1
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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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2
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Xiao YQ, Long J, Zhang SS, Zhu YY, Gu SX. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorg Chem 2024; 147:107380. [PMID: 38636432 DOI: 10.1016/j.bioorg.2024.107380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.
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Affiliation(s)
- Ya-Qi Xiao
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
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3
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Xia Y, Pan X, Shen HB. A comprehensive survey on protein-ligand binding site prediction. Curr Opin Struct Biol 2024; 86:102793. [PMID: 38447285 DOI: 10.1016/j.sbi.2024.102793] [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: 12/20/2023] [Revised: 02/18/2024] [Accepted: 02/18/2024] [Indexed: 03/08/2024]
Abstract
Protein-ligand binding site prediction is critical for protein function annotation and drug discovery. Biological experiments are time-consuming and require significant equipment, materials, and labor resources. Developing accurate and efficient computational methods for protein-ligand interaction prediction is essential. Here, we summarize the key challenges associated with ligand binding site (LBS) prediction and introduce recently published methods from their input features, computational algorithms, and ligand types. Furthermore, we investigate the specificity of allosteric site identification as a particular LBS type. Finally, we discuss the prospective directions for machine learning-based LBS prediction in the near future.
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Affiliation(s)
- Ying Xia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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4
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Ku AF, Sharma KL, Ta HM, Sutton CM, Bohren KM, Wang Y, Chamakuri S, Chen R, Hakenjos JM, Jimmidi R, Kent K, Li F, Li JY, Ma L, Madasu C, Palaniappan M, Palmer SS, Qin X, Robers MB, Sankaran B, Tan Z, Vasquez YM, Wang J, Wilkinson J, Yu Z, Ye Q, Young DW, Teng M, Kim C, Matzuk MM. Reversible male contraception by targeted inhibition of serine/threonine kinase 33. Science 2024; 384:885-890. [PMID: 38781365 DOI: 10.1126/science.adl2688] [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: 10/09/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024]
Abstract
Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.
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Affiliation(s)
- Angela F Ku
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hai Minh Ta
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruihong Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lang Ma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandrashekhar Madasu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen S Palmer
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasmin M Vasquez
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Choel Kim
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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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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Luo A, Zhou H, Wang X, Zeng F, Yu W, Yang K, Duchemin N, Hu YJ. Development of on-DNA Formation of Benzofuran for DNA-Encoded Library Synthesis. Org Lett 2024; 26:1688-1693. [PMID: 38385779 DOI: 10.1021/acs.orglett.4c00187] [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: 02/23/2024]
Abstract
Using a novel homologation-heterocyclization cascade, the on-DNA synthesis of benzofurans from aldehydes has been developed. The methodology, based on an innovative use of the Seyferth-Gilbert homologation, followed by a high yielding Sonogashira coupling in situ intramolecular cyclization one-pot, two-step reaction, provides a powerful and unique pathway for DNA-encoded library (DEL) synthesis of a wide array of pharmaceutically relevant benzofuran-based scaffolds.
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Affiliation(s)
- Ayun Luo
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Xiuming Wang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Fanming Zeng
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Weina Yu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Nicolas Duchemin
- Pharmaron U.K., Ltd., Innovation Park, West Cl, Hertford Road, Hoddesdon EN11 9FH, U.K
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
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7
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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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8
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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9
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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10
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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11
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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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12
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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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13
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Jimmidi R, Chamakuri S, Lu S, Ucisik MN, Chen PJ, Bohren KM, Moghadasi SA, Versteeg L, Nnabuife C, Li JY, Qin X, Chen YC, Faver JC, Nyshadham P, Sharma KL, Sankaran B, Judge A, Yu Z, Li F, Pollet J, Harris RS, Matzuk MM, Palzkill T, Young DW. DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors. Commun Chem 2023; 6:164. [PMID: 37542196 PMCID: PMC10403511 DOI: 10.1038/s42004-023-00961-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023] Open
Abstract
The development of SARS-CoV-2 main protease (Mpro) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate Mpro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of Mpro. An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using Mpro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of Mpro with low nanomolar Ki values. Furthermore, these compounds demonstrate efficacy against mutant forms of Mpro that have shown resistance to the standard-of-care drug nirmatrelvir. Overall, this work demonstrates that DEC-Tec can efficiently generate novel and potent inhibitors without preliminary chemical or structural information.
