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Jiang Z, Hu YT, Guo SY, Li YX, Zhao DD, Wei LY, Lin YW, Xu SM, Huang SL, Li Q, Tan JH, Rao Y, Chen SB, Huang ZS. Development of Novel N-Acylhydrazone Derivatives with High Anti-obesity Activity and Improved Safety by Exploring the Pharmaceutical Properties of Aldehyde Group. J Med Chem 2024; 67:12439-12458. [PMID: 38996004 DOI: 10.1021/acs.jmedchem.4c01242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
The discovery of effective and safe antiobesity agents remains a challenging yet promising field. Our previous studies identified Bouchardatine derivatives as potential antiobesity agents. However, the 8a-aldehyde moiety rendered them unsuitable for drug development. In this study, we designed two series of novel derivatives to modify this structural feature. Through a structure-activity relationship study, we elucidated the role of the 8a-aldehyde group in toxicity induction. We identified compound 14d, featuring an 8a-N-acylhydrazone moiety, which exhibited significant lipid-lowering activity and reduced toxicity. Compound 14d shares a similar lipid-lowering mechanism with our lead compound 3, but demonstrates improved pharmacokinetic properties and safety profile. Both oral and injectable administration of 14d significantly reduced body weight gain and ameliorated metabolic syndrome in diet-induced obese mice. Our findings identify 14d as a promising antiobesity agent and highlight the potential of substituting the aldehyde group with an N-acylhydrazone to enhance drug-like properties.
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Affiliation(s)
- Zhi Jiang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu-Tao Hu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Yao Guo
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yi-Xian Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan-Dan Zhao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Yuan Wei
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu-Wei Lin
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shu-Min Xu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingjiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Rao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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2
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Chen J, Zhao Y, Cheng J, Wang H, Pan S, Liu Y. The Antiviral Potential of Perilla frutescens: Advances and Perspectives. Molecules 2024; 29:3328. [PMID: 39064906 PMCID: PMC11279397 DOI: 10.3390/molecules29143328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses pose a significant threat to human health, causing widespread diseases and impacting the global economy. Perilla frutescens, a traditional medicine and food homologous plant, is well known for its antiviral properties. This systematic review examines the antiviral potential of Perilla frutescens, including its antiviral activity, chemical structure and pharmacological parameters. Utilizing bioinformatics analysis, we revealed the correlation between Perilla frutescens and antiviral activity, identified overlaps between Perilla frutescens target genes and virus-related genes, and explored related signaling pathways. Moreover, a classified summary of the active components of Perilla frutescens, focusing on compounds associated with antiviral activity, provides important clues for optimizing the antiviral drug development of Perilla frutescens. Our findings indicate that Perilla frutescens showed a strong antiviral effect, and its active ingredients can effectively inhibit the replication and spread of a variety of viruses in this review. The antiviral mechanisms of Perilla frutescens may involve several pathways, including enhanced immune function, modulation of inflammatory responses, and inhibition of key enzyme activities such as viral replicase. These results underscore the potential antiviral application of Perilla frutescens as a natural plant and provide important implications for the development of new antiviral drugs.
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Affiliation(s)
- Jing Chen
- Department of Bioinformatics and Intelligent Diagnosis, School of Medicine, Jiangsu University, Zhenjiang 212003, China; (J.C.); (Y.Z.); (J.C.); (H.W.)
| | - Yi Zhao
- Department of Bioinformatics and Intelligent Diagnosis, School of Medicine, Jiangsu University, Zhenjiang 212003, China; (J.C.); (Y.Z.); (J.C.); (H.W.)
| | - Jie Cheng
- Department of Bioinformatics and Intelligent Diagnosis, School of Medicine, Jiangsu University, Zhenjiang 212003, China; (J.C.); (Y.Z.); (J.C.); (H.W.)
| | - Haoran Wang
- Department of Bioinformatics and Intelligent Diagnosis, School of Medicine, Jiangsu University, Zhenjiang 212003, China; (J.C.); (Y.Z.); (J.C.); (H.W.)
| | - Shu Pan
- Computer Science School, Jiangsu University of Science and Technology, Zhenjiang 212003, China;
| | - Yuwei Liu
- Department of Bioinformatics and Intelligent Diagnosis, School of Medicine, Jiangsu University, Zhenjiang 212003, China; (J.C.); (Y.Z.); (J.C.); (H.W.)
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3
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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4
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Shukla G, Singh M, Singh S, Singh MS. Iridium(III)-catalyzed photoredox cross-coupling of alkyl bromides with trialkyl amines: access to α-alkylated aldehydes. Chem Commun (Camb) 2024. [PMID: 38686503 DOI: 10.1039/d4cc01043d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
A C(sp3)-C(sp3) cross coupling approach based on an iridium-photocatalytic radical process has been developed enabling the synthesis of various α-alkylated aldehydes from easily available/synthesized alkyl bromides and trialkyl amines under mild photocatalytic conditions. The synthesized aldehydes are also explored as a functional handle for various useful products such as carboxylic acid, alcohol and N-heterocycle synthesis.
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Affiliation(s)
- Gaurav Shukla
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-211005, India.
| | - Malkeet Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-211005, India.
| | - Saurabh Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-211005, India.
| | - Maya Shankar Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-211005, India.
