DOI: 10.1021/acs.orglett.4c01398] [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: 05/16/2024]
Abstract
DNA-encoded libraries (DELs) are a key technology for identifying small-molecule hits in both the pharmaceutical industry and academia, but their chemical diversity is largely limited to water-compatible reactions to aid in the solubility and integrity of encoding DNA tags. To broaden the DEL chemical space, we present a workflow utilizing DNA-cationic surfactant complexation that enables dissolution and reactions on-DNA in anhydrous organic solvents. We demonstrate its utility by developing DEL-compatible photoredox decarboxylative C(sp2)-C(sp3) coupling under water-free conditions. The workflow is optimized for the 96-well format necessary for large-scale DEL productions, and it enables screening and optimization of DEL-compatible reactions in organic solvents.
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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
| | - Zhicai Shi
- Discovery Chemistry, Janssen Research & Development, LLC, Spring House, Pennsylvania 19477, United States
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13
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Wang Y, Liu N. Silica Nanowires-Filled Glass Microporous Sensor for the Ultrasensitive Detection of Deoxyribonucleic Acid. ACS Sens 2024; 9:2050-2056. [PMID: 38632929 DOI: 10.1021/acssensors.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
DNA carries genetic information and can serve as an important biomarker for the early diagnosis and assessment of the disease prognosis. Here, we propose a bottom-up assembly method for a silica nanowire-filled glass microporous (SiNWs@GMP) sensor and develop a universal sensing platform for the ultrasensitive and specific detection of DNA. The three-dimensional network structure formed by SiNWs provides them with highly abundant and accessible binding sites, allowing for the immobilization of a large amount of capture probe DNA, thereby enabling more target DNA to hybridize with the capture probe DNA to improve detection performance. Therefore, the SiNWs@GMP sensor achieves ultrasensitive detection of target DNA. In the detection range of 1 aM to 100 fM, there is a good linear relationship between the decrease rate of current signal and the concentration of target DNA, and the detection limit is as low as 1 aM. The developed SiNWs@GMP sensor can distinguish target DNA sequences that are 1-, 3-, and 5-mismatched, and specifically recognize target DNA from complex mixed solution. Furthermore, based on this excellent selectivity and specificity, we validate the universality of this sensing strategy by detecting DNA (H1N1 and H5N1) sequences associated with the avian influenza virus. By replacing the types of nucleic acid aptamers, it is expected to achieve a wide range and low detection limit sensitive detection of various biological molecules. The results indicate that the developed universal sensing platform has ultrahigh sensitivity, excellent selectivity, stability, and acceptable reproducibility, demonstrating its potential application in DNA bioanalysis.
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Affiliation(s)
- Shiwei Xu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Guofeng Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yueyue Feng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Juanjuan Zheng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Liying Huang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yajun Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Nannan Liu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
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14
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Zeng H, Li Y, Wu R, Liu D, Zhang Y, Xu S, Niu D. Carbohydrate-DNA Conjugation Enabled by Glycosyl Radicals Generated from Glycosyl Sulfinates. Org Lett 2024; 26:2686-2690. [PMID: 37125782 DOI: 10.1021/acs.orglett.3c00833] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Herein, we report a method that enables the synthesis of carbohydrate-DNA conjugates by radical addition. Key to the success is the use of readily available, bench-stable, and unprotected glycosyl sulfinates as precursors to glycosyl radicals. The redox neutral reaction proceeds under mild and simple conditions and tolerates a broad substrate scope. A small library of carbohydrate-DNA conjugates was prepared.
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Affiliation(s)
- Hongxin Zeng
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Yanjing Li
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Rongfeng Wu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Daqi Liu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Yang Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Shiyang Xu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and School of Chemical Engineering, Sichuan University, Chengdu 610041, China
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15
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Wang T, Chen X, Yang G, Shi X. Selection of Leptin Surrogates by a General Phenotypic Screening Method for Receptor Agonists. Biomolecules 2024; 14:457. [PMID: 38672473 PMCID: PMC11047824 DOI: 10.3390/biom14040457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
There is a high demand for agonist biomolecules such as cytokine surrogates in both biological and medicinal research fields. These are typically sourced through natural ligand engineering or affinity-based screening, followed by individual functional validation. However, efficient screening methods for identifying rare hits within immense libraries are very limited. In this research article, we introduce a phenotypic screening method utilizing biological receptor activation-dependent cell survival (BRADS). This method offers a high-throughput, low-background, and cost-effective approach that can be implemented in virtually any biochemical laboratory setting. As a proof-of-concept, we successfully identified a surrogate for human leptin following a two-week cell culture process, without the need for specialized high-throughput equipment or reagents. This surrogate effectively emulates the activity of native human leptin in cell validation assays. Our findings not only underscore the effectiveness of BRADS but also suggest its potential applicability to a broad range of biological receptors, including Notch and GPCRs.