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Affiliation(s)
- Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Shuo Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Melek Nihan Ucisik
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Peng-Jen Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - Leroy Versteeg
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Christina Nnabuife
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ying-Chu Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - John C Faver
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jeroen Pollet
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
- Center for Vaccine Development, Texas Children's Hospital, 1102 Bates Street, Houston, Texas, 77030, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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14
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Luo A, Duchemin N, Wang X, Zhou H, Zeng F, Zhao X, Yu W, Yang K, Jin Hu Y. Development of On-DNA Thiophene Synthesis for DEL Construction. Chem Asian J 2023; 18:e202300458. [PMID: 37339942 DOI: 10.1002/asia.202300458] [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: 05/23/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
Thiophene and its substituted derivatives are a highly important class of heterocyclic compounds, with noteworthy applications in pharmaceutical ingredients. In this study, we leverage the unique reactivity of alkynes to generate thiophenes on-DNA, using a cascade iodination, Cadiot-Chodkiewicz coupling and heterocyclization. This approach, tackling on-DNA thiophene synthesis for the first time, generates diverse, and unprecedented structural and chemical features, which could be significant motifs in DEL screening as molecular recognition agents for drug discovery.
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Affiliation(s)
- Ayun Luo
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Nicolas Duchemin
- Pharmaron UK, Ltd., Innovation Park, West Cl, Hertford Rd, Hoddesdon, EN11 9FH, UK
| | - Xiuming Wang
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Fanming Zeng
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Xue Zhao
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Weina Yu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Kexin Yang
- Pharmaron Beijing Co., Ltd, 6 Taihe Road, BDA, Beijing, 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
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15
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Xue L, Ma H, Liu W, Duchemin N, Zeng F, Zhang J, Zhang H, Yang K, Hu YJ. Constructive on-DNA Thiol Aerial Oxidization for DNA-Encoded Library Synthesis. ACS OMEGA 2023; 8:24072-24077. [PMID: 37426273 PMCID: PMC10324384 DOI: 10.1021/acsomega.3c03160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
A novel on-DNA oxidative disulfide formation method has been developed. Under ambient conditions, the methodology showcased wide applicability and swift implementation in routine DNA-encoded library synthesis to access pharmaceutically relevant motifs.
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Affiliation(s)
- Lijun Xue
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Hangke Ma
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Weijie Liu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Nicolas Duchemin
- Pharmaron
UK, Ltd., Innovation Park, West Cl, Hertford Road, Hoddesdon EN11 9FH, U.K.
