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Patil BR, Bhadane KV, Ahmad I, Agrawal YJ, Shimpi AA, Dhangar MS, Patel HM. Exploring the structural activity relationship of the Osimertinib: A covalent inhibitor of double mutant EGFR L858R/T790M tyrosine kinase for the treatment of Non-Small Cell Lung Cancer (NSCLC). Bioorg Med Chem 2024; 109:117796. [PMID: 38879996 DOI: 10.1016/j.bmc.2024.117796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/13/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
The USFDA granted regular approval to Osimertinib (AZD9291) on March 2017, for treating individuals with metastatic Non-Small Cell Lung Cancer having EGFR T790M mutation. Clinically, Osimertinib stands at the forefront for the treatment of patients with Non-Small Cell Lung Cancer. Osimertinib forms a covalent bond with the Cys797 residue and predominantly spares binding to WT-EGFR, thereby reducing toxicity and enabling the administration of doses that effectively inhibit T790M. However, a high percentage of patients treated with Osimertinib (AZD9291) developed a tertiary cysteine797 to serine797 (C797S) mutation in the EGFR kinase domain, rendering resistance to it. This comprehensive review sheds light on the chemistry, computational aspects, structural features, and expansive spectrum of biological activities of Osimertinib and its analogues. The in-depth exploration of these facets serves as a valuable resource for medicinal chemists, empowering them to design better Osimertinib analogues. This exhaustive study not only provides insights into improving potency but also emphasizes considerations for mutant selectivity and optimizing pharmacokinetic properties. This review acts as a guiding beacon for the strategic design and development of next-generation Osimertinib analogues.
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Affiliation(s)
- Bhatu R Patil
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Kunal V Bhadane
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Yogesh J Agrawal
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Amit A Shimpi
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Mayur S Dhangar
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India.
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2
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Tin G, Cigler M, Hinterndorfer M, Dong KD, Imrichova H, Gygi SP, Winter GE. Discovery of a DCAF11-dependent cyanoacrylamide-containing covalent degrader of BET-proteins. Bioorg Med Chem Lett 2024; 107:129779. [PMID: 38729317 DOI: 10.1016/j.bmcl.2024.129779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Targeted protein degradation is mediated by small molecules that induce or stabilize protein-protein interactions between targets and the ubiquitin-proteasome machinery. Currently, there remains a need to expand the repertoire of viable E3 ligases available for hijacking. Notably, covalent chemistry has been employed to engage a handful of E3 ligases, including DCAF11. Here, we disclose a covalent PROTAC that enables DCAF11-dependent degradation, featuring a cyanoacrylamide warhead. Our findings underscore DCAF11 as an interesting candidate with a capacity to accommodate diverse electrophilic chemistries compatible with targeted protein degradation.
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Affiliation(s)
- Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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3
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Chiodi D, Ishihara Y. The role of the methoxy group in approved drugs. Eur J Med Chem 2024; 273:116364. [PMID: 38781921 DOI: 10.1016/j.ejmech.2024.116364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 05/25/2024]
Abstract
The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, Takeda Pharmaceuticals, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, 92121, USA.
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4
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Liu C, Zhang H. Data processing for high-throughput mass spectrometry in drug discovery. Expert Opin Drug Discov 2024; 19:815-825. [PMID: 38785418 DOI: 10.1080/17460441.2024.2354871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION High-throughput mass spectrometry that could deliver > 10 times faster sample readout speed than traditional LC-based platforms has emerged as a powerful analytical technique, enabling the rapid analysis of complex biological samples. This increased speed of MS data acquisition has brought a critical demand for automatic data processing capabilities that should match or surpass the speed of data acquisition. Those data processing capabilities should serve the different requirements of drug discovery workflows. AREAS COVERED This paper introduced the key steps of the automatic data processing workflows for high-throughput MS technologies. Specific examples and requirements are detailed for different drug discovery applications. EXPERT OPINION The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications.
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Affiliation(s)
| | - Hui Zhang
- Iambic Therapeutics, San Diego, CA, USA
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5
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Samuel Rajan IAP, Rajendran S. DABCO-catalyzed esterification of N-pivaloyl-activated amides. Org Biomol Chem 2024; 22:5170-5180. [PMID: 38864233 DOI: 10.1039/d4ob00752b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
A previously elusive organocatalytic protocol for the esterification of amides is disclosed. DABCO (10 mol%) is identified as an effective catalyst for the esterification of N-pivaloyl amides. Although N-pivaloyl amides are nearly planar (amide bond twist (τ) = 4.54° and pyramidalization (χN = 6.39°)) and resonance stabilized, esterification is achieved with high efficiency. The developed protocol is generic, phenols, thiophenols, aliphatic alcohols, and thiols were identified as effective substrates. Furthermore, the reaction features a broad substrate scope and excellent functional group tolerance. To exemplify the practical applicability of the developed protocol, the esterification of bioactive natural products, pterostilbene and menthol, is demonstrated. In addition, a series of competitive experiments were conducted to establish the reactivity pattern of alcohols, thiols, and phenols, which could serve as selectivity principles for future synthetic design. Our findings signify a notable advancement in utilizing amides as versatile synthetic building blocks in organic synthesis under metal-free conditions.
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Affiliation(s)
- Ida Angel Priya Samuel Rajan
- Dept. of Chemistry, Vellore Institute of Technology Chennai Campus, Vandalur-Kelambakkam Road, Chennai - 600127, Tamil Nadu, India.
| | - Saravanakumar Rajendran
- Dept. of Chemistry, Vellore Institute of Technology Chennai Campus, Vandalur-Kelambakkam Road, Chennai - 600127, Tamil Nadu, India.
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Lucas SCC, Milbradt AG, Blackwell JH, Bonomo S, Brierley A, Cassar DJ, Freeman J, Hadfield TE, Morrill LA, Riemens R, Sarda S, Schiesser S, Wiktelius D, Ahmed S, Bostock MJ, Börjesson U, De Fusco C, Guerot C, Hargreaves D, Hewitt S, Lamb ML, Su N, Whatling R, Wheeler M, Kettle JG. Design of a Lead-Like Cysteine-Targeting Covalent Library and the Identification of Hits to Cys55 of Bfl-1. J Med Chem 2024. [PMID: 38916990 DOI: 10.1021/acs.jmedchem.4c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Covalent hit identification is a viable approach to identify chemical starting points against difficult-to-drug targets. While most researchers screen libraries of <2k electrophilic fragments, focusing on lead-like compounds can be advantageous in terms of finding hits with improved affinity and with a better chance of identifying cryptic pockets. However, due to the increased molecular complexity, larger numbers of compounds (>10k) are desirable to ensure adequate coverage of chemical space. Herein, the approach taken to build a library of 12k covalent lead-like compounds is reported, utilizing legacy compounds, robust library chemistry, and acquisitions. The lead-like covalent library was screened against the antiapoptotic protein Bfl-1, and six promising hits that displaced the BIM peptide from the PPI interface were identified. Intriguingly, X-ray crystallography of lead-like compound 8 showed that it binds to a previously unobserved conformation of the Bfl-1 protein and is an ideal starting point for the optimization of Bfl-1 inhibitors.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - J Henry Blackwell
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Silvia Bonomo
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andrew Brierley
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Doyle J Cassar
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jared Freeman
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolic Disorders (CVRM), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Thomas E Hadfield
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Lucas A Morrill
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Rick Riemens
- Medicinal Chemistry, Oncology R&D, Acerta B. V., a Part of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Sunil Sarda
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Stefan Schiesser
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Daniel Wiktelius
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Samiyah Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Claudia De Fusco
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Carine Guerot
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - David Hargreaves
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Sarah Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Michelle L Lamb
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nancy Su
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Ryan Whatling
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthew Wheeler
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jason G Kettle
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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7
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Lou J, Zhou Q, Lyu X, Cen X, Liu C, Yan Z, Li Y, Tang H, Liu Q, Ding J, Lu Y, Huang H, Xie H, Zhao Y. Discovery of a Covalent Inhibitor That Overcame Resistance to Venetoclax in AML Cells Overexpressing BFL-1. J Med Chem 2024. [PMID: 38913996 DOI: 10.1021/acs.jmedchem.4c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Clinical and biological studies have shown that overexpression of BFL-1 is one contributing factor to venetoclax resistance. The resistance might be overcome by a potent BFL-1 inhibitor, but such an inhibitor is rare. In this study, we show that 56, featuring an acrylamide moiety, inhibited the BFL-1/BID interaction with a Ki value of 105 nM. More interestingly, 56 formed an irreversible conjugation adduct at the C55 residue of BFL-1. 56 was a selective BFL-1 inhibitor, and its MCL-1 binding affinity was 10-fold weaker, while it did not bind BCL-2 and BCL-xL. Mechanistic studies showed that 56 overcame venetoclax resistance in isogenic AML cell lines MOLM-13-OE and MV4-11-OE, which both overexpressed BFL-1. More importantly, 56 and venetoclax combination promoted stronger apoptosis induction than either single agent. Collectively, our data show that 56 overcame resistance to venetoclax in AML cells overexpressing BFL-1. These attributes make 56 a promising candidate for future optimization.
