1
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Wang N, Chai T, Wang XR, Zheng YD, Sang CY, Yang JL. Pin1: Advances in pancreatic cancer therapeutic potential and inhibitors research. Bioorg Chem 2024; 153:107869. [PMID: 39418844 DOI: 10.1016/j.bioorg.2024.107869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/18/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024]
Abstract
The peptidyl-prolyl cis/trans isomerase NIMA-interaction 1 (Pin1) catalyzes the transition of the proline ring from the cis to trans conformation, resulting in conformational and functional changes in proteins that are regulated by proline-guided serine/threonine phosphorylation. In recent years, Pin1 has emerged as a novel molecular target for the diagnosis and treatment of various malignant tumors. Notably, it has been found that Pin1 is highly expressed in pancreatic cancer. This article focuses on the mechanisms by which Pin1 orchestrates multiple oncogenic functions in the development of pancreatic cancer. By exploring the intricate interactions between Pin1 and the pancreatic tumor microenvironment, we provide an overview of Pin1's role in modifying glycolytic metabolism, redox balance, and the hypoxic microenvironment of pancreatic cancer. Furthermore, we summarize the potential anticancer effects of Pin1 inhibitors, aiming to elucidate Pin1's promise as a potential anticancer agent, particularly in the context of pancreatic cancer.
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Affiliation(s)
- Nan Wang
- College of Pharmacy, Gansu University of Chinese Medicine; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Tian Chai
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Xing-Rong Wang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Yi-Dan Zheng
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Chun-Yan Sang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Jun-Li Yang
- College of Pharmacy, Gansu University of Chinese Medicine; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou 730000, China.
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2
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Liu C, Chen Z, Chen T, Song H, Shen J, Yuan X, Xia S, Liu Q, Chen Q, Tian Q, Meng X, Han Z, Dong X, Yang Y, Cai L, Cheng X, Jia Y, Liu G, Li J, Ge J, Dou D. Re-Evaluating PIN1 as a Therapeutic Target in Oncology Using Neutral Inhibitors and PROTACs. J Med Chem 2024; 67:15780-15795. [PMID: 39229909 DOI: 10.1021/acs.jmedchem.4c01412] [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: 09/05/2024]
Abstract
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1) has emerged as a promising therapeutic target for cancer treatment. However, the current PIN1 inhibitors have shown limited efficacy in animal models, leaving the question of whether PIN1 is a proper oncologic target still unanswered. By screening a 1 trillion DNA-encoded library (DEL), we identified novel nonacidic compounds. Among resynthesized DEL compounds, DEL1067-56-469 (A0) is the most potent one (KD = 430 nM, IC50 = 420 nM). Further optimization of A0 resulted in compound C10 with much improved potency (KD = 25 nM, IC50 = 150 nM). As an alternative approach, C10 was then converted into proteolysis targeting chimeras (PROTACs) in order to achieve deeper downregulation of the PIN1 protein in cancer cell lines. Unfortunately, neither PIN1 inhibitors nor PIN1 PROTACs demonstrated meaningful antiproliferation activity. In addition, siRNA knock-down experiments provided unfavorable evidence of PIN1 as an oncologic target. Our findings highlight the complexity of targeting PIN1 for cancer therapy.
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Affiliation(s)
- Chuan Liu
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Zhonghui Chen
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Tao Chen
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Hongmei Song
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Jianbo Shen
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Xiaoxi Yuan
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Shuai Xia
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Qian Liu
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Qiuxia Chen
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Qiang Tian
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Xiaoyun Meng
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Zhu Han
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Xiaofei Dong
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Yu Yang
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Longying Cai
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Xuemin Cheng
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Yangyang Jia
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Guansai Liu
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Jin Li
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
| | - Junyou Ge
- Sichuan Kelun-Biotech Biopharmaceutical Co., Ltd., Wenjiang District, Chengdu, Sichuan 611138, P. R. China
| | - Dengfeng Dou
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610200, P. R. China
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3
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Han S, Guo X, Wang M, Liu H, Song Y, He Y, Hsueh KL, Cui W, Su W, Kuai L, Deng J. Highly Selective Novel Heme Oxygenase-1 Hits Found by DNA-Encoded Library Machine Learning beyond the DEL Chemical Space. ACS Med Chem Lett 2024; 15:1456-1466. [PMID: 39291011 PMCID: PMC11403747 DOI: 10.1021/acsmedchemlett.4c00121] [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: 03/15/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 09/19/2024] Open
Abstract
DNA-encoded library (DEL) technology, especially when combined with machine learning (ML), is a powerful method to discover novel inhibitors. DEL-ML can expand a larger chemical space and boost cost-effectiveness during hit finding. Heme oxygenase-1 (HO-1), a heme-degrading enzyme, is linked to diseases such as cancer and neurodegenerative disorders. The discovery of five series of new scaffold HO-1 hits is reported here, using a DEL-ML workflow, which emphasizes the model's uncertainty quantification and domain of applicability. This model exhibits a strong extrapolation ability, identifying new structures beyond the DEL chemical space. About 37% of predicted molecules showed a binding affinity of K D < 20 μM, with the strongest being 141 nM, amd 14 of those molecules displayed >100-fold selectivity for HO-1 over heme oxygenase-2 (HO-2). These molecules also showed structural novelty compared to existing HO-1 inhibitors. Docking simulations provided insights into possible selectivity rationale.