| | - Fanming Zeng
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Jie Zhang
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Huanqing Zhang
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
| | - Kexin Yang
- Pharmaron
Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176 P. R. China
| | - Yun Jin Hu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo 315336 China
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16
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Ye Q, Belabed H, Wang Y, Yu Z, Palaniappan M, Li JY, Kalovidouris SA, MacKenzie KR, Teng M, Young DW, Fujihara Y, Matzuk MM. Advancing ASMS with LC-MS/MS for the discovery of novel PDCL2 ligands from DNA-encoded chemical library selections. Andrology 2023; 11:808-815. [PMID: 36209044 PMCID: PMC11299427 DOI: 10.1111/andr.13309] [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: 07/18/2022] [Revised: 09/30/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND A safe, effective, and reversible nonhormonal male contraceptive drug is greatly needed for male contraception as well as for circumventing the side effects of female hormonal contraceptives. Phosducin-like 2 (PDCL2) is a testis-specific phosphoprotein in mice and humans. We recently found that male PDCL2 knockout mice are sterile due to globozoospermia caused by impaired sperm head formation, indicating that PDCL2 is a potential target for male contraception. Herein, our study for the first time developed a biophysical assay for PDCL2 allowing us to screen a series of small molecules, to study structure-activity relationships, and to discover two PDCL2 binders with novel chemical structure. OBJECTIVE To identify a PDCL2 ligand for therapeutic male contraception, we performed DNA-encoded chemical library (DECL) screening and off-DNA hit validation using a unique affinity selection mass spectrometry (ASMS) biophysical profiling strategy. MATERIALS AND METHODS We employed the screening process of DECL, which contains billions of chemically unique DNA-barcoded compounds generated through individual sequences of reactions and different combinations of functionalized building blocks. The structures of the PDCL2 binders are proposed based on the sequencing analysis of the DNA barcode attached to each individual DECL compound. The proposed structure is synthesized through multistep reactions. To confirm and determine binding affinity between the DECL identified molecules and PDCL2, we developed an ASMS assay that incorporates liquid chromatography with tandem mass spectrometry (LC-MS/MS). RESULTS After a screening process of PDCL2 with DECLs containing >440 billion compounds, we identified a series of hits. The selected compounds were synthesized as off-DNA small molecules, characterized by spectroscopy data, and subjected to our ASMS/LC-MS/MS binding assay. By this assay, we discovered two novel compounds, which showed good binding affinity for PDCL2 in comparison to other molecules generated in our laboratory and which were further confirmed by a thermal shift assay. DISCUSSION AND CONCLUSION AND RELEVANCE With the ASMS/LC-MS/MS assay developed in this paper, we successfully discovered a PDCL2 ligand that warrants further development as a male contraceptive.
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Affiliation(s)
- Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Hassane Belabed
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Stacey A. Kalovidouris
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Kevin R. MacKenzie
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Damian W. Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yoshitaka Fujihara
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- National Cerebral and Cardiovascular Center, Suita, Japan
| | - Martin M. Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
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17
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Xia Y, Pan X, Shen HB. LigBind: identifying binding residues for over 1000 ligands with relation-aware graph neural networks. J Mol Biol 2023; 435:168091. [PMID: 37054909 DOI: 10.1016/j.jmb.2023.168091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Identifying the interactions between proteins and ligands is significant for drug discovery and design. Considering the diverse binding patterns of ligands, the ligand-specific methods are trained per ligand to predict binding residues. However, most of the existing ligand-specific methods ignore shared binding preferences among various ligands and generally only cover a limited number of ligands with a sufficient number of known binding proteins. In this study, we propose a relation-aware framework LigBind with graph-level pre-training to enhance the ligand-specific binding residue predictions for 1159 ligands, which can effectively cover the ligands with a few known binding proteins. LigBind first pre-trains a graph neural network-based feature extractor for ligand-residue pairs and relation-aware classifiers for similar ligands. Then, LigBind is fine-tuned with ligand-specific binding data, where a domain adaptive neural network is designed to automatically leverage the diversity and similarity of various ligand-binding patterns for accurate binding residue prediction. We construct ligand-specific benchmark datasets of 1159 ligands and 16 unseen ligands, which are used to evaluate the effectiveness of LigBind. The results demonstrate the LigBind's efficacy on the large-scale ligand-specific benchmark datasets, and generalizes well to unseen ligands. LigBind also enables accurate identification of the ligand-binding residues in the main protease, papain-like protease and the RNA-dependent RNA polymerase of SARS-CoV-2. The webserver and source codes of LigBind are available at http://www.csbio.sjtu.edu.cn/bioinf/LigBind/ and https://github.com/YYingXia/LigBind/ for academic use.