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Affiliation(s)
- Jianfeng Lou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qianqian Zhou
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Xinyi Cen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Yan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Haotian Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Qiupei Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Jian Ding
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Ye Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - He Huang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hua Xie
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
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8
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Raouf YS. Covalent Inhibitors: To Infinity and Beyond. J Med Chem 2024. [PMID: 38913822 DOI: 10.1021/acs.jmedchem.4c01308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Affiliation(s)
- Yasir S Raouf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE
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9
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Robinson SA, Co JA, Banik SM. Molecular glues and induced proximity: An evolution of tools and discovery. Cell Chem Biol 2024; 31:1089-1100. [PMID: 38688281 DOI: 10.1016/j.chembiol.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.
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Affiliation(s)
| | | | - Steven Mark Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
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10
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Zimmermann T, Feng J, de Campos LJ, Knight LA, Schlötzer J, Ramirez YA, Schwickert K, Zehe M, Adler TB, Schirmeister T, Kisker C, Sotriffer C, Conda-Sheridan M, Decker M. Structure-Based Design and Synthesis of Covalent Inhibitors for Deubiquitinase and Acetyltransferase ChlaDUB1 of Chlamydia trachomatis. J Med Chem 2024. [PMID: 38897928 DOI: 10.1021/acs.jmedchem.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Upon infection by an intracellular pathogen, host cells activate apoptotic pathways to limit pathogen replication. Consequently, efficient proliferation of the obligate intracellular pathogen Chlamydia trachomatis, a major cause of trachoma and sexually transmitted diseases, depends on the suppression of host cell apoptosis. C. trachomatis secretes deubiquitinase ChlaDUB1 into the host cell, leading among other interactions to the stabilization of antiapoptotic proteins and, thus, suppression of host cell apoptosis. Targeting the bacterial effector protein may, therefore, lead to new therapeutic possibilities. To explore the active site of ChlaDUB1, an iterative cycle of computational docking, synthesis, and enzymatic screening was applied with the aim of lead structure development. Hereby, covalent inhibitors were developed, which show enhanced inhibition with a 22-fold increase in IC50 values compared to previous work. Comprehensive insights into the binding prerequisites to ChlaDUB1 are provided, establishing the foundation for an additional specific antichlamydial therapy by small molecules.
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Affiliation(s)
- Thomas Zimmermann
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Jiachen Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Luana Janaína de Campos
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Lindsey A Knight
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jan Schlötzer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, Julius-Maximilians-Universität Würzburg (JMU), 97080 Wurzburg, Germany
| | - Yesid A Ramirez
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Markus Zehe
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Thomas B Adler
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, Julius-Maximilians-Universität Würzburg (JMU), 97080 Wurzburg, Germany
| | - Christoph Sotriffer
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Michael Decker
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
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11
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Ren X, Li H, Peng H, Yang Y, Su H, Huang C, Wang X, Zhang J, Liu Z, Wei W, Cheng K, Zhu T, Lu Z, Li Z, Zhao Q, Tang BZ, Yao SQ, Song X, Sun H. Reactivity-Tunable Fluorescent Platform for Selective and Biocompatible Modification of Cysteine or Lysine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402838. [PMID: 38896788 DOI: 10.1002/advs.202402838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Chemoselective modification of specific residues within a given protein poses a significant challenge, as the microenvironment of amino acid residues in proteins is variable. Developing a universal molecular platform with tunable chemical warheads can provide powerful tools for precisely labeling specific amino acids in proteins. Cysteine and lysine are hot targets for chemoselective modification, but current cysteine/lysine-selective warheads face challenges due to cross-reactivity and unstable reaction products. In this study, a versatile fluorescent platform is developed for highly selective modification of cysteine/lysine under biocompatible conditions. Chloro- or phenoxy-substituted NBSe derivatives effectively labeled cysteine residues in the cellular proteome with high specificity. This finding also led to the development of phenoxy-NBSe phototheragnostic for the diagnosis and activatable photodynamic therapy of GSH-overexpressed cancer cells. Conversely, alkoxy-NBSe derivatives are engineered to selectively react with lysine residues in the cellular environment, exhibiting excellent anti-interfering ability against thiols. Leveraging a proximity-driven approach, alkoxy-NBSe probes are successfully designed to demonstrate their utility in bioimaging of lysine deacetylase activity. This study also achieves integrating a small photosensitizer into lysine residues of proteins in a regioselective manner, achieving photoablation of cancer cells activated by overexpressed proteins.
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Affiliation(s)
- Xiaojie Ren
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Haokun Li
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Hui Peng
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Yang Yang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, China
| | - Hang Su
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Chen Huang
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Xuan Wang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Zhang
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Zhiyang Liu
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Wenyu Wei
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Ke Cheng
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Tianyang Zhu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, China
| | - Zhenpin Lu
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, 999077, China
| | - Ben Zhong Tang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Xiangzhi Song
- College of Chemistry & Chemical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Hongyan Sun
- Department of Chemistry and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
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12
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024:10.1038/s41573-024-00958-9. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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13
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Song Q, Zhang Q, Fan X, Kayaat F, Lv R, Li J, Wang Y. The discovery of novel imidazo[1,2- a]pyridine derivatives as covalent anticancer agents. Org Biomol Chem 2024. [PMID: 38869445 DOI: 10.1039/d4ob00694a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The success of targeted covalent inhibitors (TCIs) for treating cancers has spurred the search for novel scaffolds to install covalent warheads. In our endeavour, using a scaffold hopping strategy, we managed to utilize imidazo[1,2-a]pyridine as the core backbone and explored its potential for the development of covalent inhibitors, therefore, synthesizing a series of novel KRAS G12C inhibitors facilitated by the Groebke-Blackburn-Bienaymè reaction (GBB reaction). Preliminary bio-evaluation screening delivered compound I-11 as a potent anticancer agent for KRAS G12C-mutated NCI-H358 cells, whose effects were further clarified by a series of cellular, biochemical, and molecular docking experiments. These results not only indicate the potential of compound I-11 as a lead compound for the treatment of intractable cancers, but also validate the unique role of imidazo[1,2-a]pyridine as a novel scaffold suitable for the discovery of covalent anticancer agents.