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Affiliation(s)
- Shuai Han
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Xinyun Guo
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Min Wang
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Huan Liu
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Yidan Song
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Yunyun He
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Kuang-Lung Hsueh
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec, 22 Strathmore Road, Natick, Massachusetts 01760, United States
| | - Jason Deng
- WuXi AppTec, 22 Strathmore Road, Natick, Massachusetts 01760, United States
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4
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Xing Y, Zhang H, Wang Y, Zong Z, Bogyo M, Chen S. DNA encoded peptide library for SARS-CoV-2 3CL protease covalent inhibitor discovery and profiling. RSC Chem Biol 2024; 5:691-702. [PMID: 38966676 PMCID: PMC11221529 DOI: 10.1039/d4cb00097h] [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: 04/29/2024] [Accepted: 05/29/2024] [Indexed: 07/06/2024] Open
Abstract
Covalent protease inhibitors serve as valuable tools for modulating protease activity and are essential for investigating the functions of protease targets. These inhibitors typically consist of a recognition motif and a covalently reactive electrophile. Substrate peptides, featuring residues capable of fitting into the substrate pockets of proteases, undergo chemical modification at the carbonyl carbon of the P1 residue with an electrophile and have been widely applied in the development of covalent inhibitors. In this study, we utilized a DNA-encoded peptide library to replicate peptide binder sequences and introduced a vinyl sulfone warhead at the C-termini to construct the DNA-encoded peptide covalent inhibitor library (DEPCIL) for targeting cysteine proteases. Screening results toward 3CL protease demonstrated the efficacy of this library, not only in identifying protease inhibitors, but also in discovering amino acids that can conform to aligned protease pockets. The identified peptide sequences provide valuable insight into the amino acid preferences within substrate binding pockets, and our novel technology is indicative of the potential for similar strategies to discover covalent inhibitors and profile binding preferences of other proteases.
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Affiliation(s)
- Yuyu Xing
- Biotech Drug Research Center, 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
| | - Huiya Zhang
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yanhui Wang
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Zhaoyun Zong
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine Stanford CA USA
| | - Shiyu Chen
- Biotech Drug Research Center, 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
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5
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Dickson P. DNA-Encoded Library Technology─A Catalyst for Covalent Ligand Discovery. ACS Chem Biol 2024; 19:802-808. [PMID: 38527941 DOI: 10.1021/acschembio.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The identification of novel covalent ligands for therapeutic purposes has long depended on serendipity, with dedicated hit finding techniques emerging only in the early 2000s. Advances in chemoproteomics have enabled robust characterization of putative drugs to derisk the unique liabilities associated with covalent hit molecules, leading to a renewed interest in this targeting modality. DNA-encoded library (DEL) technology has similarly emerged over the past two decades as a highly efficient method to identify new chemical equity toward protein targets of interest. A number of commercial and academic groups have reported methods in covalent DEL synthesis and hit identification; however, it is evident that there is still much to be done to fully realize the power of this technology for covalent ligand discovery. This perspective will explore the current approaches in covalent DEL technology and reflect on the next steps to advance this field.