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5
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Mason M, Belvisi L, Pignataro L, Dal Corso A. A Tight Contact: The Expanding Application of Salicylaldehydes in Lysine-Targeting Covalent Drugs. Chembiochem 2024; 25:e202300743. [PMID: 37986243 DOI: 10.1002/cbic.202300743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
The installation of aldehydes into synthetic protein ligands is an efficient strategy to engage protein lysine residues in remarkably stable imine bonds and augment the compound affinity and selectivity for their biological targets. The high frequency of lysine residues in proteins and the reversibility of the covalent ligand-protein bond support the application of aldehyde-bearing ligands, holding promises for their future use as drugs. This review highlights the increasing exploitation of salicylaldehyde modules in various classes of protein binders, aimed at the reversible-covalent engagement of lysine residues.
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Affiliation(s)
- Mattia Mason
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Luca Pignataro
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Alberto Dal Corso
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
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6
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Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CTK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med 2024; 16:eadi0979. [PMID: 38478629 PMCID: PMC11193659 DOI: 10.1126/scitranslmed.adi0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/21/2024] [Indexed: 05/09/2024]
Abstract
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
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Affiliation(s)
- Michael Westberg
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Chemistry, Aarhus University; 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University; 8000 Aarhus C, Denmark
| | - Yichi Su
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Pinghan Huang
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Jaishree Garhyan
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Puja Bhavesh Patel
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University; Stanford, CA 94305, USA
- Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University; Stanford, CA 94305, USA
| | - Yan Wu
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Chenzhou Hao
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Chieh-Wen Lo
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Marwah Karim
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | | | - Vivian Tat
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Shirit Einav
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Catherine Blish
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Michael Z. Lin
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University; Stanford, CA 94305, USA
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7
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Huo T, Zhao X, Cheng Z, Wei J, Zhu M, Dou X, Jiao N. Late-stage modification of bioactive compounds: Improving druggability through efficient molecular editing. Acta Pharm Sin B 2024; 14:1030-1076. [PMID: 38487004 PMCID: PMC10935128 DOI: 10.1016/j.apsb.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Accepted: 11/13/2023] [Indexed: 03/17/2024] Open
Abstract
Synthetic chemistry plays an indispensable role in drug discovery, contributing to hit compounds identification, lead compounds optimization, candidate drugs preparation, and so on. As Nobel Prize laureate James Black emphasized, "the most fruitful basis for the discovery of a new drug is to start with an old drug"1. Late-stage modification or functionalization of drugs, natural products and bioactive compounds have garnered significant interest due to its ability to introduce diverse elements into bioactive compounds promptly. Such modifications alter the chemical space and physiochemical properties of these compounds, ultimately influencing their potency and druggability. To enrich a toolbox of chemical modification methods for drug discovery, this review focuses on the incorporation of halogen, oxygen, and nitrogen-the ubiquitous elements in pharmacophore components of the marketed drugs-through late-stage modification in recent two decades, and discusses the state and challenges faced in these fields. We also emphasize that increasing cooperation between chemists and pharmacists may be conducive to the rapid discovery of new activities of the functionalized molecules. Ultimately, we hope this review would serve as a valuable resource, facilitating the application of late-stage modification in the construction of novel molecules and inspiring innovative concepts for designing and building new drugs.
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Affiliation(s)
- Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zengrui Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
| | - Minghui Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, East China Normal University, Shanghai 200062, China
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8
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Wang E, Luo J, Zhang L, Zhang J, Jiang Y. Copper-Catalyzed Oxidative [3 + 2] Cycloaddition of Enamines and Pyridotriazoles toward Indolizines. Org Lett 2024; 26:1249-1254. [PMID: 38305700 DOI: 10.1021/acs.orglett.4c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
An efficient copper catalytic system has been established for the synthesis of highly functional indolizines through oxidative [3 + 2] cycloaddition of enamines and pyridotriazoles. This modular platform is compatible with a broad range of functional groups, including natural and complex skeletons, allowing for late-stage modifications. It features a step-economical, highly regioselective, and easy-handling procedure and has been applied in constructing small molecules of potent activity toward inhibiting the VEGF-NRP1 interaction through a one-pot reaction of pyridotriazoles, amines, and aldehydes.
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Affiliation(s)
- Enfu Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Jiangbin Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Luoman Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Jian Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Yaojia Jiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China
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9
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Bracken AK, Gekko CE, Suss NO, Lueders EE, Cui Q, Fu Q, Lui ACW, Anderson ET, Zhang S, Abbasov ME. Biomimetic Synthesis and Chemical Proteomics Reveal the Mechanism of Action and Functional Targets of Phloroglucinol Meroterpenoids. J Am Chem Soc 2024; 146:2524-2548. [PMID: 38230968 PMCID: PMC11000255 DOI: 10.1021/jacs.3c10741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Natural products perennially serve as prolific sources of drug leads and chemical probes, fueling the development of numerous therapeutics. Despite their scarcity, natural products that modulate protein function through covalent interactions with lysine residues hold immense potential to unlock new therapeutic interventions and advance our understanding of the biological processes governed by these modifications. Phloroglucinol meroterpenoids constitute one of the most expansive classes of natural products, displaying a plethora of biological activities. However, their mechanism of action and cellular targets have, until now, remained elusive. In this study, we detail the concise biomimetic synthesis, computational mechanistic insights, physicochemical attributes, kinetic parameters, molecular mechanism of action, and functional cellular targets of several phloroglucinol meroterpenoids. We harness synthetic clickable analogues of natural products to probe their disparate proteome-wide reactivity and subcellular localization through in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned lysine-targeting probe, we streamline a quantitative activity-based protein profiling, enabling the direct mapping of global reactivity and ligandability of proteinaceous lysines in human cells. Leveraging this framework, we identify numerous lysine-meroterpenoid interactions in breast cancer cells at tractable protein sites across diverse structural and functional classes, including those historically deemed undruggable. We validate that phloroglucinol meroterpenoids perturb biochemical functions through stereoselective and site-specific modification of lysines in proteins vital for breast cancer metabolism, including lipid signaling, mitochondrial respiration, and glycolysis. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.