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Affiliation(s)
- Ying Xia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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18
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Moghadasi SA, Heilmann E, Khalil AM, Nnabuife C, Kearns FL, Ye C, Moraes SN, Costacurta F, Esler MA, Aihara H, von Laer D, Martinez-Sobrido L, Palzkill T, Amaro RE, Harris RS. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. SCIENCE ADVANCES 2023; 9:eade8778. [PMID: 36989354 PMCID: PMC10058310 DOI: 10.1126/sciadv.ade8778] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/28/2023] [Indexed: 05/05/2023]
Abstract
Vaccines and drugs have helped reduce disease severity and blunt the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus transmission, continuous evolution, and increasing selective pressures have the potential to yield viral variants capable of resisting these interventions. Here, we investigate the susceptibility of natural variants of the main protease [Mpro; 3C-like protease (3CLpro)] of SARS-CoV-2 to protease inhibitors. Multiple single amino acid changes in Mpro confer resistance to nirmatrelvir (the active component of Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different resistance mutation profile. Importantly, phylogenetic analyses indicate that several of these resistant variants have pre-existed the introduction of these drugs into the human population and are capable of spreading. These results encourage the monitoring of resistance variants and the development of additional protease inhibitors and other antiviral drugs with different mechanisms of action and resistance profiles for combinatorial therapy.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Christina Nnabuife
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | | | - Morgan A. Esler
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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19
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Guterres Fernandes OL, Tizziani T, Dambrós BP, Ferreira de Sousa N, Mansur Pontes CL, da Silva LAL, Escorteganha Pollo LA, de Assis FF, Scotti MT, Scotti L, Braga AL, Steindel M, Sandjo LP. Studies of Cytotoxicity Effects, SARS-CoV-2 Main Protease Inhibition, and in Silico Interactions of Synthetic Chalcones. Chem Biodivers 2023; 20:e202201151. [PMID: 36740573 DOI: 10.1002/cbdv.202201151] [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: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 main protease (Mpro ) plays an essential role in proteolysis cleavage that promotes coronavirus replication. Thus, attenuating the activity of this enzyme represents a strategy to develop antiviral agents. We report inhibitory effects against Mpro of 40 synthetic chalcones, and cytotoxicity activities, hemolysis, and in silico interactions of active compounds. Seven of them bearing a (E)-3-(furan-2-yl)-1-arylprop-2-en-1-one skeleton (10, 28, and 35-39) showed enzyme inhibition with IC50 ranging from 13.76 and 36.13 μM. Except for 35 and 36, other active compounds were not cytotoxic up to 150 μM against THP-1 and Vero cell lines. Compounds 10, and 35-39 showed no hemolysis while 28 was weakly hemotoxic at 150 μM. Moreover, molecular docking showed interactions between compound 10 and Mpro (PDBID 5RG2 and 5RG3) with proximity to cys145 and His41, suggesting a covalent binding. Products of the reaction between chalcones and cyclohexanethiol indicated that this binding could be a Michael addition type.
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Affiliation(s)
- Octavio L Guterres Fernandes
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Tiago Tizziani
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Bibiana P Dambrós
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Natália Ferreira de Sousa
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Carime L Mansur Pontes
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Layzon A L da Silva
- Postgraduate Program in Pharmacy, Department of Pharmaceutical Sciences, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Luiz A Escorteganha Pollo
- Postgraduate Program in Pharmacy, Department of Pharmaceutical Sciences, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Francisco F de Assis
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Marcus T Scotti
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Bioactive Synthetic Products, Department of Pharmaceutical Sciences, Universidade Federal de Paraíba, 50670-910, João Pessoa, Paraíba, Brazil
| | - Antonio L Braga
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
| | - Mario Steindel
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, Santa Catarina, Brazil
| | - Louis P Sandjo
- Postgraduate Program in Chemistry, Department of Chemistry, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, 88040-900, Florianópolis, SC, Brazil
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20
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Brewitz L, Dumjahn L, Zhao Y, Owen CD, Laidlaw SM, Malla TR, Nguyen D, Lukacik P, Salah E, Crawshaw AD, Warren AJ, Trincao J, Strain-Damerell C, Carroll MW, Walsh MA, Schofield CJ. Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. J Med Chem 2023; 66:2663-2680. [PMID: 36757959 PMCID: PMC9924091 DOI: 10.1021/acs.jmedchem.2c01627] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Indexed: 02/10/2023]
Abstract
Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of Mpro and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.