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Affiliation(s)
- Qin Song
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Qianer Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Xuejing Fan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Fatmata Kayaat
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Ruicheng Lv
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
| | - Yong Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, Qingdao 26003, Shandong, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, P. R. China
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14
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Zhang J, Wang X, Huang Q, Ye J, Wang J. Genetically Encoded Epoxide Warhead for Precise and Versatile Covalent Targeting of Proteins. J Am Chem Soc 2024; 146:16173-16183. [PMID: 38819260 PMCID: PMC11177858 DOI: 10.1021/jacs.4c03974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
Genetically encoding a proximal reactive warhead into the protein binder/drug has emerged as an efficient strategy for covalently binding to protein targets, enabling broad applications. To expand the reactivity scope for targeting the diverse natural residues under physiological conditions, the development of a genetically encoded reactive warhead with excellent stability and broad reactivity is highly desired. Herein, we reported the genetic encoding of epoxide-containing tyrosine (EPOY) for developing covalent protein drugs. Our study demonstrates that EPOY, when incorporated into a nanobody (KN035), can cross-link with different side chains (mutations) at the same position of PD-L1 protein. Significantly, a single genetically encoded reactive warhead that is capable of covalent and site-specific targeting to 10 different nucleophilic residues was achieved for the first time. This would largely expand the scope of covalent warhead and inspire the development of covalent warheads for both small-molecule drugs and protein drugs. Furthermore, we incorporate the EPOY into a designed ankyrin repeat protein (DarpinK13) to create the covalent binders of KRAS. This covalent KRAS binder holds the potential to achieve pan-covalent targeting of KRAS based on the structural similarity among all oncogenic KRAS mutants while avoiding off-target binding to NRAS/HRAS through a covalent interaction with KRAS-specific residues (H95 and E107). We envision that covalently targeting to H95 will be a promising strategy for the development of covalent pan-KRAS inhibitors in the future.
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Affiliation(s)
| | | | | | - Jinsong Ye
- Department of Chemistry,
Research Center for Chemical Biology and Omics Analysis, College of
Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jie Wang
- Department of Chemistry,
Research Center for Chemical Biology and Omics Analysis, College of
Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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15
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Matsuo K, Yamaoka S, Waku T, Kobori A. In-cell chemical construction of a photoswitchable CENP-E using a photochromic covalent inhibitor. Org Biomol Chem 2024; 22:4651-4655. [PMID: 38787760 DOI: 10.1039/d4ob00647j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
An arylazopyrazole-based covalent inhibitor targeting the mitotic motor protein of centromere-associated protein E (CENP-E) was developed. Using this photoswitchable inhibitor, a photoswitchable CENP-E was chemically constructed in cells, which enabled to local control of mitotic cell division with light illumination.
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Affiliation(s)
- Kazuya Matsuo
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Shusuke Yamaoka
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
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16
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Gowans FA, Forte N, Hatcher J, Huang OW, Wang Y, Altamirano Poblano BE, Wertz IE, Nomura DK. Covalent Degrader of the Oncogenic Transcription Factor β-Catenin. J Am Chem Soc 2024. [PMID: 38848252 DOI: 10.1021/jacs.4c05174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
β-catenin (CTNNB1) is an oncogenic transcription factor that is important in cell-cell adhesion and transcription of cell proliferation and survival genes that drive the pathogenesis of many different types of cancers. However, direct pharmacological targeting of CTNNB1 has remained challenging. Here, we have performed a screen with a library of cysteine-reactive covalent ligands to identify the monovalent degrader EN83 that depletes CTNNB1 in a ubiquitin-proteasome-dependent manner. We show that EN83 directly and covalently targets CTNNB1 three cysteines C466, C520, and C619, leading to destabilization and degradation of CTNNB1. Through structural optimization, we generate a highly potent and relatively selective destabilizing degrader that acts through the targeting of only C619 on CTNNB1. Our results show that chemoproteomic approaches can be used to covalently target and degrade challenging transcription factors like CTNNB1 through destabilization-mediated degradation.
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Affiliation(s)
- Flor A Gowans
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
| | - Nafsika Forte
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
| | - Justin Hatcher
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
| | - Oscar W Huang
- Bristol Myers Squibb, San Francisco, California 94158, United States
| | - Yangzhi Wang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
| | - Belen E Altamirano Poblano
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
| | - Ingrid E Wertz
- Bristol Myers Squibb, San Francisco, California 94158, United States
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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17
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McCarthy WJ, van der Zouwen AJ, Bush JT, Rittinger K. Covalent fragment-based drug discovery for target tractability. Curr Opin Struct Biol 2024; 86:102809. [PMID: 38554479 DOI: 10.1016/j.sbi.2024.102809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/01/2024]
Abstract
An important consideration in drug discovery is the prioritization of tractable protein targets that are not only amenable to binding small molecules, but also alter disease biology in response to small molecule binding. Covalent fragment-based drug discovery has emerged as a powerful approach to aid in the identification of such protein targets. The application of irreversible binding mechanisms enables the identification of fragment hits for challenging-to-target proteins, allows proteome-wide screening in a cellular context, and makes it possible to determine functional effects with modestly potent ligands without the requirement for extensive compound optimization. Here, we provide an overview of recent approaches to covalent fragment-based screening and discuss how these have been applied to establish the tractability of unexplored binding sites on protein targets.
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Affiliation(s)
- William J McCarthy
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Antonie J van der Zouwen
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. https://twitter.com/Jake_T_Bush
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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18
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Cui XY, Li Z, Kong Z, Liu Y, Meng H, Wen Z, Wang C, Chen J, Xu M, Li Y, Gao J, Zhu W, Hao Z, Huo L, Liu S, Yang Z, Liu Z. Covalent targeted radioligands potentiate radionuclide therapy. Nature 2024; 630:206-213. [PMID: 38778111 DOI: 10.1038/s41586-024-07461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Targeted radionuclide therapy, in which radiopharmaceuticals deliver potent radionuclides to tumours for localized irradiation, has addressed unmet clinical needs and improved outcomes for patients with cancer1-4. A therapeutic radiopharmaceutical must achieve both sustainable tumour targeting and fast clearance from healthy tissue, which remains a major challenge5,6. A targeted ligation strategy that selectively fixes the radiopharmaceutical to the target protein in the tumour would be an ideal solution. Here we installed a sulfur (VI) fluoride exchange (SuFEx) chemistry-based linker on radiopharmaceuticals to prevent excessively fast tumour clearance. When the engineered radiopharmaceutical binds to the tumour-specific protein, the system undergoes a binding-to-ligation transition and readily conjugates to the tyrosine residues through the 'click' SuFEx reaction. The application of this strategy to a fibroblast activation protein (FAP) inhibitor (FAPI) triggered more than 80% covalent binding to the protein and almost no dissociation for six days. In mice, SuFEx-engineered FAPI showed 257% greater tumour uptake than did the original FAPI, and increased tumour retention by 13-fold. The uptake in healthy tissues was rapidly cleared. In a pilot imaging study, this strategy identified more tumour lesions in patients with cancer than did other methods. SuFEx-engineered FAPI also successfully achieved targeted β- and α-radionuclide therapy, causing nearly complete tumour regression in mice. Another SuFEx-engineered radioligand that targets prostate-specific membrane antigen (PSMA) also showed enhanced therapeutic efficacy. Considering the broad scope of proteins that can potentially be ligated to SuFEx warheads, it might be possible to adapt this strategy to other cancer targets.
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Affiliation(s)
- Xi-Yang Cui
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Zhu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Ziren Kong
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yu Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Hao Meng
- Changping Laboratory, Beijing, P. R. China
| | - Zihao Wen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Changlun Wang
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Junyi Chen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mengxin Xu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Yiyan Li
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jingyue Gao
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wenjia Zhu
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhixin Hao
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Li Huo
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Shaoyan Liu
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhi Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Zhibo Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China.
- Peking University-Tsinghua University Center for Life Sciences, Peking University, Beijing, P. R. China.
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19
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Wang L, Liang Y, Luo P, Huang M, Wan Y. Novel partially reversible NDM-1 inhibitors based on the naturally occurring houttuynin. Bioorg Chem 2024; 147:107328. [PMID: 38583248 DOI: 10.1016/j.bioorg.2024.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
Discovering novel NDM-1 inhibitors is an urgent task for treatment of 'superbug' infectious diseases. In this study, we found that naturally occurring houttuynin and its sulfonate derivatives might be effective NDM-1 inhibitors with novel mechanism, i.e. the attribute of partially covalent inhibition of sulfonate derivatives of houttuynin against NDM-1. Primary structure-activity relationship study showed that both the long aliphatic side chain and the warhead of aldehyde group are vital for the efficiency against NDM-1. The homologs with longer chains (SNH-2 to SNH-5) displayed stronger inhibitory activities with IC50 range of 1.1-1.5 μM, while the shorter chain the weaker inhibition. Further synergistic experiments in cell level confirmed that all these 4 compounds (at 32 μg/mL) recovered the antibacterial activity of meropenem (MER) against E. coli BL21/pET15b-blaNDM-1.