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Affiliation(s)
- Tao Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (T.W.); (X.C.); (G.Y.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xixi Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (T.W.); (X.C.); (G.Y.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (T.W.); (X.C.); (G.Y.)
| | - Xiaojie Shi
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (T.W.); (X.C.); (G.Y.)
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16
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Hou W, Zhang Y, Huang F, Chen W, Gu Y, Wang Y, Pang J, Dong H, Pan K, Zhang S, Ma P, Xu H. Bioinspired Selenium-Nitrogen Exchange (SeNEx) Click Chemistry Suitable for Nanomole-Scale Medicinal Chemistry and Bioconjugation. Angew Chem Int Ed Engl 2024; 63:e202318534. [PMID: 38343199 DOI: 10.1002/anie.202318534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Click chemistry is a powerful molecular assembly strategy for rapid functional discovery. The development of click reactions with new connecting linkage is of great importance for expanding the click chemistry toolbox. We report the first selenium-nitrogen exchange (SeNEx) click reaction between benzoselenazolones and terminal alkynes (Se-N to Se-C), which is inspired by the biochemical SeNEx between Ebselen and cysteine (Cys) residue (Se-N to Se-S). The formed selenoalkyne connection is readily elaborated, thus endowing this chemistry with multidimensional molecular diversity. Besides, this reaction is modular, predictable, and high-yielding, features fast kinetics (k2≥14.43 M-1 s-1), excellent functional group compatibility, and works well at miniaturization (nanomole-scale), opening up many interesting opportunities for organo-Se synthesis and bioconjugation, as exemplified by sequential click chemistry (coupled with ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC) and sulfur-fluoride exchange (SuFEx)), selenomacrocycle synthesis, nanomole-scale synthesis of Se-containing natural product library and DNA-encoded library (DEL), late-stage peptide modification and ligation, and multiple functionalization of proteins. These results indicated that SeNEx is a useful strategy for new click chemistry developments, and the established SeNEx chemistry will serve as a transformative platform in multidisciplinary fields such as synthetic chemistry, material science, chemical biology, medical chemistry, and drug discovery.
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Affiliation(s)
- Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Fuchao Huang
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Jiacheng Pang
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Kangyin Pan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, 201210, Shanghai, China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
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17
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Zhou Y, Shen W, Gao Y, Peng J, Li Q, Wei X, Liu S, Lam FS, Mayol-Llinàs J, Zhao G, Li G, Li Y, Sun H, Cao Y, Li X. Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries. Nat Chem 2024; 16:543-555. [PMID: 38326646 DOI: 10.1038/s41557-024-01442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.
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Grants
- AoE/P-705/16, 17301118, 17111319, 17303220, 17300321, 17318322, C7005-20G, C7016-22G, and 2122-7S04 Research Grants Council, University Grants Committee (RGC, UGC)
- 21877093, 22222702, and 91953119 National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
- Health@InnoHK Innovation and Technology Commission (ITF)
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Gao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qingrong Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shihao Liu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Joan Mayol-Llinàs
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Hongzhe Sun
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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18
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Kodadek T. Catalytic Protein Inhibitors. Angew Chem Int Ed Engl 2024; 63:e202316726. [PMID: 38064411 DOI: 10.1002/anie.202316726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Indexed: 01/13/2024]
Abstract
Many of the highest priority targets in a wide range of disease states are difficult-to-drug proteins. The development of reversible small molecule inhibitors for the active sites of these proteins with sufficient affinity and residence time on-target is an enormous challenge. This has engendered interest in strategies to increase the potency of a given protein inhibitor by routes other than further improvement in gross affinity. Amongst these, the development of catalytic protein inhibitors has garnered the most attention and investment, particularly with respect to protein degraders, which catalyze the destruction of the target protein. This article discusses the genesis of the burgeoning field of catalytic inhibitors, the current state of the art, and exciting future directions.