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Affiliation(s)
- Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Leo Dumjahn
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yilin Zhao
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Stephen M. Laidlaw
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Dung Nguyen
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Adam D. Crawshaw
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Anna J. Warren
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jose Trincao
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Miles W. Carroll
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research
Complex at Harwell, Harwell Science and
Innovation Campus, Didcot OX11 0FA, United
Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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21
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Modukuri RK, Monsivais D, Li F, Palaniappan M, Bohren KM, Tan Z, Ku AF, Wang Y, Madasu C, Li JY, Tang S, Miklossy G, Palmer SS, Young DW, Matzuk MM. Discovery of Highly Potent and BMPR2-Selective Kinase Inhibitors Using DNA-Encoded Chemical Library Screening. J Med Chem 2023; 66:2143-2160. [PMID: 36719862 PMCID: PMC9924264 DOI: 10.1021/acs.jmedchem.2c01886] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/01/2023]
Abstract
The discovery of monokinase-selective inhibitors for patients is challenging because the 500+ kinases encoded by the human genome share highly conserved catalytic domains. Until now, no selective inhibitors unique for a single transforming growth factor β (TGFβ) family transmembrane receptor kinase, including bone morphogenetic protein receptor type 2 (BMPR2), have been reported. This dearth of receptor-specific kinase inhibitors hinders therapeutic options for skeletal defects and cancer as a result of an overactivated BMP signaling pathway. By screening 4.17 billion "unbiased" and "kinase-biased" DNA-encoded chemical library molecules, we identified hits CDD-1115 and CDD-1431, respectively, that were low-nanomolar selective kinase inhibitors of BMPR2. Structure-activity relationship studies addressed metabolic lability and high-molecular-weight issues, resulting in potent and BMPR2-selective inhibitor analogs CDD-1281 (IC50 = 1.2 nM) and CDD-1653 (IC50 = 2.8 nM), respectively. Our work demonstrates that DNA-encoded chemistry technology (DEC-Tec) is reliable for identifying novel first-in-class, highly potent, and selective kinase inhibitors.
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Affiliation(s)
- Ram K. Modukuri
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Diana Monsivais
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Feng Li
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas77030, United States
| | - Murugesan Palaniappan
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Kurt M. Bohren
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Zhi Tan
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas77030, United States
| | - Angela F. Ku
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Yong Wang
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Chandrashekhar Madasu
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Jian-Yuan Li
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Suni Tang
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Gabriella Miklossy
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Stephen S. Palmer
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
| | - Damian W. Young
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas77030, United States
| | - Martin M. Matzuk
- Center
for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas77030, United States
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas77030, United States
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22
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Shell DJ, Rectenwald JM, Buttery PH, Johnson RL, Foley CA, Guduru SKR, Uguen M, Rubiano JS, Zhang X, Li F, Norris-Drouin JL, Axtman M, Brian Hardy P, Vedadi M, Frye SV, James LI, Pearce KH. Discovery of hit compounds for methyl-lysine reader proteins from a target class DNA-encoded library. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:428-439. [PMID: 36272689 DOI: 10.1016/j.slasd.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
Methyl-lysine (Kme) reader domains are prevalent in chromatin regulatory proteins which bind post-translational modification sites to recruit repressive and activating factors; therefore, these proteins play crucial roles in cellular signaling and epigenetic regulation. Proteins that contain Kme domains are implicated in various diseases, including cancer, making them attractive therapeutic targets for drug and chemical probe discovery. Herein, we report on expanding the utility of a previously reported, Kme-focused DNA-encoded library (DEL), UNCDEL003, as a screening tool for hit discovery through the specific targeting of Kme reader proteins. As an efficient method for library generation, focused DELs are designed based on structural and functional features of a specific class of proteins with the intent of novel hit discovery. To broadly assess the applicability of our library, UNCDEL003 was screened against five diverse Kme reader protein domains (53BP1 TTD, KDM7B JmjC-PHD, CDYL2 CD, CBX2 CD, and LEDGF PWWP) with varying structures and functions. From these screening efforts, we identified hit compounds which contain unique chemical scaffolds distinct from previously reported ligands. The selected hit compounds were synthesized off-DNA and confirmed using primary and secondary assays and assessed for binding selectivity. Hit compounds from these efforts can serve as starting points for additional development and optimization into chemical probes to aid in further understanding the functionality of these therapeutically relevant proteins.