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Affiliation(s)
- Lifang Wang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Yaowen Liang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Pan Luo
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Manna Huang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China.
| | - Yiqian Wan
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
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20
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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21
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Petruzzella A, Bruand M, Santamaria-Martínez A, Katanayeva N, Reymond L, Wehrle S, Georgeon S, Inel D, van Dalen FJ, Viertl D, Lau K, Pojer F, Schottelius M, Zoete V, Verdoes M, Arber C, Correia BE, Oricchio E. Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins. Nat Chem Biol 2024:10.1038/s41589-024-01627-z. [PMID: 38811854 DOI: 10.1038/s41589-024-01627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterious side effects. To address this problem, we developed a modular antibody-based platform for targeted drug delivery by conjugating non-natural peptide inhibitors (NNPIs) to antibodies. NNPIs were functionalized with reactive warheads for covalent inhibition, optimized with deep saturation mutagenesis and conjugated to antibodies to enable cell-type-specific delivery. Our antibody-peptide inhibitor conjugates specifically blocked the activity of cathepsins in different cancer cells, as well as osteoclasts, and showed therapeutic efficacy in vitro and in vivo. Overall, our approach allows for the rapid design of selective cathepsin inhibitors and can be generalized to inhibit a broad class of proteases in cancer and other diseases.
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Affiliation(s)
- Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Marine Bruand
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Albert Santamaria-Martínez
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Luc Reymond
- Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Damla Inel
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Floris J van Dalen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - David Viertl
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- In Vivo Imaging Facility, Department of Research and Training, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Margret Schottelius
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- AGORA Pôle de Recherche sur le Cancer, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Martijn Verdoes
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Caroline Arber
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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22
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Maso L, Rajak E, Bang I, Koide A, Hattori T, Neel BG, Koide S. Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes. Proc Natl Acad Sci U S A 2024; 121:e2319029121. [PMID: 38781214 PMCID: PMC11145297 DOI: 10.1073/pnas.2319029121] [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] [Accepted: 02/14/2024] [Indexed: 05/25/2024] Open
Abstract
The HapImmuneTM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the VH and VL domains, binds HLAs in an unconventional, angled way, with VL making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.
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Affiliation(s)
- Lorenzo Maso
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Epsa Rajak
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Medicine, New York University School of Medicine, New York, NY10016
| | - Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Medicine, New York University School of Medicine, New York, NY10016
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
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23
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Lian X, Chatterjee S, Sun Y, Dilliard SA, Moore S, Xiao Y, Bian X, Yamada K, Sung YC, Levine RM, Mayberry K, John S, Liu X, Smith C, Johnson LT, Wang X, Zhang CC, Liu DR, Newby GA, Weiss MJ, Yen JS, Siegwart DJ. Bone-marrow-homing lipid nanoparticles for genome editing in diseased and malignant haematopoietic stem cells. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01680-8. [PMID: 38783058 DOI: 10.1038/s41565-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Therapeutic genome editing of haematopoietic stem cells (HSCs) would provide long-lasting treatments for multiple diseases. However, the in vivo delivery of genetic medicines to HSCs remains challenging, especially in diseased and malignant settings. Here we report on a series of bone-marrow-homing lipid nanoparticles that deliver mRNA to a broad group of at least 14 unique cell types in the bone marrow, including healthy and diseased HSCs, leukaemic stem cells, B cells, T cells, macrophages and leukaemia cells. CRISPR/Cas and base editing is achieved in a mouse model expressing human sickle cell disease phenotypes for potential foetal haemoglobin reactivation and conversion from sickle to non-sickle alleles. Bone-marrow-homing lipid nanoparticles were also able to achieve Cre-recombinase-mediated genetic deletion in bone-marrow-engrafted leukaemic stem cells and leukaemia cells. We show evidence that diverse cell types in the bone marrow niche can be edited using bone-marrow-homing lipid nanoparticles.
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Affiliation(s)
- Xizhen Lian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sumanta Chatterjee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yehui Sun
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean A Dilliard
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Moore
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yufen Xiao
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoyan Bian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohki Yamada
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yun-Chieh Sung
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rachel M Levine
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin Mayberry
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Samuel John
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoye Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Caroline Smith
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lindsay T Johnson
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xu Wang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan S Yen
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel J Siegwart
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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24
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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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25
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Merten EM, Sears JD, Leisner TM, Hardy PB, Ghoshal A, Hossain MA, Asressu KH, Brown PJ, Stashko MA, Herring L, Mordant AL, Webb TS, Mills CA, Barker NK, Streblow ZJ, Perveen S, Arrowsmith C, Arnold JJ, Cameron CE, Streblow DN, Moorman NJ, Heise M, Willson TM, Popov K, Pearce KH. Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586341. [PMID: 38562906 PMCID: PMC10983941 DOI: 10.1101/2024.03.22.586341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC 50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a k inact /K I of 6.4 x 10 3 M -1 s -1 . LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic. Significance Statement Chikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.
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26
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Himmelbauer M, Bajrami B, Basile R, Capacci A, Chen T, Choi CK, Gilfillan R, Gonzalez-Lopez de Turiso F, Gu C, Hoemberger M, Johnson DS, Jones JH, Kadakia E, Kirkland M, Lin EY, Liu Y, Ma B, Magee T, Mantena S, Marx IE, Metrick CM, Mingueneau M, Murugan P, Muste CA, Nadella P, Nevalainen M, Parker Harp CR, Pattaropong V, Pietrasiewicz A, Prince RJ, Purgett TJ, Santoro JC, Schulz J, Sciabola S, Tang H, Vandeveer HG, Wang T, Yousaf Z, Helal CJ, Hopkins BT. Discovery and Preclinical Characterization of BIIB129, a Covalent, Selective, and Brain-Penetrant BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2024; 67:8122-8140. [PMID: 38712838 PMCID: PMC11129193 DOI: 10.1021/acs.jmedchem.4c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024]
Abstract
Multiple sclerosis (MS) is a chronic disease with an underlying pathology characterized by inflammation-driven neuronal loss, axonal injury, and demyelination. Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase and member of the TEC family of kinases, is involved in the regulation, migration, and functional activation of B cells and myeloid cells in the periphery and the central nervous system (CNS), cell types which are deemed central to the pathology contributing to disease progression in MS patients. Herein, we describe the discovery of BIIB129 (25), a structurally distinct and brain-penetrant targeted covalent inhibitor (TCI) of BTK with an unprecedented binding mode responsible for its high kinome selectivity. BIIB129 (25) demonstrated efficacy in disease-relevant preclinical in vivo models of B cell proliferation in the CNS, exhibits a favorable safety profile suitable for clinical development as an immunomodulating therapy for MS, and has a low projected total human daily dose.