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Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, FL 33458, USA
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19
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Chen B, Sultan MM, Karaletsos T. Compositional Deep Probabilistic Models of DNA-Encoded Libraries. J Chem Inf Model 2024; 64:1123-1133. [PMID: 38335055 DOI: 10.1021/acs.jcim.3c01699] [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: 02/12/2024]
Abstract
DNA-encoded library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly efficient screening experiments. These selection experiments, involving multiple stages of washing, elution, and identification of potent binders via unique DNA barcodes, often generate complex data. This complexity can potentially mask the underlying signals, necessitating the application of computational tools, such as machine learning, to uncover valuable insights. We introduce a compositional deep probabilistic model of DEL data, DEL-Compose, which decomposes molecular representations into their monosynthon, disynthon, and trisynthon building blocks and capitalizes on the inherent hierarchical structure of these molecules by modeling latent reactions between embedded synthons. Additionally, we investigate methods to improve the observation models for DEL count data, such as integrating covariate factors to more effectively account for data noise. Across two popular public benchmark data sets (CA-IX and HRP), our model demonstrates strong performance compared to count baselines, enriches the correct pharmacophores, and offers valuable insights via its intrinsic interpretable structure, thereby providing a robust tool for the analysis of DEL data.
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Affiliation(s)
- Benson Chen
- Insitro, South San Francisco, California 94080, United States
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20
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Plais L, Trachsel L, Scheuermann J. Asymmetry of Dual-Display DNA-Encoded Chemical Libraries. Bioconjug Chem 2024; 35:147-153. [PMID: 38266192 DOI: 10.1021/acs.bioconjchem.3c00559] [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: 01/26/2024]
Abstract
While dual-display DNA-encoded chemical libraries (DELs) are increasingly employed for ligand discovery, some of their fundamental properties have not yet been studied in-depth. Aided with fluorescence polarization experiments, we demonstrate that dual-display DELs are intrinsically asymmetrical entities, and we deduce practical guidelines to perform better-informed on-DNA hit validation from these libraries.
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Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Louis Trachsel
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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21
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Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
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Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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22
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Zhang S, Zhang H, Liu X, Qi P, Tan T, Wang S, Gao H, Xu H, Zhou Z, Yi W. Mask and Release Strategy-Enabled Diversity-Oriented Synthesis for DNA-Encoded Library. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307049. [PMID: 38044314 PMCID: PMC10853742 DOI: 10.1002/advs.202307049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Indexed: 12/05/2023]
Abstract
An ideal DNA-encoded library (DEL) selection requires the library to consist of diverse core skeletons and cover chemical space as much as possible. However, the lack of efficient on-DNA synthetic approaches toward core skeletons has greatly restricted the diversity of DEL. To mitigate this issue, this work disclosed a "Mask & Release" strategy to streamline the challenging on-DNA core skeleton synthesis. N-phenoxyacetamide is used as a masked phenol and versatile directing group to mediate diversified DNA-compatible C-H functionalization, introducing the 1st-dimensional diversity at a defined site, and simultaneously releasing the phenol functionality, which can facilitate the introduction of the 2nd diversity. This work not only provides a set of efficient syntheses toward DNA-conjugated drug-like core skeletons such as ortho-alkenyl/sulfiliminyl/cyclopropyl phenol, benzofuran, dihydrobenzofuran but also provides a paradigm for on-DNA core skeleton synthetic method development.
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Affiliation(s)
- Silin Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Haiman Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Xiawen Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Ping Qi
- Guangzhou Institute for Food InspectionGuangzhou511400China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Shengdong Wang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Hui Gao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical PharmacologyThe NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou511436China
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23
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Sharique M, Matsuo B, Granados A, Kim S, Arshad M, Oh H, Wu VE, Huang M, Csakai A, Marcaurelle LA, Molander GA. On-DNA hydroalkylation of N-vinyl heterocycles via photoinduced EDA-complex activation. Chem Sci 2023; 14:14193-14199. [PMID: 38098729 PMCID: PMC10717525 DOI: 10.1039/d3sc03731b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/22/2023] [Indexed: 12/17/2023] Open
Abstract
The emergence of DNA-encoded library (DEL) technology has provided a considerable advantage to the pharmaceutical industry in the pursuit of discovering novel therapeutic candidates for their drug development initiatives. This combinatorial technique not only offers a more economical, spatially efficient, and time-saving alternative to the existing ligand discovery methods, but also enables the exploration of additional chemical space by utilizing novel DNA-compatible synthetic transformations to leverage multifunctional building blocks from readily available substructures. In this report, a decarboxylative-based hydroalkylation of DNA-conjugated N-vinyl heterocycles enabled by single-electron transfer (SET) and subsequent hydrogen atom transfer through electron-donor/electron-acceptor (EDA) complex activation is detailed. The simplicity and robustness of this method permits inclusion of a broad array of alkyl radical precursors and DNA-tethered nitrogenous heterocyles to generate medicinally relevant substituted heterocycles with pendant functional groups. Moreover, a successful telescoped route provides the opportunity to access a broad range of intricate structural scaffolds by employing basic carboxylic acid feedstocks.