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Affiliation(s)
- Amy K Bracken
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Colby E Gekko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Nina O Suss
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emma E Lueders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qi Cui
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Andy C W Lui
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
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10
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Radwan MO, Abd-Alla HI, Alsaggaf AT, El-Mezayen H, Abourehab MAS, El-Beeh ME, Tateishi H, Otsuka M, Fujita M. Gypsogenin Battling for a Front Position in the Pentacyclic Triterpenes Game of Thrones on Anti-Cancer Therapy: A Critical Review-Dedicated to the Memory of Professor Hanaa M. Rady. Molecules 2023; 28:5677. [PMID: 37570648 PMCID: PMC10420691 DOI: 10.3390/molecules28155677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
In the last decade, gypsogenin has attracted widespread attention from medicinal chemists by virtue of its prominent anti-cancer potential. Despite its late identification, gypsogenin has proved itself as a new anti-proliferative player battling for a frontline position among other classic pentacyclic triterpenes such as oleanolic acid, glycyrrhetinic acid, ursolic acid, betulinic acid, and celastrol. Herein, we present the most important reactions of gypsogenin via modification of its four functional groups. Furthermore, we demonstrate insights into the anti-cancer activity of gypsogenin and its semisynthetic derivatives and go further by introducing our perspective to judiciously guide the prospective rational design. The present article opens a new venue for a better exploitation of gypsogenin chemical entity as a lead compound in cancer chemotherapy. To the best of our knowledge, this is the first review article exploring the anti-cancer activity of gypsogenin derivatives.
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Affiliation(s)
- Mohamed O. Radwan
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Chemistry of Natural Compounds Department, National Research Centre, Giza 12622, Egypt
| | - Howaida I. Abd-Alla
- Chemistry of Natural Compounds Department, National Research Centre, Giza 12622, Egypt
| | - Azhaar T. Alsaggaf
- Department of Chemistry, Taibah University, Madinah 42353, Saudi Arabia;
| | | | - Mohammed A. S. Abourehab
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed E. El-Beeh
- Biology Department, Al-Jumum University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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11
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Monticelli S, Talbot A, Gotico P, Caillé F, Loreau O, Del Vecchio A, Malandain A, Sallustrau A, Leibl W, Aukauloo A, Taran F, Halime Z, Audisio D. Unlocking full and fast conversion in photocatalytic carbon dioxide reduction for applications in radio-carbonylation. Nat Commun 2023; 14:4451. [PMID: 37488106 PMCID: PMC10366225 DOI: 10.1038/s41467-023-40136-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Harvesting sunlight to drive carbon dioxide (CO2) valorisation represents an ideal concept to support a sustainable and carbon-neutral economy. While the photochemical reduction of CO2 to carbon monoxide (CO) has emerged as a hot research topic, the full CO2-to-CO conversion remains an often-overlooked criterion that prevents a productive and direct valorisation of CO into high-value-added chemicals. Herein, we report a photocatalytic process that unlocks full and fast CO2-to-CO conversion (<10 min) and its straightforward valorisation into human health related field of radiochemistry with carbon isotopes. Guided by reaction-model-based kinetic simulations to rationalize reaction optimisations, this manifold opens new opportunities for the direct access to 11C- and 14C-labeled pharmaceuticals from their primary isotopic sources [11C]CO2 and [14C]CO2.
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Affiliation(s)
- Serena Monticelli
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Alex Talbot
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Philipp Gotico
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, F-91191, Gif-sur-Yvette, France
| | - Fabien Caillé
- Université Paris-Saclay, Inserm, CNRS, CEA, Laboratoire d'Imagerie Biomédicale Multimodale Paris-Saclay (BioMaps), F-91401, Orsay, France
| | - Olivier Loreau
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Antonio Del Vecchio
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Augustin Malandain
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Antoine Sallustrau
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Winfried Leibl
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, F-91191, Gif-sur-Yvette, France
| | - Ally Aukauloo
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, F-91191, Gif-sur-Yvette, France
- Université Paris-Saclay, CNRS, Institut de chimie moléculaire et des matériaux d'Orsay, F-91400,, Orsay, France
| | - Frédéric Taran
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France
| | - Zakaria Halime
- Université Paris-Saclay, CNRS, Institut de chimie moléculaire et des matériaux d'Orsay, F-91400,, Orsay, France.
| | - Davide Audisio
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et Marquage, DMTS, F-91191, Gif-sur-Yvette, France.
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12
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Lucero B, Francisco KR, Liu LJ, Caffrey CR, Ballatore C. Protein-protein interactions: developing small-molecule inhibitors/stabilizers through covalent strategies. Trends Pharmacol Sci 2023; 44:474-488. [PMID: 37263826 PMCID: PMC11003449 DOI: 10.1016/j.tips.2023.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
The development of small-molecule inhibitors or stabilizers of selected protein-protein interactions (PPIs) of interest holds considerable promise for the development of research tools as well as candidate therapeutics. In this context, the covalent modification of selected residues within the target protein has emerged as a promising mechanism of action to obtain small-molecule modulators of PPIs with appropriate selectivity and duration of action. Different covalent labeling strategies are now available that can potentially allow for a rational, ground-up discovery and optimization of ligands as PPI inhibitors or stabilizers. This review article provides a synopsis of recent developments and applications of such tactics, with a particular focus on site-directed fragment tethering and proximity-enabled approaches.