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Affiliation(s)
- Martin
K. Himmelbauer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rebecca Basile
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Andrew Capacci
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Colin K. Choi
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rab Gilfillan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | | | - Chungang Gu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas S. Johnson
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J. Howard Jones
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ekta Kadakia
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Melissa Kirkland
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Edward Y. Lin
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ying Liu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Srinivasa Mantena
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Isaac E. Marx
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M. Metrick
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Cathy A. Muste
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Prasad Nadella
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marta Nevalainen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Chelsea R. Parker Harp
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Vatee Pattaropong
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Alicia Pietrasiewicz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Robin J. Prince
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas J. Purgett
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Joseph C. Santoro
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jurgen Schulz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Simone Sciabola
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - H. George Vandeveer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ti Wang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zain Yousaf
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Christopher J. Helal
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T. Hopkins
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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27
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Eiken AP, Smith AL, Skupa SA, Schmitz E, Rana S, Singh S, Kumar S, Mallareddy JR, de Cubas AA, Krishna A, Kalluchi A, Rowley MJ, D'Angelo CR, Lunning MA, Bociek RG, Vose JM, Natarajan A, El-Gamal D. Novel Spirocyclic Dimer, SpiD3, Targets Chronic Lymphocytic Leukemia Survival Pathways with Potent Preclinical Effects. CANCER RESEARCH COMMUNICATIONS 2024; 4:1328-1343. [PMID: 38687198 PMCID: PMC11110724 DOI: 10.1158/2767-9764.crc-24-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Chronic lymphocytic leukemia (CLL) cell survival and growth is fueled by the induction of B-cell receptor (BCR) signaling within the tumor microenvironment (TME) driving activation of NFκB signaling and the unfolded protein response (UPR). Malignant cells have higher basal levels of UPR posing a unique therapeutic window to combat CLL cell growth using pharmacologic agents that induce accumulation of misfolded proteins. Frontline CLL therapeutics that directly target BCR signaling such as Bruton tyrosine kinase (BTK) inhibitors (e.g., ibrutinib) have enhanced patient survival. However, resistance mechanisms wherein tumor cells bypass BTK inhibition through acquired BTK mutations, and/or activation of alternative survival mechanisms have rendered ibrutinib ineffective, imposing the need for novel therapeutics. We evaluated SpiD3, a novel spirocyclic dimer, in CLL cell lines, patient-derived CLL samples, ibrutinib-resistant CLL cells, and in the Eµ-TCL1 mouse model. Our integrated multi-omics and functional analyses revealed BCR signaling, NFκB signaling, and endoplasmic reticulum stress among the top pathways modulated by SpiD3. This was accompanied by marked upregulation of the UPR and inhibition of global protein synthesis in CLL cell lines and patient-derived CLL cells. In ibrutinib-resistant CLL cells, SpiD3 retained its antileukemic effects, mirrored in reduced activation of key proliferative pathways (e.g., PRAS, ERK, MYC). Translationally, we observed reduced tumor burden in SpiD3-treated Eµ-TCL1 mice. Our findings reveal that SpiD3 exploits critical vulnerabilities in CLL cells including NFκB signaling and the UPR, culminating in profound antitumor properties independent of TME stimuli. SIGNIFICANCE SpiD3 demonstrates cytotoxicity in CLL partially through inhibition of NFκB signaling independent of tumor-supportive stimuli. By inducing the accumulation of unfolded proteins, SpiD3 activates the UPR and hinders protein synthesis in CLL cells. Overall, SpiD3 exploits critical CLL vulnerabilities (i.e., the NFκB pathway and UPR) highlighting its use in drug-resistant CLL.
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MESH Headings
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Humans
- Animals
- Mice
- Signal Transduction/drug effects
- Piperidines/pharmacology
- Piperidines/therapeutic use
- Cell Line, Tumor
- Unfolded Protein Response/drug effects
- Adenine/analogs & derivatives
- Adenine/pharmacology
- Drug Resistance, Neoplasm/drug effects
- NF-kappa B/metabolism
- Spiro Compounds/pharmacology
- Spiro Compounds/therapeutic use
- Cell Survival/drug effects
- Tumor Microenvironment/drug effects
- Receptors, Antigen, B-Cell/metabolism
- Cell Proliferation/drug effects
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Affiliation(s)
- Alexandria P. Eiken
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Audrey L. Smith
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sydney A. Skupa
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Elizabeth Schmitz
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Siddhartha Kumar
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| | - Aguirre A de Cubas
- Department of Microbiology and Immunology, College of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Akshay Krishna
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - M. Jordan Rowley
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Christopher R. D'Angelo
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Matthew A. Lunning
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - R. Gregory Bociek
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Julie M. Vose
- Division of Hematology and Oncology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Dalia El-Gamal
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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28
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Gayatri, Brewitz L, Ibbotson L, Salah E, Basak S, Choudhry H, Schofield CJ. Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation. Chem Sci 2024; 15:7667-7678. [PMID: 38784729 PMCID: PMC11110133 DOI: 10.1039/d4sc01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Enzyme inhibitors working by O-acylation of nucleophilic serine residues are of immense medicinal importance, as exemplified by the β-lactam antibiotics. By contrast, inhibition of nucleophilic cysteine enzymes by S-acylation has not been widely exploited for medicinal applications. The SARS-CoV-2 main protease (Mpro) is a nucleophilic cysteine protease and a validated therapeutic target for COVID-19 treatment using small-molecule inhibitors. The clinically used Mpro inhibitors nirmatrelvir and simnotrelvir work via reversible covalent reaction of their electrophilic nitrile with the Mpro nucleophilic cysteine (Cys145). We report combined structure activity relationship and mass spectrometric studies revealing that appropriately functionalized γ-lactams can potently inhibit Mpro by reversible covalent reaction with Cys145 of Mpro. The results suggest that γ-lactams have potential as electrophilic warheads for development of covalently reacting small-molecule inhibitors of Mpro and, by implication, other nucleophilic cysteine enzymes.
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Affiliation(s)
- Gayatri
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lewis Ibbotson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Shyam Basak
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Hani Choudhry
- Department of Biochemistry, Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University Jeddah Saudi Arabia
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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29
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Zhang X, Shen C, Zhang H, Kang Y, Hsieh CY, Hou T. Advancing Ligand Docking through Deep Learning: Challenges and Prospects in Virtual Screening. Acc Chem Res 2024; 57:1500-1509. [PMID: 38577892 DOI: 10.1021/acs.accounts.4c00093] [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: 04/06/2024]
Abstract
Molecular docking, also termed ligand docking (LD), is a pivotal element of structure-based virtual screening (SBVS) used to predict the binding conformations and affinities of protein-ligand complexes. Traditional LD methodologies rely on a search and scoring framework, utilizing heuristic algorithms to explore binding conformations and scoring functions to evaluate binding strengths. However, to meet the efficiency demands of SBVS, these algorithms and functions are often simplified, prioritizing speed over accuracy.The emergence of deep learning (DL) has exerted a profound impact on diverse fields, ranging from natural language processing to computer vision and drug discovery. DeepMind's AlphaFold2 has impressively exhibited its ability to accurately predict protein structures solely from amino acid sequences, highlighting the remarkable potential of DL in conformation prediction. This groundbreaking advancement circumvents the traditional search-scoring frameworks in LD, enhancing both accuracy and processing speed and thereby catalyzing a broader adoption of DL algorithms in binding pose prediction. Nevertheless, a consensus on certain aspects remains elusive.In this Account, we delineate the current status of employing DL to augment LD within the VS paradigm, highlighting our contributions to this domain. Furthermore, we discuss the challenges and future prospects, drawing insights from our scholarly investigations. Initially, we present an overview of VS and LD, followed by an introduction to DL paradigms, which deviate significantly from traditional search-scoring frameworks. Subsequently, we delve into the challenges associated with the development of DL-based LD (DLLD), encompassing evaluation metrics, application scenarios, and physical plausibility of the predicted conformations. In the evaluation of LD algorithms, it is essential to recognize the multifaceted nature of the metrics. While the accuracy of binding pose prediction, often measured by the success rate, is a pivotal aspect, the scoring/screening power and computational speed of these algorithms are equally important given the pivotal role of LD tools in VS. Regarding application scenarios, early methods focused on blind docking, where the binding site is unknown. However, recent studies suggest a shift toward identifying binding sites rather than solely predicting binding poses within these models. In contrast, LD with a known pocket in VS has been shown to be more practical. Physical plausibility poses another significant challenge. Although DLLD models often achieve higher success rates compared to traditional methods, they may generate poses with implausible local structures, such as incorrect bond angles or lengths, which are disadvantageous for postprocessing tasks like visualization. Finally, we discuss the future perspectives for DLLD, emphasizing the need to improve generalization ability, strike a balance between speed and accuracy, account for protein conformation flexibility, and enhance physical plausibility. Additionally, we delve into the comparison between generative and regression algorithms in this context, exploring their respective strengths and potential.