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Affiliation(s)
- Mohammed Sharique
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Bianca Matsuo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Albert Granados
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Saegun Kim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Mahwish Arshad
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Hyunjung Oh
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Victoria E Wu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Minxue Huang
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Adam Csakai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Lisa A Marcaurelle
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
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24
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Jiang L, Liu S, Jia X, Gong Q, Wen X, Lu W, Yang J, Wu X, Wang X, Suo Y, Li Y, Uesugi M, Qu ZB, Tan M, Lu X, Zhou L. ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries. J Am Chem Soc 2023; 145:25283-25292. [PMID: 37857329 DOI: 10.1021/jacs.3c08852] [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: 10/21/2023]
Abstract
DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.
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Affiliation(s)
- Lulu Jiang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xinglong Jia
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qinting Gong
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jintong Yang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yilin Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Motonari Uesugi
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Zhi-Bei Qu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
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25
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Wang H, Zhao G, Zhang T, Li Y, Zhang G, Li Y. Comparative Study of DNA Barcode Integrity Evaluation Approaches in the Early-Stage Development of DNA-Compatible Chemical Transformation. ACS Pharmacol Transl Sci 2023; 6:1724-1733. [PMID: 37974618 PMCID: PMC10644510 DOI: 10.1021/acsptsci.3c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 11/19/2023]
Abstract
DNA-encoded libraries (DEL) have emerged as an important drug discovery technical platform for target-based compound library selection. The success rate of DEL depends on both the chemical diversity of combinatorial libraries and the accuracy of DNA barcoding. Therefore, it is critical that the chemistry applied to library construction should efficiently transform on a wide range of substrates while preserving the integrity of DNA tags. Although several analytical methods have been developed to measure DNA damage caused by DEL chemical reactions, efficient and cost-effective evaluation criteria for DNA damage detection are still demanding. Herein, we set standards for evaluating the DNA compatibility of chemistry development at the laboratory level. Based on four typical DNA damage models of three different DEL formats, we evaluated the detection capabilities of four analytical methods, including ultraperformance liquid chromatography (UPLC-MS), electrophoresis, quantitative polymerase chain reaction (qPCR), and Sanger sequencing. This work systematically revealed the scope and capability of different analytical methods in assessing DNA damages caused by chemical transformation. Based on the results, we recommended UPLC-MS and qPCR as efficient methods for DNA barcode integrity analysis in the early-stage development of DNA-compatible chemistry. Meanwhile, we identified that Sanger sequencing was unreliable to assess DNA damage in this application.
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Affiliation(s)
- Huicong Wang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Tianyang Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, 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
| | - Gong Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, 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, 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
- Beijing
National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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26
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Puglioli S, Oehler S, Prati L, Scheuermann J, Bassi G, Cazzamalli S, Neri D, Favalli N. Impact of library input on the hit discovery rate in DNA-encoded chemical library selections. Chem Sci 2023; 14:12026-12033. [PMID: 37969600 PMCID: PMC10631129 DOI: 10.1039/d3sc03688j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/29/2023] [Indexed: 11/17/2023] Open
Abstract
DNA-encoded chemical libraries (DELs) are powerful drug discovery tools, enabling the parallel screening of millions of DNA-barcoded compounds. We investigated how the DEL input affects the hit discovery rate in DEL screenings. Evaluation of selection fingerprints revealed that the use of approximately 105 copies of each library member is required for the confident identification of nanomolar hits, using generally applicable methodologies.
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Affiliation(s)
- Sara Puglioli
- Philochem AG, R&D Department 8112 Otelfingen Switzerland
| | | | - Luca Prati
- Philochem AG, R&D Department 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich) Zürich Switzerland
| | - Gabriele Bassi
- Philochem AG, R&D Department 8112 Otelfingen Switzerland
| | | | - Dario Neri
- Philochem AG, R&D Department 8112 Otelfingen Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich) Zürich Switzerland
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27
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Lessing A, Petrov D, Scheuermann J. Advancing small-molecule drug discovery by encoded dual-display technologies. Trends Pharmacol Sci 2023; 44:817-831. [PMID: 37739829 DOI: 10.1016/j.tips.2023.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023]
Abstract
DNA-encoded chemical library technology (DECL or DEL) has become an important pillar for small-molecule drug discovery. The technology rapidly identifies small-molecule hits for relevant target proteins at low cost and with a high success rate, including ligands for targeted protein degradation (TPD). More recently, the setup of DNA- or peptide nucleic acid (PNA)-encoded chemical libraries based on the simultaneous display of ligand pairs, termed dual-display, allows for more sophisticated applications which will be reviewed herein. Both stable and dynamic dual-display DEL technologies enable innovative affinity-based selection modalities, even on and in cells. Novel methods for a seamless conversion between single- and double-stranded library formats allow for even more versatility. We present the first candidates emerging from dual-display technologies and discuss the future potential of dual-display for drug discovery.