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Affiliation(s)
- Bobby Lucero
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Karol R Francisco
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lawrence J Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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13
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Chen P, Tang G, Zhu C, Sun J, Wang X, Xiang M, Huang H, Wang W, Li L, Zhang ZM, Gao L, Yao SQ. 2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases. J Am Chem Soc 2023; 145:3844-3849. [PMID: 36774655 DOI: 10.1021/jacs.2c11595] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Lysine-targeting irreversible covalent inhibitors have attracted growing interests in recent years, especially in the fields of kinase research. Despite encouraging progress, few chemistries are available to develop inhibitors that are exclusively lysine-targeting, selective, and cell-active. We report herein a 2-ethynylbenzaldehyde (EBA)-based, lysine-targeting strategy to generate potent and selective small-molecule inhibitors of ABL kinase by selectively targeting the conserved catalytic lysine in the enzyme. We showed the resulting compounds were cell-active, capable of covalently engaging endogenous ABL kinase in K562 cells with long-residence time and few off-targets. We further validated the generality of this strategy by developing EBA-based irreversible inhibitors against EGFR (a kinase) and Mcl-1 (a nonkinase) that covalently reacted with the catalytic and noncatalytic lysine within each target.
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Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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14
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Stini NA, Poursaitidis ET, Nikitas NF, Kartsinis M, Spiliopoulou N, Ananida-Dasenaki P, Kokotos CG. Light-accelerated "on-water" hydroacylation of dialkyl azodicarboxylates. Org Biomol Chem 2023; 21:1284-1293. [PMID: 36645430 DOI: 10.1039/d2ob02204d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The hydroacylation of dialkyl azodicarboxylates has received a lot of attention lately due to the great importance of acyl hydrazides in organic chemistry. Herein, we report an inexpensive and green photochemical approach, where light irradiation (390 nm) significantly accelerates the reaction between dialkyl azodicarboxylates and aldehydes, while water is employed as the solvent. A variety of aromatic and aliphatic aldehydes were converted into their corresponding acyl hydrazides in good to excellent yields in really short reaction times (15-210 min) and the reaction mechanism was also studied. Applications of this reaction in the syntheses of Vorinostat and Moclobemide were demonstrated.
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Affiliation(s)
- Naya A Stini
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Efthymios T Poursaitidis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Nikolaos F Nikitas
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Michail Kartsinis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Nikoleta Spiliopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Phoebe Ananida-Dasenaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
| | - Christoforos G Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis 15771, Athens, Greece.
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15
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Nasiri A, Mokhtari S, Daraei B, Yazdanpanah H, Faizi M, Kobarfard F. A Neglected Challenge in the Analysis of Active Pharmaceutical Substances with Aldehyde Functional Group in Aqueous Matrices. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2022; 21:e127036. [PMID: 36060912 PMCID: PMC9420214 DOI: 10.5812/ijpr-127036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/05/2022] [Indexed: 06/15/2023]
Abstract
Aldehydes are compounds that are widely used and popular in organic synthesis due to their high reactivity. This advantage is a disadvantage in medicinal chemistry. Due to the ability of aldehydes to participate in nucleophilic reactions (especially in aqueous biological media) and access to nucleophiles such as amino acids and nucleic acids, drugs with aldehyde functional groups are always used with caution and carefully quantified in biological fluids. Our experience in working on biologically active aldehydes indicates the transformation of these groups of compounds in aqueous or alcoholic solution and thus the failure of analytical methods for their accurate monitoring in such media. Both mass spectrometry and Proton nuclear magnetic resonance spectroscopic findings indicate the reaction of spiramycin with water molecules in an aqueous solution, resulting in the conversion of spiramycin to a new molecule with 18 mass unit difference and thus, the residue amount which is measured and reported based on a mass spectrometries method does not show the correct amount of spiramycin in these samples.
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Affiliation(s)
- Azadeh Nasiri
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Food Safety Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaya Mokhtari
- Central Research Laboratories, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Daraei
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Yazdanpanah
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Food Safety Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad Faizi
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Kobarfard
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Central Research Laboratories, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Yang T, Cuesta A, Wan X, Craven GB, Hirakawa B, Khamphavong P, May JR, Kath JC, Lapek JD, Niessen S, Burlingame AL, Carelli JD, Taunton J. Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Nat Chem Biol 2022; 18:934-941. [PMID: 35590003 PMCID: PMC9970282 DOI: 10.1038/s41589-022-01019-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022]
Abstract
The expansion of the target landscape of covalent inhibitors requires the engagement of nucleophiles beyond cysteine. Although the conserved catalytic lysine in protein kinases is an attractive candidate for a covalent approach, selectivity remains an obvious challenge. Moreover, few covalent inhibitors have been shown to engage the kinase catalytic lysine in animals. We hypothesized that reversible, lysine-targeted inhibitors could provide sustained kinase engagement in vivo, with selectivity driven in part by differences in residence time. By strategically linking benzaldehydes to a promiscuous kinase binding scaffold, we developed chemoproteomic probes that reversibly and covalently engage >200 protein kinases in cells and mice. Probe-kinase residence time was dramatically enhanced by a hydroxyl group ortho to the aldehyde. Remarkably, only a few kinases, including Aurora A, showed sustained, quasi-irreversible occupancy in vivo, the structural basis for which was revealed by X-ray crystallography. We anticipate broad application of salicylaldehyde-based probes to proteins that lack a druggable cysteine.