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Affiliation(s)
- Xujun Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Haotian Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chang-Yu Hsieh
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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30
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Kopranovic A, Meyer-Almes FJ. Rapid Determination of Kinetic Constants for Slow-Binding Inhibitors and Inactivators of Human Histone Deacetylase 8. Int J Mol Sci 2024; 25:5593. [PMID: 38891780 PMCID: PMC11171933 DOI: 10.3390/ijms25115593] [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: 04/21/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The kinetics and mechanism of drug binding to its target are critical to pharmacological efficacy. A high throughput (HTS) screen often results in hundreds of hits, of which usually only simple IC50 values are determined during reconfirmation. However, kinetic parameters such as residence time for reversible inhibitors and the kinact/KI ratio, which is the critical measure for evaluating covalent inactivators, are early predictive measures to assess the chances of success of the hits in the clinic. Using the promising cancer target human histone deacetylase 8 as an example, we present a robust method that calculates concentration-dependent apparent rate constants for the inhibition or inactivation of HDAC8 from dose-response curves recorded after different pre-incubation times. With these data, hit compounds can be classified according to their mechanism of action, and the relevant kinetic parameters can be calculated in a highly parallel fashion. HDAC8 inhibitors with known modes of action were correctly assigned to their mechanism, and the binding mechanisms of some hits from an internal HDAC8 screening campaign were newly determined. The oxonitriles SVE04 and SVE27 were classified as fast reversible HDAC8 inhibitors with moderate time-constant IC50 values of 4.2 and 2.6 µM, respectively. The hit compound TJ-19-24 and SAH03 behave like slow two-step inactivators or reversible inhibitors, with a very low reverse isomerization rate.
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Affiliation(s)
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
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31
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Cremosnik G, Mesrouze Y, Zueger P, Furkert D, Grandjean F, Argoti D, Mermet-Meillon F, Bauer MR, Brittain S, Rogemoser P, Yang W, Giovannoni J, McGregor L, Tang J, Knapp M, Holzinger S, Buhr S, Muller L, Leder L, Xie L, Fernandez C, Nieto-Oberhuber C, Chène P, Galli GG, Sesterhenn F. mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B. ACS Chem Biol 2024; 19:1142-1150. [PMID: 38655884 PMCID: PMC11106749 DOI: 10.1021/acschembio.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.
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Affiliation(s)
- Gregor
S. Cremosnik
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Yannick Mesrouze
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Patrik Zueger
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - David Furkert
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Frédéric Grandjean
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Dayana Argoti
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | | | - Matthias R. Bauer
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Scott Brittain
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Phuong Rogemoser
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Winnie Yang
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jerome Giovannoni
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lynn McGregor
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jenny Tang
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Mark Knapp
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Sandra Holzinger
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Sylvia Buhr
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lionel Muller
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lukas Leder
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lili Xie
- Discovery
Sciences, Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Cesar Fernandez
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | | | - Patrick Chène
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Giorgio G. Galli
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Fabian Sesterhenn
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
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32
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Ye H, Zhu Y, Kong Y, Wen H, Lu W, Wang D, Tang S, Zhan M, Lu G, Shao C, Wang N, Hao H. Carbene Footprinting Directs Design of Genetically Encoded Proximity-Reactive Protein Binders. Anal Chem 2024; 96:7566-7576. [PMID: 38684118 DOI: 10.1021/acs.analchem.4c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Genetically encoding proximal-reactive unnatural amino acids (PrUaas), such as fluorosulfate-l-tyrosine (FSY), into natural proteins of interest (POI) confer the POI with the ability to covalently bind to its interacting proteins (IPs). The PrUaa-incorporated POIs hold promise for blocking undesirable POI-IP interactions. Selecting appropriate PrUaa anchor sites is crucial, but it remains challenging with the current methodology, which heavily relies on crystallography to identify the proximal residues between the POIs and the IPs for the PrUaa anchorage. To address the challenge, here, we propose a footprinting-directed genetically encoded covalent binder (footprinting-GECB) approach. This approach employs carbene footprinting, a structural mass spectrometry (MS) technique that quantifies the extent of labeling of the POI following the addition of its IP, and thus identifies the responsive residues. By genetically encoding PrUaa into these responsive sites, POI variants with covalent bonding ability to its IP can be produced without the need for crystallography. Using the POI-IP model, KRAS/RAF1, we showed that engineering FSY at the footprint-assigned KRAS residue resulted in a KRAS variant that can bind irreversibly to RAF1. Additionally, we inserted FSY at the responsive residue in RAF1 upon footprinting the oncogenic KRASG12D/RAF1, which lacks crystal structure, and generated a covalent binder to KRASG12D. Together, we demonstrated that by adopting carbene footprinting to direct PrUaa anchorage, we can greatly expand the opportunities for designing covalent protein binders for PPIs without relying on crystallography. This holds promise for creating effective PPI inhibitors and supports both fundamental research and biotherapeutics development.
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Affiliation(s)
- Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Yinxue Zhu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Ying Kong
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Hongtao Wen
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Wenjie Lu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Dexiang Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Shuo Tang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Mengru Zhan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Gaoyuan Lu
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
| | - Nanxi Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing 210023, Jiangsu, China
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
- School of Pharmacy, China Pharmaceutical University, Tongjiaxiang No. 24, Nanjing 210009, Jiangsu, China
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33
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Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell 2024; 187:2536-2556.e30. [PMID: 38653237 PMCID: PMC11143475 DOI: 10.1016/j.cell.2024.03.027] [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: 10/01/2023] [Revised: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.
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Affiliation(s)
- Mariko Takahashi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.
| | - Harrison B Chong
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Siwen Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Tzu-Yi Yang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Matthew J Lazarov
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Stefan Harry
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Kira Vordermark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Jonathan Assaad
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Magdy Gohar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Benedikt R Dürr
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Marianne Richter
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Himani Patel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | | | | | - Karla Rubio
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Antonio Villanueva
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Junbing Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farah Makram
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Hanna Griesshaber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Drew Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Barbara Karakyriakou
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Alexander Healy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - George Popoola
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neha Khandelwal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | - Pei-Chieh Tien
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Nicholas Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Tobias Hosp
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sanne van den Ouweland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Toshiro Hara
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lillian Bussema
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Martin Q Rasmussen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ana Carolina Domingues
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Aleigha Lawless
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacy Fang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satoshi Yoda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Linh Phuong Nguyen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Marie Reeves
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farrah Nicole Wakefield
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Adam Acker
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Elizabeth Clark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Taronish Dubash
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - John Kastanos
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Eugene Oh
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel A Haber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Moshe Sade-Feldman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Russell W Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Aaron N Hata
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Nabeel M Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Mario L Suvà
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA.
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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Ohata J. Friedel-Crafts reactions for biomolecular chemistry. Org Biomol Chem 2024; 22:3544-3558. [PMID: 38624091 DOI: 10.1039/d4ob00406j] [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: 04/17/2024]
Abstract
Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used synthetic methods for the preparation of small molecules but their use in biological and medical fields is relatively less frequent than the other reactions, possibly owing to the notion of their plausible incompatibility with biological systems. This review demonstrates advances in Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or -assisted processes, these reactions have garnered considerable interest in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated their utility for the construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides, lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic chemistry courses, this review is intended for both experts and nonexperts by discussing their basic reaction patterns (with the depiction of each reaction mechanism in the ESI) and relevant real-world impacts in order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described here is a testament to their broad importance and utility, and further development and investigations of the reactions will surely be the focus in the organic biomolecular chemistry fields.
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Affiliation(s)
- Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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Ma S, Patel H, Peeples CA, Shen J. QM/MM simulations of EFGR with afatinib reveal the role of the β-dimethylaminomethyl substitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.18.580887. [PMID: 38766221 PMCID: PMC11100610 DOI: 10.1101/2024.02.18.580887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a β-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state β-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Heeral Patel
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Craig A Peeples
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
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Xerxa E, Bajorath J. Data-oriented protein kinase drug discovery. Eur J Med Chem 2024; 271:116413. [PMID: 38636127 DOI: 10.1016/j.ejmech.2024.116413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
The continued growth of data from biological screening and medicinal chemistry provides opportunities for data-driven experimental design and decision making in early-phase drug discovery. Approaches adopted from data science help to integrate internal and public domain data and extract knowledge from historical in-house data. Protein kinase (PK) drug discovery is an exemplary area where large amounts of data are accumulating, providing a valuable knowledge base for discovery projects. Herein, the evolution of PK drug discovery and development of small molecular PK inhibitors (PKIs) is reviewed, highlighting milestone developments in the field and discussing exemplary studies providing a basis for increasing data orientation of PK discovery efforts.