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Affiliation(s)
- Alice Lessing
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Dimitar Petrov
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Jörg Scheuermann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland.
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28
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Stuart DD, Guzman-Perez A, Brooijmans N, Jackson EL, Kryukov GV, Friedman AA, Hoos A. Precision Oncology Comes of Age: Designing Best-in-Class Small Molecules by Integrating Two Decades of Advances in Chemistry, Target Biology, and Data Science. Cancer Discov 2023; 13:2131-2149. [PMID: 37712571 PMCID: PMC10551669 DOI: 10.1158/2159-8290.cd-23-0280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Small-molecule drugs have enabled the practice of precision oncology for genetically defined patient populations since the first approval of imatinib in 2001. Scientific and technology advances over this 20-year period have driven the evolution of cancer biology, medicinal chemistry, and data science. Collectively, these advances provide tools to more consistently design best-in-class small-molecule drugs against known, previously undruggable, and novel cancer targets. The integration of these tools and their customization in the hands of skilled drug hunters will be necessary to enable the discovery of transformational therapies for patients across a wider spectrum of cancers. SIGNIFICANCE Target-centric small-molecule drug discovery necessitates the consideration of multiple approaches to identify chemical matter that can be optimized into drug candidates. To do this successfully and consistently, drug hunters require a comprehensive toolbox to avoid following the "law of instrument" or Maslow's hammer concept where only one tool is applied regardless of the requirements of the task. Combining our ever-increasing understanding of cancer and cancer targets with the technological advances in drug discovery described below will accelerate the next generation of small-molecule drugs in oncology.
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Affiliation(s)
| | | | | | | | | | | | - Axel Hoos
- Scorpion Therapeutics, Boston, Massachusetts
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29
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Oehler S, Lucaroni L, Migliorini F, Elsayed A, Prati L, Puglioli S, Matasci M, Schira K, Scheuermann J, Yudin D, Jia M, Ban N, Bushnell D, Kornberg R, Cazzamalli S, Neri D, Favalli N, Bassi G. A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition. Nat Chem 2023; 15:1431-1443. [PMID: 37400597 DOI: 10.1038/s41557-023-01257-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.
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Affiliation(s)
| | | | | | - Abdullah Elsayed
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Kristina Schira
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Denis Yudin
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Min Jia
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | - Roger Kornberg
- NeoTX Therapeutics LTD, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | - Dario Neri
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Philogen SPA, Siena, Italy
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30
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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.
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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
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31
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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.
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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.
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32
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Merrifield JL, Pimentel EB, Peters-Clarke TM, Nesbitt DJ, Coon JJ, Martell JD. DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries. Bioconjug Chem 2023; 34:1380-1386. [PMID: 37540561 PMCID: PMC10831869 DOI: 10.1021/acs.bioconjchem.3c00254] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Aldehydes are important synthons for DNA-encoded library (DEL) construction, but the development of a DNA-compatible method for the oxidation of alcohols to aldehydes remains a significant challenge in the field of DEL chemistry. We report that a copper/TEMPO catalyst system enables the solution-phase DNA-compatible oxidation of DNA-linked primary activated alcohols to aldehydes. The semiaqueous, room-temperature reaction conditions afford oxidation of benzylic, heterobenzylic, and allylic alcohols in high yield, with DNA compatibility verified by mass spectrometry, qPCR, Sanger sequencing, and ligation assays. Subsequent transformations of the resulting aldehydes demonstrate the potential of this method for robust library diversification.