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Affiliation(s)
- Tangpo Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Gregory B. Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Brad Hirakawa
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Penney Khamphavong
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jeffrey R. May
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John C. Kath
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John D. Lapek
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Sherry Niessen
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jordan D. Carelli
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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17
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Vankadara S, Dawson MD, Fong JY, Oh QY, Ang QA, Liu B, Chang HY, Koh J, Koh X, Tan QW, Joy J, Chia CSB. A Warhead Substitution Study on the Coronavirus Main Protease Inhibitor Nirmatrelvir. ACS Med Chem Lett 2022; 13:1345-1350. [PMID: 35971455 PMCID: PMC9331150 DOI: 10.1021/acsmedchemlett.2c00260] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 01/08/2023] Open
Abstract
![]()
The SARS-CoV-2 pandemic is currently causing an unprecedented
global
health emergency since its emergence in December 2019. In December
2021, the FDA granted emergency use authorization to nirmatrelvir,
a SARS-CoV-2 main protease inhibitor, for treating infected patients.
This peptidomimetic is designed with a nitrile warhead, which forms
a covalent bond to the viral protease. Herein, we investigate nirmatrelvir
analogs with different warheads and their inhibitory activities. In
addition, antiviral activities against human alphacoronavirus 229E
was also investigated along with a cell-based assay. We discovered
that the hydroxymethylketone and ketobenzothiazole warheads were equipotent
to the nitrile warhead, suggesting that these analogs can also be
used for treating coronavirus infections.
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Affiliation(s)
- Subramanyam Vankadara
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | | | - Jia Yi Fong
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Qin Yao Oh
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Qi An Ang
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Boping Liu
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Hong Yun Chang
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Judice Koh
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Xiaoying Koh
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Qian Wen Tan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Joma Joy
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
| | - Cheng San Brian Chia
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, 138670 Singapore
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18
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Zhu J, Li L, Drelich A, Chenna BC, Mellott DM, Taylor ZW, Tat V, Garcia CZ, Katzfuss A, Tseng CTK, Meek TD. Self-Masked Aldehyde Inhibitors of Human Cathepsin L Are Potent Anti-CoV-2 Agents. Front Chem 2022; 10:867928. [PMID: 35860632 PMCID: PMC9291521 DOI: 10.3389/fchem.2022.867928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine proteases comprise an important class of drug targets, especially for infectious diseases such as Chagas disease (cruzain) and COVID-19 (3CL protease, cathepsin L). Peptide aldehydes have proven to be potent inhibitors for all of these proteases. However, the intrinsic, high electrophilicity of the aldehyde group is associated with safety concerns and metabolic instability, limiting the use of aldehyde inhibitors as drugs. We have developed a novel class of compounds, self-masked aldehyde inhibitors (SMAIs) which are based on the dipeptide aldehyde inhibitor (Cbz-Phe-Phe-CHO, 1), for which the P1 Phe group contains a 1′-hydroxy group, effectively, an o-tyrosinyl aldehyde (Cbz-Phe-o-Tyr-CHO, 2; (Li et al. (2021) J. Med. Chem. 64, 11,267–11,287)). Compound 2 and other SMAIs exist in aqueous mixtures as stable δ-lactols, and apparent catalysis by the cysteine protease cruzain, the major cysteine protease of Trypanosoma cruzi, results in the opening of the lactol ring to afford the aldehydes which then form reversible thiohemiacetals with the enzyme. These SMAIs are also potent, time-dependent inhibitors of human cathepsin L (Ki = 11–60 nM), an enzyme which shares 36% amino acid identity with cruzain. As inactivators of cathepsin L have recently been shown to be potent anti-SARS-CoV-2 agents in infected mammalian cells (Mellott et al. (2021) ACS Chem. Biol. 16, 642–650), we evaluated SMAIs in VeroE6 and A549/ACE2 cells infected with SARS-CoV-2. These SMAIs demonstrated potent anti-SARS-CoV-2 activity with values of EC50 = 2–8 μM. We also synthesized pro-drug forms of the SMAIs in which the hydroxyl groups of the lactols were O-acylated. Such pro-drug SMAIs resulted in significantly enhanced anti-SARS-CoV-2 activity (EC50 = 0.3–0.6 μM), demonstrating that the O-acylated-SMAIs afforded a level of stability within infected cells, and are likely converted to SMAIs by the action of cellular esterases. Lastly, we prepared and characterized an SMAI in which the sidechain adjacent to the terminal aldehyde is a 2-pyridonyl-alanine group, a mimic of both phenylalanine and glutamine. This compound (9) inhibited both cathepsin L and 3CL protease at low nanomolar concentrations, and also exerted anti-CoV-2 activity in an infected human cell line.