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Affiliation(s)
- Elena Xerxa
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115, Bonn, Germany.
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37
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Shirley JD, Nauta KM, Gillingham JR, Diwakar S, Carlson EE. kinact / KI Value Determination for Penicillin-Binding Proteins in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592586. [PMID: 38746240 PMCID: PMC11092749 DOI: 10.1101/2024.05.05.592586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Penicillin-binding proteins (PBPs) are an essential family of bacterial enzymes that are inhibited by the β-lactam class of antibiotics. PBP inhibition disrupts cell wall biosynthesis, which results in deficient growth and proliferation, and ultimately leads to lysis. IC 50 values are often employed as descriptors of enzyme inhibition and inhibitor selectivity but can be misleading in the study of time-dependent, irreversible inhibitors. Due to this disconnect, the second order rate constant k inact / K I is a more appropriate metric of covalent inhibitor potency. Despite being the gold standard measurement of potency, k inact / K I values are typically obtained from in vitro assays, which limits assay throughput if investigating an enzyme family with multiple homologs (such as the PBPs). Therefore, we developed a whole-cell k inact / K I assay to define inhibitor potency for the PBPs in Streptococcus pneumoniae using the fluorescent activity-based probe Bocillin-FL. Our results align with in vitro k inact / K I data and show a comparable relationship to previously established IC 50 values. These results support the validity of our in vivo k inact / K I method as a means of obtaining a full picture of β-lactam potency for a suite of PBPs. Abstract Figure
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Jerye K, Lüken H, Steffen A, Schlawis C, Jänsch L, Schulz S, Brönstrup M. Activity-Based Protein Profiling Identifies Protein Disulfide-Isomerases as Target Proteins of the Volatile Salinilactones. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309515. [PMID: 38430530 PMCID: PMC11095149 DOI: 10.1002/advs.202309515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/05/2024] [Indexed: 03/04/2024]
Abstract
The salinilactones, volatile marine natural products secreted from Salinispora arenicola, feature a unique [3.1.0]-lactone ring system and cytotoxic activities through a hitherto unknown mechanism. To find their molecular target, an activity-based protein profiling with a salinilactone-derived probe is applied that disclosed the protein disulfide-isomerases (PDIs) as the dominant mammalian targets of salinilactones, and thioredoxin (TRX1) as secondary target. The inhibition of protein disulfide-isomerase A1 (PDIA1) and TRX1 is confirmed by biochemical assays with recombinant proteins, showing that (1S,5R)-salinilactone B is more potent than its (1R,5S)-configured enantiomer. The salinilactones bound covalently to C53 and C397, the catalytically active cysteines of the isoform PDIA1 according to tandem mass spectrometry. Reactions with a model substrate demonstrated that the cyclopropyl group is opened by an attack of the thiol at C6. Fluorophore labeling experiments showed the cell permeability of a salinilactone-BODIPY (dipyrrometheneboron difluoride) conjugate and its co-localization with PDIs in the endoplasmic reticulum. The study is one of the first to pinpoint a molecular target for a volatile microbial natural product, and it demonstrates that salinilactones can achieve high selectivity despite their small size and intrinsic reactivity.
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Affiliation(s)
- Karoline Jerye
- Department of Chemical BiologyHelmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
| | - Helko Lüken
- Department of Chemical BiologyHelmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
| | - Anika Steffen
- Department of Cell BiologyHelmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
| | - Christian Schlawis
- Institute of Organic ChemistryTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Lothar Jänsch
- Research Group Cellular Proteome ResearchHelmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
| | - Stefan Schulz
- Institute of Organic ChemistryTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Mark Brönstrup
- Department of Chemical BiologyHelmholtz Centre for Infection ResearchInhoffenstraße 738124BraunschweigGermany
- Biomolecular Drug Research Center (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- German Center for Infection ResearchSite Hannover‐BraunschweigInhoffenstraße 738124BraunschweigGermany
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Yin H, Tang Q, Xia H, Bi F. Targeting RAF dimers in RAS mutant tumors: From biology to clinic. Acta Pharm Sin B 2024; 14:1895-1923. [PMID: 38799634 PMCID: PMC11120325 DOI: 10.1016/j.apsb.2024.02.018] [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: 10/09/2023] [Revised: 01/02/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024] Open
Abstract
RAS mutations occur in approximately 30% of tumors worldwide and have a poor prognosis due to limited therapies. Covalent targeting of KRAS G12C has achieved significant success in recent years, but there is still a lack of efficient therapeutic approaches for tumors with non-G12C KRAS mutations. A highly promising approach is to target the MAPK pathway downstream of RAS, with a particular focus on RAF kinases. First-generation RAF inhibitors have been authorized to treat BRAF mutant tumors for over a decade. However, their use in RAS-mutated tumors is not recommended due to the paradoxical ERK activation mainly caused by RAF dimerization. To address the issue of RAF dimerization, type II RAF inhibitors have emerged as leading candidates. Recent clinical studies have shown the initial effectiveness of these agents against RAS mutant tumors. Promisingly, type II RAF inhibitors in combination with MEK or ERK inhibitors have demonstrated impressive efficacy in RAS mutant tumors. This review aims to clarify the importance of RAF dimerization in cellular signaling and resistance to treatment in tumors with RAS mutations, as well as recent progress in therapeutic approaches to address the problem of RAF dimerization in RAS mutant tumors.
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Affiliation(s)
- Huanhuan Yin
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiulin Tang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongwei Xia
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Bi
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
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40
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Zhao J, Li X, Ma T, Chang B, Zhang B, Fang J. Glutathione-triggered prodrugs: Design strategies, potential applications, and perspectives. Med Res Rev 2024; 44:1013-1054. [PMID: 38140851 DOI: 10.1002/med.22007] [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: 10/17/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023]
Abstract
The burgeoning prodrug strategy offers a promising avenue toward improving the efficacy and specificity of cytotoxic drugs. Elevated intracellular levels of glutathione (GSH) have been regarded as a hallmark of tumor cells and characteristic feature of the tumor microenvironment. Considering the pivotal involvement of elevated GSH in the tumorigenic process, a diverse repertoire of GSH-triggered prodrugs has been developed for cancer therapy, facilitating the attenuation of deleterious side effects associated with conventional chemotherapeutic agents and/or the attainment of more efficacious therapeutic outcomes. These prodrug formulations encompass a spectrum of architectures, spanning from small molecules to polymer-based and organic-inorganic nanomaterial constructs. Although the GSH-triggered prodrugs have been gaining increasing interests, a comprehensive review of the advancements made in the field is still lacking. To fill the existing lacuna, this review undertakes a retrospective analysis of noteworthy research endeavors, based on a categorization of these molecules by their diverse recognition units (i.e., disulfides, diselenides, Michael acceptors, and sulfonamides/sulfonates). This review also focuses on explaining the distinct benefits of employing various chemical architecture strategies in the design of these prodrug agents. Furthermore, we highlight the potential for synergistic functionality by incorporating multiple-targeting conjugates, theranostic entities, and combinational treatment modalities, all of which rely on the GSH-triggering. Overall, an extensive overview of the emerging field is presented in this review, highlighting the obstacles and opportunities that lie ahead. Our overarching goal is to furnish methodological guidance for the development of more efficacious GSH-triggered prodrugs in the future. By assessing the pros and cons of current GSH-triggered prodrugs, we expect that this review will be a handful reference for prodrug design, and would provide a guidance for improving the properties of prodrugs and discovering novel trigger scaffolds for constructing GSH-triggered prodrugs.