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Affiliation(s)
- Justice L. Merrifield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Daniel J. Nesbitt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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33
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An Y, Glavatskikh M, Lim J, Wang X, Norris-Drouin J, Hardy PB, Leisner TM, Pearce KH, Kireev D. Machine Learning-driven Fragment-based Discovery of CIB1-directed Anti-Tumor Agents by FRASE-bot. RESEARCH SQUARE 2023:rs.3.rs-3197490. [PMID: 37645935 PMCID: PMC10462244 DOI: 10.21203/rs.3.rs-3197490/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Chemical probes are an indispensable tool for translating biological discoveries into new therapies, though are increasingly difficult to identify. Novel therapeutic targets are often hard-to-drug proteins, such as messengers or transcription factors. Computational strategies arise as a promising solution to expedite drug discovery for unconventional therapeutic targets. FRASE-bot exploits big data and machine learning (ML) to distill 3D information relevant to the target protein from thousands of protein-ligand complexes to seed it with ligand fragments. The seeded fragments can then inform either (i) de novo design of 3D ligand structures or (ii) ultra-large-scale virtual screening of commercially available compounds. Here, FRASE-bot was applied to identify ligands for Calcium and Integrin Binding protein 1 (CIB1), a promising but ligand-orphan drug target implicated in triple negative breast cancer. The signaling function of CIB1 relies on protein-protein interactions and its structure does not feature any natural ligand-binding pocket. FRASE-based virtual screening identified the first small-molecule CIB1 ligand (with binding confirmed in a TR-FRET assay) showing specific cell-killing activity in CIB1-dependent cancer cells, but not in CIB1-depleted cells.
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Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Jiwoong Lim
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Xiaowen Wang
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - P. Brian Hardy
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Tina M. Leisner
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27513
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211
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34
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Pan K, Yao Y, Zhang Y, Gu Y, Wang Y, Ma P, Hou W, Yang G, Zhang S, Xu H. Enolate-Azide [3 + 2]-Cycloaddition Reaction Suitable for DNA-Encoded Library Synthesis. Bioconjug Chem 2023; 34:1459-1466. [PMID: 37443440 DOI: 10.1021/acs.bioconjchem.3c00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The DNA-encoded chemical library (DEL) is a powerful hit selection technique in either basic science or innovative drug discovery. With the aim to circumvent the issue concerning DNA barcode damage in a conventional on-DNA copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), we have successfully developed the first DNA-compatible enolate-azide [3 + 2] cycloaddition reaction. The merits of this DEL chemistry include metal-free reaction and high DNA fidelity, high conversions and easy operation, broad substrate scope, and ready access to the highly substituted 1,4,5-trisubstituted triazoles. Thus, it will not only further enrich the DEL chemistry toolbox but also will have great potential in practical DEL synthesis.
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Affiliation(s)
- Kangyin Pan
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Ying Yao
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
| | - Wei Hou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
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35
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:4930. [PMID: 37582753 PMCID: PMC10427684 DOI: 10.1038/s41467-023-40575-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
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Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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36
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Salvini CLA, Darlot B, Davison J, Martin MP, Tudhope SJ, Turberville S, Kawamura A, Noble MEM, Wedge SR, Crawford JJ, Waring MJ. Fragment expansion with NUDELs - poised DNA-encoded libraries. Chem Sci 2023; 14:8288-8294. [PMID: 37564419 PMCID: PMC10411621 DOI: 10.1039/d3sc01171b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes and is a process that takes many years. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, the evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming and complex. Here, we introduce a paradigm for fragment hit optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL, a partially constructed library that retains a reactive handle, allows the coupling of any active fragment for a specific target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with 51 nM affinity in a single step, representing an increase in potency of several orders of magnitude from an original fragment. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.
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Affiliation(s)
- Catherine L A Salvini
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Benoit Darlot
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jack Davison
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Susan J Tudhope
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Shannon Turberville
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Akane Kawamura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - James J Crawford
- Genentech Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
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37
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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.
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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
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38
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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.
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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
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39
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Thompson AA, Harbut MB, Kung PP, Karpowich NK, Branson JD, Grant JC, Hagan D, Pascual HA, Bai G, Zavareh RB, Coate HR, Collins BC, Côte M, Gelin CF, Damm-Ganamet KL, Gholami H, Huff AR, Limon L, Lumb KJ, Mak PA, Nakafuku KM, Price EV, Shih AY, Tootoonchi M, Vellore NA, Wang J, Wei N, Ziff J, Berger SB, Edwards JP, Gardet A, Sun S, Towne JE, Venable JD, Shi Z, Venkatesan H, Rives ML, Sharma S, Shireman BT, Allen SJ. Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc Natl Acad Sci U S A 2023; 120:e2216342120. [PMID: 37098070 PMCID: PMC10160951 DOI: 10.1073/pnas.2216342120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ+, and CD8+ T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein-protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure-activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.