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Affiliation(s)
- Devan J Shell
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justin M Rectenwald
- School of Medicine, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peter H Buttery
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca L Johnson
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline A Foley
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiva K R Guduru
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mélanie Uguen
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juanita Sanchez Rubiano
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xindi Zhang
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jacqueline L Norris-Drouin
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Axtman
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - P Brian Hardy
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephen V Frye
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I James
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth H Pearce
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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23
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [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: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a “good” hit in the course of a screening campaign still rely on a lot of luck – which is within the reach of academics –, that the hit to lead process requires a lot of chemistry and that if public–private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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24
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Xu H, Tan T, Zhang Y, Wang Y, Pan K, Yao Y, Zhang S, Gu Y, Chen W, Li J, Dong H, Meng Y, Ma P, Hou W, Yang G. Metal-Free and Open-Air Arylation Reactions of Diaryliodonium Salts for DNA-Encoded Library Synthesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202790. [PMID: 35853237 PMCID: PMC9475524 DOI: 10.1002/advs.202202790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
A successful DNA-encoded library (DEL) will consist of diverse skeletons and cover chemical space as comprehensive as possible to fully realize its potential in drug discovery and chemical biology. However, the lack of versatile on-DNA arylation methods for phenols that are less nucleophilic and reactive poses a great hurdle for DEL to include diaryl ether, a privileged chemotype in pharmaceuticals and natural products. This work describes the use of "substrate activation" approach to address the arylation of DNA-conjugated phenols. Diaryliodonium salt, a highly electrophilic and reactive arylation reagent, is employed as Ar+ sources to ensure highly selective on-DNA arylation of phenols and oximes with both high yields and DNA fidelity. Notably, the new on-DNA arylation reaction can be applied to the late-stage modification of peptides containing tyrosine side-chain and to synthesize DNA-tagged analogues of existing drug molecules such as sorafenib, a known pan-kinase inhibitor. The new on-DNA diaryliodonium salts chemistry affords a greater flexibility in DEL design and synthesis.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Kangyin Pan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Ying Yao
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Yu Meng
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
- Shanghai Key Laboratory of Orthopedic ImplantsDepartment of Orthopedic SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong UniversitySchool of MedicineShanghai200011P. R. China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
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25
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Abstract
The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here, we report quantitative reporters for Mpro function in living cells in which protease inhibition by genetic or chemical methods results in robust signal readouts by fluorescence (enhanced green fluorescent protein [eGFP]) or bioluminescence (firefly luciferase). These gain-of-signal systems are scalable to high-throughput platforms for quantitative discrimination between Mpro mutants and/or inhibitor potencies as evidenced by validation of several reported inhibitors. Additional utility is shown by single Mpro amino acid variants and structural information combining to demonstrate that both inhibitor conformational dynamics and amino acid differences are able to influence inhibitor potency. We further show that a recent variant of concern (Omicron) has an unchanged response to a clinically approved drug, nirmatrelvir, whereas proteases from divergent coronavirus species show differential susceptibility. Together, we demonstrate that these gain-of-signal systems serve as robust, facile, and scalable assays for live cell quantification of Mpro inhibition, which will help expedite the development of next-generation antivirals and enable the rapid testing of emerging variants. IMPORTANCE The main protease, Mpro, of SARS-CoV-2 is an essential viral protein required for the earliest steps of infection. It is therefore an attractive target for antiviral drug development. Here, we report the development and implementation of two complementary cell-based systems for quantification of Mpro inhibition by genetic or chemical approaches. The first is fluorescence based (eGFP), and the second is luminescence based (firefly luciferase). Importantly, both systems rely upon gain-of-signal readouts such that stronger inhibitors yield higher fluorescent or luminescent signal. The high versatility and utility of these systems are demonstrated by characterizing Mpro mutants and natural variants, including Omicron, as well as a panel of existing inhibitors. These systems rapidly, safely, and sensitively identify Mpro variants with altered susceptibilities to inhibition, triage-nonspecific, or off-target molecules and validate bona fide inhibitors, with the most potent thus far being the first-in-class drug nirmatrelvir.