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Affiliation(s)
- Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
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6
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Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
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7
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Zhang YJ, Liang JX, Xu YS, Liu YX, Cui Y, Qiao ZY, Wang H. Covalent drugs based on small molecules and peptides for disease theranostics. Biomater Sci 2024; 12:564-580. [PMID: 37975197 DOI: 10.1039/d3bm01138k] [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: 11/19/2023]
Abstract
Biomacromolecules, such as proteins, nucleic acids and polysaccharides, are widely distributed in the human body, and some of them have been recognized as the targets of drugs for disease theranostics. Drugs typically act on targets in two ways: non-covalent bond and covalent bond. Non-covalent bond-based drugs have some disadvantages, such as structural instability and environmental sensitivity. Covalent interactions between drugs and targets have a longer action time, higher affinity and controllability than non-covalent interactions of conventional drugs. With the development of artificial intelligence, covalent drugs have received more attention and have been developed rapidly in pharmaceutical research in recent years. From the perspective of covalent drugs, this review summarizes the design methods and the effects of covalent drugs. Finally, we discuss the application of covalent peptide drugs and expect to provide a new reference for cancer treatment.
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Affiliation(s)
- Ying-Jin Zhang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Jian-Xiao Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Yin-Sheng Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Yi-Xuan Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Yingying Cui
- Department of Food and Drug, Laiwu Vocational and Technical, College, Jinan, China
| | - Zeng-Ying Qiao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Hao Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
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8
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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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9
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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: 37] [Impact Index Per Article: 37.0] [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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10
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Seydimemet M, Yang Y, Lv Y, Liu J, Yan Z, Zhao Y, Wang X, Lu X. Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries. ACS Med Chem Lett 2023; 14:1073-1078. [PMID: 37583819 PMCID: PMC10424316 DOI: 10.1021/acsmedchemlett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.
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Affiliation(s)
- Mengnisa Seydimemet
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yixuan Yang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yuhan Lv
- School
of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong P.R. China
| | - Jiaxiang Liu
- Alphama
Biotechnology Suzhou Co., Ltd., 108 Yuxin Road, Suzhou City, Jiangsu Province 215123, China
| | - Ziqin Yan
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yujun Zhao
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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11
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Iskandar SE, Chiou LF, Leisner TM, Shell DJ, Norris-Drouin JL, Vaziri C, Pearce KH, Bowers AA. Identification of Covalent Cyclic Peptide Inhibitors in mRNA Display. J Am Chem Soc 2023; 145:15065-15070. [PMID: 37395736 PMCID: PMC11246720 DOI: 10.1021/jacs.3c04833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Peptides have historically been underutilized for covalent inhibitor discovery, despite their unique abilities to interact with protein surfaces and interfaces. This is in part due to a lack of methods for screening and identifying covalent peptide ligands. Here, we report a method to identify covalent cyclic peptide inhibitors in mRNA display. We combine co- and post-translational library diversification strategies to create cyclic libraries with reactive dehydroalanines (Dhas), which we employ in selections against two model targets. The most potent hits exhibit low nanomolar inhibitory activities and disrupt known protein-protein interactions with their selected targets. Overall, we establish Dhas as electrophiles for covalent inhibition and showcase how separate library diversification methods can work synergistically to dispose mRNA display to novel applications like covalent inhibitor discovery.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Lilly F Chiou
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Devan J Shell
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L Norris-Drouin
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Cyrus Vaziri
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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Alves ETM, Pernichelle FG, Nascimento LA, Ferreira GM, Ferreira EI. Covalent Inhibitors for Neglected Diseases: An Exploration of Novel Therapeutic Options. Pharmaceuticals (Basel) 2023; 16:1028. [PMID: 37513939 PMCID: PMC10385647 DOI: 10.3390/ph16071028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Neglected diseases, primarily found in tropical regions of the world, present a significant challenge for impoverished populations. Currently, there are 20 diseases considered neglected, which greatly impact the health of affected populations and result in difficult-to-control social and economic consequences. Unfortunately, for the majority of these diseases, there are few or no drugs available for patient treatment, and the few drugs that do exist often lack adequate safety and efficacy. As a result, there is a pressing need to discover and design new drugs to address these neglected diseases. This requires the identification of different targets and interactions to be studied. In recent years, there has been a growing focus on studying enzyme covalent inhibitors as a potential treatment for neglected diseases. In this review, we will explore examples of how these inhibitors have been used to target Human African Trypanosomiasis, Chagas disease, and Malaria, highlighting some of the most promising results so far. Ultimately, this review aims to inspire medicinal chemists to pursue the development of new drug candidates for these neglected diseases, and to encourage greater investment in research in this area.
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Affiliation(s)
- Erick Tavares Marcelino Alves
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Filipe Gomes Pernichelle
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Lucas Adriano Nascimento
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
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Wen X, Wu X, Jin R, Lu X. Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization. Eur J Med Chem 2023; 248:115079. [PMID: 36669370 DOI: 10.1016/j.ejmech.2022.115079] [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: 10/09/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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