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Affiliation(s)
- Aaron A. Thompson
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Michael B. Harbut
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Pei-Pei Kung
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Nathan K. Karpowich
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Jeffrey D. Branson
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Joanna C. Grant
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Deborah Hagan
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Heather A. Pascual
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Guoyun Bai
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | | | - Heather R. Coate
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Bernard C. Collins
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Marjorie Côte
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Christine F. Gelin
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | | | - Hadi Gholami
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Adam R. Huff
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Luis Limon
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Kevin J. Lumb
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Puiying A. Mak
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Kohki M. Nakafuku
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Edmund V. Price
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Amy Y. Shih
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Mandana Tootoonchi
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Nadeem A. Vellore
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Jocelyn Wang
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Na Wei
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Jeannie Ziff
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Scott B. Berger
- Discovery Immunology, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - James P. Edwards
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Agnès Gardet
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Siquan Sun
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | - Jennifer E. Towne
- Discovery Immunology, Janssen Research & Development, San Diego, CA92121
| | | | - Zhicai Shi
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | | | - Marie-Laure Rives
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Sujata Sharma
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
| | - Brock T. Shireman
- Therapeutics Discovery, Janssen Research & Development, San Diego, CA92121
| | - Samantha J. Allen
- Therapeutics Discovery, Janssen Research & Development, Lower Gwynedd Township, PA19002
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40
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Sadybekov AV, Katritch V. Computational approaches streamlining drug discovery. Nature 2023; 616:673-685. [PMID: 37100941 DOI: 10.1038/s41586-023-05905-z] [Citation(s) in RCA: 184] [Impact Index Per Article: 184.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 04/28/2023]
Abstract
Computer-aided drug discovery has been around for decades, although the past few years have seen a tectonic shift towards embracing computational technologies in both academia and pharma. This shift is largely defined by the flood of data on ligand properties and binding to therapeutic targets and their 3D structures, abundant computing capacities and the advent of on-demand virtual libraries of drug-like small molecules in their billions. Taking full advantage of these resources requires fast computational methods for effective ligand screening. This includes structure-based virtual screening of gigascale chemical spaces, further facilitated by fast iterative screening approaches. Highly synergistic are developments in deep learning predictions of ligand properties and target activities in lieu of receptor structure. Here we review recent advances in ligand discovery technologies, their potential for reshaping the whole process of drug discovery and development, as well as the challenges they encounter. We also discuss how the rapid identification of highly diverse, potent, target-selective and drug-like ligands to protein targets can democratize the drug discovery process, presenting new opportunities for the cost-effective development of safer and more effective small-molecule treatments.
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Affiliation(s)
- Anastasiia V Sadybekov
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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41
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Rui H, Ashton KS, Min J, Wang C, Potts PR. Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem Biol 2023; 4:192-215. [PMID: 36908699 PMCID: PMC9994104 DOI: 10.1039/d2cb00207h] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
Molecular glues are a class of small molecules that stabilize the interactions between proteins. Naturally occurring molecular glues are present in many areas of biology where they serve as central regulators of signaling pathways. Importantly, several clinical compounds act as molecular glue degraders that stabilize interactions between E3 ubiquitin ligases and target proteins, leading to their degradation. Molecular glues hold promise as a new generation of therapeutic agents, including those molecular glue degraders that can redirect the protein degradation machinery in a precise way. However, rational discovery of molecular glues is difficult in part due to the lack of understanding of the protein-protein interactions they stabilize. In this review, we summarize the structures of known molecular glue-induced ternary complexes and the interface properties. Detailed analysis shows different mechanisms of ternary structure formation. Additionally, we also review computational approaches for predicting protein-protein interfaces and highlight the promises and challenges. This information will ultimately help inform future approaches for rational molecular glue discovery.
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Affiliation(s)
- Huan Rui
- Center for Research Acceleration by Digital Innovation, Amgen Research Thousand Oaks CA 91320 USA
| | - Kate S Ashton
- Medicinal Chemistry, Amgen Research Thousand Oaks CA 91320 USA
| | - Jaeki Min
- Induced Proximity Platform, Amgen Research Thousand Oaks CA 91320 USA
| | - Connie Wang
- Digital, Technology & Innovation, Amgen Thousand Oaks CA 91320 USA
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42
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Rössler SL, Grob NM, Buchwald SL, Pentelute BL. Abiotic peptides as carriers of information for the encoding of small-molecule library synthesis. Science 2023; 379:939-945. [PMID: 36862767 PMCID: PMC10064805 DOI: 10.1126/science.adf1354] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/24/2023] [Indexed: 03/04/2023]
Abstract
Encoding small-molecule information in DNA has been leveraged to accelerate the discovery of ligands for therapeutic targets such as proteins. However, oligonucleotide-based encoding is hampered by inherent limitations of information stability and density. In this study, we establish abiotic peptides for next-generation information storage and apply them for the encoding of diverse small-molecule synthesis. The chemical stability of the peptide-based tag allows the use of palladium-mediated reactions to efficiently synthesize peptide-encoded libraries (PELs) with broad chemical diversity and high purity. We demonstrate the successful de novo discovery of small-molecule protein ligands from PELs by affinity selection against carbonic anhydrase IX and the oncogenic protein targets BRD4(1) and MDM2. Collectively, this work establishes abiotic peptides as carriers of information for the encoding of small-molecule synthesis, leveraged herein for the discovery of protein ligands.