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26
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Deodato D, Asad N, Dore TM. Discovery of 2-Thiobenzimidazoles as Noncovalent Inhibitors of SARS-CoV-2 Main Protease. Bioorg Med Chem Lett 2022; 72:128867. [PMID: 35760254 PMCID: PMC9225965 DOI: 10.1016/j.bmcl.2022.128867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/03/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
Abstract
The discovery of antiviral agents against SARS-CoV-2 is an important step toward ending the COVID-19 pandemic and to tackle future outbreaks. In this context, the main protease (Mpro) represents an ideal target for developing coronavirus antivirals, being conserved among different strains and essential for survival. In this work, using in silico tools, we created and validated a docking protocol able to predict binders to the catalytic site of Mpro. The following structure-based virtual screening of a subset of the ZINC library (over 4.3 million unique structures), led to the identification of a hit compound having a 2-thiobenzimidazole scaffold. The inhibitory activity was confirmed using a FRET-based proteolytic assay against recombinant Mpro. Structure-activity relationships were obtained with the synthesis of a small library of analogs, guided by the analysis of the docking pose. Our efforts led to the identification of a micromolar Mpro inhibitor (IC50 = 14.9 µM) with an original scaffold possessing ideal drug-like properties (predicted using the QikProp function) and representing a promising lead for the development of a novel class of coronavirus antivirals.
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Affiliation(s)
- Davide Deodato
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Nadeem Asad
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Timothy M Dore
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates; Department of Chemistry, University of Georgia, Athens, GA 30602, USA
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27
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Siripuram VK, Sunkari YK, Nguyen TL, Flajolet M. DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries. Front Chem 2022; 10:894603. [PMID: 35774858 PMCID: PMC9237475 DOI: 10.3389/fchem.2022.894603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
An efficient method for the C-C bond formation via water soluble Na2PdCl4/sSPhos mediated Suzuki-Miyaura cross-coupling reaction of DNA-conjugated aryl iodide with (het)aryl boronic acids has been developed. This reaction proceeds at 37°C in water and acetonitrile (4:1) system. We also demonstrated that numerous aromatic and heteroaromatic boronic acids of different electronic natures, and harboring various functional groups, were highly compatible providing the desired coupling products in good to excellent yields. This DNA-compatible Suzuki-Miyaura cross-coupling reaction has strong potential to construct DNA-Encoded Libraries (DELs) in the context of drug discovery.
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Affiliation(s)
| | | | | | - Marc Flajolet
- *Correspondence: Vijay Kumar Siripuram, ; Marc Flajolet,
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28
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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29
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Fang X, Wang Y, He P, Liao H, Zhang G, Li Y, Li Y. Visible Light-Promoted Divergent Benzoheterocyclization from Aldehydes for DNA-Encoded Chemical Libraries. Org Lett 2022; 24:3291-3296. [PMID: 35467894 DOI: 10.1021/acs.orglett.2c01187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Benzoheterocyclics have been widely adopted as drug-like core scaffolds that can be incorporated into DNA-encoded chemical library technology for high-throughput hit discovery. Here, we present a visible light-promoted divergent synthesis of on-DNA benzoheterocycles from aldehydes. Four types of DNA-conjugated benzoheterocyclics were obtained under mild conditions with a broad substrate scope. A cross substrate scope study, together with enzymatic ligation and subsequent chemical diversifications, were conducted, demonstrating the feasibility of this approach in DNA-encoded chemical library construction.