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Affiliation(s)
- Jiyun Zhu
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Linfeng Li
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Bala C. Chenna
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Drake M. Mellott
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Zane W. Taylor
- Department of Chemistry, College of Science, Texas A&M University College Station, College Station, TX, United States
| | - Vivian Tat
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Christopher Z. Garcia
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
- *Correspondence: Thomas D. Meek,
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19
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Liu Y, Wang L, Zhao L, Zhang Y. Structure, properties of gossypol and its derivatives-from physiological activities to drug discovery and drug design. Nat Prod Rep 2022; 39:1282-1304. [PMID: 35587693 DOI: 10.1039/d1np00080b] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Covering up to 2022Gossypol is a polyphenolic compound isolated from cottonseed. There are two optical enantiomers of gossypol, (-)-gossypol and (+)-gossypol. Gossypol exists as three different tautomers, aldehyde, ketone and lactol. Gossypol is toxic and provides a protective mechanism for cotton plants against pests. Gossypol was used as a male contraceptive in China in the 1970s. It was eventually abandoned due to noticeable side effects, disruption of potassium uptake and incomplete reversibility. Gossypol has gained considerable research interest due to its attractive biological activities, especially antitumor and antivirus. Gossypol derivatives are prepared by a structural modification to reduce toxicity and improve their therapeutic effect. This review depicts the bioactivity and regulation mechanisms of gossypol and its derivatives as drug lead compounds, with emphasis on its antitumor mechanism. The design and synthesis of pharmacologically active derivatives based on the structure of gossypol, such as gossypol Schiff bases, apogossypol, gossypolone, are thoroughly discussed. This review aims to serve as a reference for gossypol-based drug discovery and drug design.
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Affiliation(s)
- Yanxia Liu
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Lulu Wang
- State Key Laboratory of Chemistry and Utilization of Carbon-based Energy Resource, School of Chemistry and Chemical Engineering, Xinjiang University, Urumqi, China
| | - Lin Zhao
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Yagang Zhang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China.
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20
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Zhang Z, Wang Y, Chen X, Song X, Tu Z, Chen Y, Zhang Z, Ding K. Characterization of an aromatic trifluoromethyl ketone as a new warhead for covalently reversible kinase inhibitor design. Bioorg Med Chem 2021; 50:116457. [PMID: 34670167 DOI: 10.1016/j.bmc.2021.116457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
An aromatic trifluoromethyl ketone moiety was characterized as a new warhead for covalently reversible kinase inhibitor design to target the non-catalytic cysteine residue. Potent and selective covalently reversible inhibitors of FGFR4 kinase were successfully designed and synthesized by utilizing this new warhead. The binding mode of a representative inhibitor was fully characterized by using multiple technologies including MALDI-TOF mass spectrometry, dialysis assay and X-ray crystallographic studies etc. This functional group was also successfully applied to discovery of a new JAK3 inhibitor, suggesting its potential application in designing other kinase inhibitors.
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Affiliation(s)
- Zhen Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yongjin Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Song
- Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; Drug Discovery Pipeline & Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Guangzhou 510530, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhimin Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of PR China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; The First Affiliated Hospital, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
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21
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Shen J, Jiang X, Wu H, Xu J, Zhu Q, Zhang P. Copper-catalyzed selective oxidation of hydrazones through C(sp 3)-H functionalization. Org Biomol Chem 2021; 19:8917-8923. [PMID: 34617555 DOI: 10.1039/d1ob01563j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A simple and mild protocol for copper-catalyzed oxidation of hydrazones at the α-position has been reported. Various substrates are compatible, providing the corresponding products in moderate to good yields. This strategy provides an efficient and convenient solution for the synthesis of carbonyl hydrazone. A free radical pathway mechanism is suggested for the transformation.
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Affiliation(s)
- Jiabin Shen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China. .,College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, People's Republic of China.
| | - Xiaoying Jiang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, People's Republic of China. .,College of Chemistry and Chemical Engineering, Central south University, Changsha, 410083, P.R. China
| | - Haifeng Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China. .,College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, People's Republic of China.
| | - Jun Xu
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, People's Republic of China.
| | - Qing Zhu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Pengfei Zhang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, People's Republic of China.
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22
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Chia CSB, Xu W, Shuyi Ng P. A Patent Review on SARS Coronavirus Main Protease (3CL pro ) Inhibitors. ChemMedChem 2021; 17:e202100576. [PMID: 34651447 PMCID: PMC8653044 DOI: 10.1002/cmdc.202100576] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/11/2021] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic is an unprecedented global health emergency causing more than 4.2 million fatalities as of 30 July 2021. Only three antiviral therapies have been approved or granted emergency use authorization by the FDA. The SARS‐CoV‐2 3CL protease (3CLpro) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis, although no inhibitors have been approved. This patent review discusses SARS coronavirus 3CLpro inhibitors that have been filed up to 30 July 2021, giving an overview on the types of inhibitors that have generated commercial interest, especially amongst drug companies. Insights into the common structural motifs required for active site binding is also discussed.