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Affiliation(s)
- Simon L. Rössler
- Massachusetts Institute of Technology, Department of Chemistry; Cambridge, MA 02139, United States of America
| | - Nathalie M. Grob
- Massachusetts Institute of Technology, Department of Chemistry; Cambridge, MA 02139, United States of America
| | - Stephen L. Buchwald
- Massachusetts Institute of Technology, Department of Chemistry; Cambridge, MA 02139, United States of America
| | - Bradley L. Pentelute
- Massachusetts Institute of Technology, Department of Chemistry; Cambridge, MA 02139, United States of America
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02139, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, United States of America
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, United States of America
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43
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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44
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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45
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Chen Q, Liu C, Wang W, Meng X, Cheng X, Li X, Cai L, Luo L, He X, Qu H, Luo J, Wei H, Gao S, Liu G, Wan J, Israel DI, Li J, Dou D. Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach. ACS Chem Biol 2023; 18:25-33. [PMID: 36606710 PMCID: PMC9872815 DOI: 10.1021/acschembio.2c00797] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023]
Abstract
The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.
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Affiliation(s)
- Qiuxia Chen
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Chuan Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Wei Wang
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xiaoyun Meng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xuemin Cheng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xianyang Li
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Longying Cai
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Linfu Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xu He
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Huan Qu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jing Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Hong Wei
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Sen Gao
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Guansai Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jinqiao Wan
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | | | - Jin Li
- HitGen
Inc., Chengdu, Sichuan 610200, China
| | - Dengfeng Dou
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
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46
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Chheda PR, Simmons N, Schuman DP, Shi Z. Photoredox-Mediated Deoxygenative Alkylation of DNA-Tagged Alkenes with Activated Alcohols. Org Lett 2022; 24:9514-9519. [PMID: 36541781 DOI: 10.1021/acs.orglett.2c03994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA-encoded library (DEL) screens have become a key technology to find small molecule binders to biological targets for drug discovery applications. The development of new DNA-compatible chemistries to expand the accessible DEL chemical space is imperative to enhance screen success across broad target classes and modalities. Additionally, reactions that use commonly available building blocks as well as those that enable the fsp3 of library members to be increased would have high impact for accessing diverse drug-like structures. Herein, we report a DNA-compatible Giese-type addition of nonstabilized C-centered radicals generated by the deoxygenation of preactivated alcohols into on-DNA olefins. Although alcohols have been historically underused as a building block class within DEL synthesis, their activation to a xanthate enables Csp3-Csp3 coupling to furnish sp3-rich products. This reaction is compatible with multiple classes of functional groups, does not damage the DNA tag, and is suitable for use in DEL productions.
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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
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47
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Wang Y, Liu L, Le Z, Tay A. Analysis of Nanomedicine Efficacy for Osteoarthritis. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yuwen Wang
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
| | - Ling Liu
- Institute of Health Innovation and Technology National University of Singapore Singapore 117599 Singapore
| | - Zhicheng Le
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
| | - Andy Tay
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
- Institute of Health Innovation and Technology National University of Singapore Singapore 117599 Singapore
- Tissue Engineering Programme National University of Singapore Singapore 117510 Singapore
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48
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Puglioli S, Schmidt E, Pellegrino C, Prati L, Oehler S, De Luca R, Galbiati A, Comacchio C, Nadal L, Scheuermann J, Manz MG, Neri D, Cazzamalli S, Bassi G, Favalli N. Selective tumor targeting enabled by picomolar fibroblast activation protein inhibitors isolated from a DNA-encoded affinity maturation library. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Highly sensitive molecularly imprinted polymer-based electrochemical sensor for voltammetric determination of Adenine and Guanine in real samples using gold screen-printed electrode. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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50
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Zhang Y, Xia S, Shi WX, Lin B, Su XC, Lu W, Wu X, Wang X, Lu X, Yan M, Zhang XJ. Radical C–H Sulfonation of Arenes: Its Applications on Bioactive and DNA-Encoded Molecules. Org Lett 2022; 24:7961-7966. [DOI: 10.1021/acs.orglett.2c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
| | - Shengdi Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wen-xia Shi
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
| | - Bizhen Lin
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
| | - Xiao-can Su
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Yan
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
| | - Xue-jing Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University; Guangzhou, 510006, China
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