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Affiliation(s)
- Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Pengyang He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Huilin Liao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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30
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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31
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Rossetti GG, Ossorio MA, Rempel S, Kratzel A, Dionellis VS, Barriot S, Tropia L, Gorgulla C, Arthanari H, Thiel V, Mohr P, Gamboni R, Halazonetis TD. Non-covalent SARS-CoV-2 M pro inhibitors developed from in silico screen hits. Sci Rep 2022; 12:2505. [PMID: 35169179 PMCID: PMC8847420 DOI: 10.1038/s41598-022-06306-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/24/2022] [Indexed: 01/03/2023] Open
Abstract
Mpro, the main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for the viral life cycle. Accordingly, several groups have performed in silico screens to identify Mpro inhibitors that might be used to treat SARS-CoV-2 infections. We selected more than five hundred compounds from the top-ranking hits of two very large in silico screens for on-demand synthesis. We then examined whether these compounds could bind to Mpro and inhibit its protease activity. Two interesting chemotypes were identified, which were further evaluated by characterizing an additional five hundred synthesis on-demand analogues. The compounds of the first chemotype denatured Mpro and were considered not useful for further development. The compounds of the second chemotype bound to and enhanced the melting temperature of Mpro. The most active compound from this chemotype inhibited Mpro in vitro with an IC50 value of 1 μM and suppressed replication of the SARS-CoV-2 virus in tissue culture cells. Its mode of binding to Mpro was determined by X-ray crystallography, revealing that it is a non-covalent inhibitor. We propose that the inhibitors described here could form the basis for medicinal chemistry efforts that could lead to the development of clinically relevant inhibitors.
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Affiliation(s)
- Giacomo G Rossetti
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland.,FoRx Therapeutics AG, 4056, Basel, Switzerland
| | - Marianna A Ossorio
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | | | - Annika Kratzel
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vasilis S Dionellis
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Samia Barriot
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Laurence Tropia
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, 02115, USA.,Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, 02138, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Peter Mohr
- NANDASI Pharma Advisors, 4123, Allschwil, Switzerland
| | - Remo Gamboni
- NANDASI Pharma Advisors, 4123, Allschwil, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland. .,FoRx Therapeutics AG, 4056, Basel, Switzerland.
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32
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Newly Emerging Strategies in Antiviral Drug Discovery: Dedicated to Prof. Dr. Erik De Clercq on Occasion of His 80th Anniversary. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030850. [PMID: 35164129 PMCID: PMC8839652 DOI: 10.3390/molecules27030850] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022]
Abstract
Viral infections pose a persistent threat to human health. The relentless epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health problem, with millions of infections and fatalities so far. Traditional approaches such as random screening and optimization of lead compounds by organic synthesis have become extremely resource- and time-consuming. Various modern innovative methods or integrated paradigms are now being applied to drug discovery for significant resistance in order to simplify the drug process. This review provides an overview of newly emerging antiviral strategies, including proteolysis targeting chimera (PROTAC), ribonuclease targeting chimera (RIBOTAC), targeted covalent inhibitors, topology-matching design and antiviral drug delivery system. This article is dedicated to Prof. Dr. Erik De Clercq, an internationally renowned expert in the antiviral drug research field, on the occasion of his 80th anniversary.
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33
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Structure-based inhibitor design and repurposing clinical drugs to target SARS-CoV-2 proteases. Biochem Soc Trans 2022; 50:151-165. [PMID: 35015073 DOI: 10.1042/bst20211180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic, encodes two proteases, 3CLpro and PLpro, two of the main antiviral research targets. Here we provide an overview of the structures and functions of 3CLpro and PLpro and examine strategies of structure-based drug designing and drug repurposing against these proteases. Rational structure-based drug design enables the generation of potent and target-specific antivirals. Drug repurposing offers an attractive prospect with an accelerated turnaround. Thus far, several protease inhibitors have been identified, and some candidates are undergoing trials that may well prove to be effective antivirals against SARS-CoV-2.
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