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Affiliation(s)
- C S Brian Chia
- Experimental Drug Development Centre, 10 Biopolis Road, 138670, Chromos #08-01, Singapore
| | - Weijun Xu
- Experimental Drug Development Centre, 10 Biopolis Road, 138670, Chromos #08-01, Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, 138670, Chromos #08-01, Singapore
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23
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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24
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DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors. Proc Natl Acad Sci U S A 2021; 118:2111172118. [PMID: 34426525 PMCID: PMC8433497 DOI: 10.1073/pnas.2111172118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed more than 4 million humans globally, but there is no bona fide Food and Drug Administration-approved drug-like molecule to impede the COVID-19 pandemic. The sluggish pace of traditional therapeutic discovery is poorly suited to producing targeted treatments against rapidly evolving viruses. Here, we used an affinity-based screen of 4 billion DNA-encoded molecules en masse to identify a potent class of virus-specific inhibitors of the SARS-CoV-2 main protease (Mpro) without extensive and time-consuming medicinal chemistry. CDD-1714, the initial three-building-block screening hit (molecular weight [MW] = 542.5 g/mol), was a potent inhibitor (inhibition constant [K i] = 20 nM). CDD-1713, a smaller two-building-block analog (MW = 353.3 g/mol) of CDD-1714, is a reversible covalent inhibitor of Mpro (K i = 45 nM) that binds in the protease pocket, has specificity over human proteases, and shows in vitro efficacy in a SARS-CoV-2 infectivity model. Subsequently, key regions of CDD-1713 that were necessary for inhibitory activity were identified and a potent (K i = 37 nM), smaller (MW = 323.4 g/mol), and metabolically more stable analog (CDD-1976) was generated. Thus, screening of DNA-encoded chemical libraries can accelerate the discovery of efficacious drug-like inhibitors of emerging viral disease targets.
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25
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Li L, Chenna BC, Yang KS, Cole TR, Goodall ZT, Giardini M, Moghadamchargari Z, Hernandez EA, Gomez J, Calvet CM, Bernatchez JA, Mellott DM, Zhu J, Rademacher A, Thomas D, Blankenship LR, Drelich A, Laganowsky A, Tseng CTK, Liu WR, Wand AJ, Cruz-Reyes J, Siqueira-Neto JL, Meek TD. Self-Masked Aldehyde Inhibitors: A Novel Strategy for Inhibiting Cysteine Proteases. J Med Chem 2021; 64:11267-11287. [PMID: 34288674 PMCID: PMC10504874 DOI: 10.1021/acs.jmedchem.1c00628] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine proteases comprise an important class of drug targets, especially for infectious diseases such as Chagas disease (cruzain) and COVID-19 (3CL protease, cathepsin L). Peptide aldehydes have proven to be potent inhibitors for all of these proteases. However, the intrinsic, high electrophilicity of the aldehyde group is associated with safety concerns and metabolic instability, limiting the use of aldehyde inhibitors as drugs. We have developed a novel class of self-masked aldehyde inhibitors (SMAIs) for cruzain, the major cysteine protease of the causative agent of Chagas disease-Trypanosoma cruzi. These SMAIs exerted potent, reversible inhibition of cruzain (Ki* = 18-350 nM) while apparently protecting the free aldehyde in cell-based assays. We synthesized prodrugs of the SMAIs that could potentially improve their pharmacokinetic properties. We also elucidated the kinetic and chemical mechanism of SMAIs and applied this strategy to the design of anti-SARS-CoV-2 inhibitors.
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Affiliation(s)
- Linfeng Li
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Bala C Chenna
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Kai S Yang
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Zachary T Goodall
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Miriam Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Elizabeth A Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jana Gomez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Claudia M Calvet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Jean A Bernatchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jiyun Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Andrew Rademacher
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Diane Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Lauren R Blankenship
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Wenshe R Liu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
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26
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Dampalla CS, Kim Y, Bickmeier N, Rathnayake AD, Nguyen HN, Zheng J, Kashipathy MM, Baird MA, Battaile KP, Lovell S, Perlman S, Chang KO, Groutas WC. Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease. J Med Chem 2021; 64:10047-10058. [PMID: 34213885 PMCID: PMC8276672 DOI: 10.1021/acs.jmedchem.1c00319] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Indexed: 12/12/2022]
Abstract
A series of nondeuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally constrained cyclohexane moiety was synthesized and found to potently inhibit severe acute respiratory syndrome coronavirus-2 3CL protease in biochemical and cell-based assays. Several of the inhibitors were also found to be nanomolar inhibitors of Middle East respiratory syndrome coronavirus 3CL protease. The corresponding latent aldehyde bisulfite adducts were found to be equipotent to the precursor aldehydes. High-resolution cocrystal structures confirmed the mechanism of action and illuminated the structural determinants involved in binding. The spatial disposition of the compounds disclosed herein provides an effective means of accessing new chemical space and optimizing pharmacological activity. The cellular permeability of the identified inhibitors and lack of cytotoxicity warrant their advancement as potential therapeutics for COVID-19.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Naemi Bickmeier
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Athri D. Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | | - Matthew A. Baird
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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27
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Vankadara S, Wong YX, Liu B, See YY, Tan LH, Tan QW, Wang G, Karuna R, Guo X, Tan ST, Fong JY, Joy J, Chia CSB. A head-to-head comparison of the inhibitory activities of 15 peptidomimetic SARS-CoV-2 3CLpro inhibitors. Bioorg Med Chem Lett 2021; 48:128263. [PMID: 34271072 PMCID: PMC8277557 DOI: 10.1016/j.bmcl.2021.128263] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/03/2021] [Accepted: 07/11/2021] [Indexed: 02/08/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has created an unprecedented global health emergency. As of July 2021, only three antiviral therapies have been approved by the FDA for treating infected patients, highlighting the urgent need for more antiviral drugs. The SARS-CoV-2 3CL protease (3CLpro) is deemed an attractive drug target due to its essential role in viral polyprotein processing and pathogenesis. Indeed, a number of peptidomimetic 3CLpro inhibitors armed with electrophilic warheads have been reported by various research groups that can potentially be developed for treating COVID-19. However, it is currently impossible to compare their relative potencies due to the different assays employed. To solve this, we conducted a head-to-head comparison of fifteen reported peptidomimetic inhibitors in a standard FRET-based SARS-CoV-2 3CLpro inhibition assay to compare and identify potent inhibitors for development. Inhibitor design and the suitability of various warheads are also discussed.
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Affiliation(s)
- Subramanyam Vankadara
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Yun Xuan Wong
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Boping Liu
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Yi Yang See
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Li Hong Tan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Qian Wen Tan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Gang Wang
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Ratna Karuna
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Xue Guo
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Shu Ting Tan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Jia Yi Fong
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - Joma Joy
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore
| | - C S Brian Chia
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos #08-01, Singapore 138670, Singapore.
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28
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Serafini M, Cargnin S, Massarotti A, Tron GC, Pirali T, Genazzani AA. What's in a Name? Drug Nomenclature and Medicinal Chemistry Trends using INN Publications. J Med Chem 2021; 64:4410-4429. [PMID: 33847110 PMCID: PMC8154580 DOI: 10.1021/acs.jmedchem.1c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 12/13/2022]
Abstract
The World Health Organization assigns international nonproprietary names (INN), also known as common names, to compounds upon request from drug developers. Structures of INNs are publicly available and represent a source, albeit underused, to understand trends in drug research and development. Here, we explain how a common drug name is composed and analyze chemical entities from 2000 to 2021. In the analysis, we describe some changes that intertwine chemical structure, newer therapeutic targets (e.g., kinases), including a significant increase in the use of fluorine and of heterocycles, and some other evolutionary modifications, such as the progressive increase in molecular weight. Alongside these, small signs of change can be spotted, such as the rise in spirocyclic scaffolds and small rings and the emergence of unconventional structural moieties that might forecast the future to come.
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Affiliation(s)
| | | | | | - Gian Cesare Tron
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Tracey Pirali
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Armando A. Genazzani
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
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29
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Qiao J, Li YS, Zeng R, Liu FL, Luo RH, Huang C, Wang YF, Zhang J, Quan B, Shen C, Mao X, Liu X, Sun W, Yang W, Ni X, Wang K, Xu L, Duan ZL, Zou QC, Zhang HL, Qu W, Long YHP, Li MH, Yang RC, Liu X, You J, Zhou Y, Yao R, Li WP, Liu JM, Chen P, Liu Y, Lin GF, Yang X, Zou J, Li L, Hu Y, Lu GW, Li WM, Wei YQ, Zheng YT, Lei J, Yang S. SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Science 2021; 371:1374-1378. [PMID: 33602867 PMCID: PMC8099175 DOI: 10.1126/science.abf1611] [Citation(s) in RCA: 303] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/12/2021] [Indexed: 02/05/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing Mpro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 Mpro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of Mpro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.
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Affiliation(s)
- Jingxin Qiao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yue-Shan Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Zeng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng-Liang Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Chong Huang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi-Fei Wang
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoxue Quan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenjian Shen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Mao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xinlei Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Weining Sun
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xincheng Ni
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Kai Wang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Zi-Lei Duan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Hai-Lin Zhang
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wang Qu
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Yang-Hao-Peng Long
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Rui-Cheng Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaolong Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing You
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yangli Zhou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Yao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wen-Pei Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing-Ming Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Pei Chen
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Gui-Feng Lin
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jun Zou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yiguo Hu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Guang-Wen Lu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei-Min Li
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. .,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Jian Lei
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. .,National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Lentini NA, Schroeder CM, Harmon NM, Huang X, Schladetsch MA, Foust BJ, Poe MM, Hsiao CHC, Wiemer AJ, Wiemer DF. Synthesis and Metabolism of BTN3A1 Ligands: Studies on Modifications of the Allylic Alcohol. ACS Med Chem Lett 2021; 12:136-142. [PMID: 33488975 DOI: 10.1021/acsmedchemlett.0c00586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
(E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) and its phosphonate analogs are potent phosphoantigens. HMBPP contains an (E)-allylic alcohol which interacts with the molecular target BTN3A1 giving an antigenic signal to activate Vγ9Vδ2 T cells. As probes of BTN3A1 function, we prepared prodrug derivatives of the HMBPP analog C-HMBP that lack the (E)-allylic alcohol or have modified it to an aldehyde or aldoxime and evaluated their biological activity. Removal of the alcohol completely abrogates phosphoantigenicity in these compounds while the aldoxime modification decreases potency relative to the (E)-allylic alcohol form. However, homoprenyl derivatives oxidized to an aldehyde stimulate Vγ9Vδ2 T cells at nanomolar concentrations. Selection of phosphonate protecting groups (i.e., prodrug forms) impacts the potency of phosphoantigen aldehydes, with mixed aryl acyloxyalkyl forms exhibiting superior activity relative to aryl amidate forms. The activity correlates with the cellular reduction of the aldehyde to the alcohol form. Thus, the functionality on this ligand framework can be altered concurrently with phosphonate protection to promote cellular transformation to highly potent phosphoantigens.
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Affiliation(s)
- Nicholas A. Lentini
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Chloe M. Schroeder
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Nyema M. Harmon
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Xueting Huang
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092,United States
| | - Megan A. Schladetsch
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092,United States
| | - Benjamin J. Foust
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Michael M. Poe
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Chia-Hung Christine Hsiao
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092,United States
| | - Andrew J. Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092,United States
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269-3092, United States
| | - David F. Wiemer
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242-1109, United States
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