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Affiliation(s)
- Jintao Zhao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Xinming Li
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, China
| | - Tao Ma
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Bingbing Chang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Jianguo Fang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, China
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41
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Danilack AD, Dickson CJ, Soylu C, Fortunato M, Rodde S, Munkler H, Hornak V, Duca JS. Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design. J Comput Aided Mol Des 2024; 38:21. [PMID: 38693331 DOI: 10.1007/s10822-024-00560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully balanced to maintain potency while avoiding unwanted side effects. While warhead reactivities are commonly measured with assays, a computational model to predict warhead reactivities could be useful for several aspects of the covalent inhibitor design process. Studies have shown correlations between covalent warhead reactivities and quantum mechanic (QM) properties that describe important aspects of the covalent reaction mechanism. However, the models from these studies are often linear regression equations and can have limitations associated with their usage. Applications of machine learning (ML) models to predict covalent warhead reactivities with QM descriptors are not extensively seen in the literature. This study uses QM descriptors, calculated at different levels of theory, to train ML models to predict reactivities of covalent acrylamide warheads. The QM/ML models are compared with linear regression models built upon the same QM descriptors and with ML models trained on structure-based features like Morgan fingerprints and RDKit descriptors. Experiments show that the QM/ML models outperform the linear regression models and the structure-based ML models, and literature test sets demonstrate the power of the QM/ML models to predict reactivities of unseen acrylamide warhead scaffolds. Ultimately, these QM/ML models are effective, computationally feasible tools that can expedite the design of new covalent inhibitors.
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Affiliation(s)
- Aaron D Danilack
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Callum J Dickson
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Cihan Soylu
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Mike Fortunato
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephane Rodde
- Biomedical Research, Novartis, Novartis Campus, 4056, Basel, Switzerland
| | - Hagen Munkler
- Technical Research & Development, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Viktor Hornak
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Jose S Duca
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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42
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Khatua K, Alugubelli YR, Yang KS, Vulupala VR, Blankenship LR, Coleman D, Atla S, Chaki SP, Geng ZZ, Ma XR, Xiao J, Chen PH, Cho CCD, Sharma S, Vatansever EC, Ma Y, Yu G, Neuman BW, Xu S, Liu WR. Azapeptides with unique covalent warheads as SARS-CoV-2 main protease inhibitors. Antiviral Res 2024; 225:105874. [PMID: 38555023 PMCID: PMC11070182 DOI: 10.1016/j.antiviral.2024.105874] [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: 01/30/2024] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
The main protease (MPro) of SARS-CoV-2, the causative agent of COVID-19, is a pivotal nonstructural protein critical for viral replication and pathogenesis. Its protease function relies on three active site pockets for substrate recognition and a catalytic cysteine for enzymatic activity. To develop potential SARS-CoV-2 antivirals, we successfully synthesized a diverse range of azapeptide inhibitors with various covalent warheads to target MPro's catalytic cysteine. Our characterization identified potent MPro inhibitors, including MPI89 that features an aza-2,2-dichloroacetyl warhead with a remarkable EC50 value of 10 nM against SARS-CoV-2 infection in ACE2+ A549 cells and a selective index of 875. MPI89 is also remarkably selective and shows no potency against SARS-CoV-2 papain-like protease and several human proteases. Crystallography analyses demonstrated that these inhibitors covalently engaged the catalytic cysteine and used the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 stands as one of the most potent MPro inhibitors, suggesting the potential for further exploration of azapeptides and the aza-2,2-dichloroacetyl warhead for developing effective therapeutics against COVID-19.
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Affiliation(s)
- Kaustav Khatua
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yugendar R Alugubelli
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Kai S Yang
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Veerabhadra R Vulupala
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Lauren R Blankenship
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Demonta Coleman
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sandeep Atla
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sankar P Chaki
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhi Zachary Geng
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Xinyu R Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Jing Xiao
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Peng-Hsun Chen
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Chia-Chuan D Cho
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Shivangi Sharma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Erol C Vatansever
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yuying Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Ge Yu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; Texas A&M Global Health Research Complex, Texas A&M University, College Station, TX 77843, USA; Health Science Centre, Department of Molecular Pathogenesis and Immunology, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA.
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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43
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Jacobs FJ, Helliwell JR, Brink A. Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development. IUCRJ 2024; 11:359-373. [PMID: 38639558 PMCID: PMC11067751 DOI: 10.1107/s2052252524002598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.
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Affiliation(s)
- Francois J.F. Jacobs
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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44
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Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024:gkae300. [PMID: 38686803 DOI: 10.1093/nar/gkae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.
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Affiliation(s)
- Marine Bugnon
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mathilde Goullieux
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology, Geneva University Hospital (HUG), CH-1205 Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, CH-1015 Lausanne, Switzerland
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45
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Liang W, Krabill AD, Gallagher KS, Muli C, Qu Z, Trader D, Zhang ZY, Dai M. Natural Product-Inspired Molecules for Covalent Inhibition of SHP2 Tyrosine Phosphatase. Tetrahedron 2024; 156:133918. [PMID: 38618612 PMCID: PMC11008911 DOI: 10.1016/j.tet.2024.133918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Natural products have been playing indispensable roles in the development of lifesaving drug molecules. They are also valuable sources for covalent protein modifiers. However, they often are scarce in nature and have complex chemical structures, which are limiting their further biomedical development. Thus, natural product-inspired small molecules which still contain the essence of the parent natural products but are readily available and amenable for structural modification, are important and desirable in searching for lead compounds for various disease treatment. Inspired by the complex and diverse ent-kaurene diterpenoids with significant biological activities, we have created a synthetically accessible and focused covalent library by incorporating the bicyclo[3.2.1]octane α-methylene ketone, which is considered as the pharmacophore of ent-kaurene diterpenoids, as half of the structure, and replacing the other half with much less complex but more druglike scaffolds. From this library, we have identified and characterized selective covalent inhibitors of protein tyrosine phosphatase SHP2, an important anti-cancer therapeutic target. The success of this study demonstrated the importance of creating and evaluating natural product-inspired library as well as their application in targeting challenging disease targets.
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Affiliation(s)
- Weida Liang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Katelyn S Gallagher
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Christine Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Zihan Qu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Darci Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, United States
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46
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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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47
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Barragan AM, Ghaby K, Pond MP, Roux B. Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. J Chem Inf Model 2024; 64:3488-3502. [PMID: 38546820 DOI: 10.1021/acs.jcim.4c00023] [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: 04/23/2024]
Abstract
Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.
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Affiliation(s)
- Angela M Barragan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Kyle Ghaby
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Matthew P Pond
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
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48
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Gu Z, Yan Y, Liu H, Wu D, Yao H, Lin K, Li X. Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. J Chem Inf Model 2024; 64:3047-3058. [PMID: 38520328 DOI: 10.1021/acs.jcim.3c01900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Covalent drugs exhibit advantages in that noncovalent drugs cannot match, and covalent docking is an important method for screening covalent lead compounds. However, it is difficult for covalent docking to screen covalent compounds on a large scale because covalent docking requires determination of the covalent reaction type of the compound. Here, we propose to use deep learning of a lateral interactions spiking neural network to construct a covalent lead compound screening model to quickly screen covalent lead compounds. We used the 3CL protease (3CL Pro) of SARS-CoV-2 as the screen target and constructed two classification models based on LISNN to predict the covalent binding and inhibitory activity of compounds. The two classification models were trained on the covalent complex data set targeting cysteine (Cys) and the compound inhibitory activity data set targeting 3CL Pro, respected, with good prediction accuracy (ACC > 0.9). We then screened the screening compound library with 6 covalent binding screening models and 12 inhibitory activity screening models. We tested the inhibitory activity of the 32 compounds, and the best compound inhibited SARS-CoV-2 3CL Pro with an IC50 value of 369.5 nM. Further assay implied that dithiothreitol can affect the inhibitory activity of the compound to 3CL Pro, indicating that the compound may covalently bind 3CL Pro. The selectivity test showed that the compound had good target selectivity to 3CL Pro over cathepsin L. These correlation assays can prove the rationality of the covalent lead compound screening model. Finally, covalent docking was performed to demonstrate the binding conformation of the compound with 3CL Pro. The source code can be obtained from the GitHub repository (https://github.com/guzh970630/Screen_Covalent_Compound_by_LISNN).
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Affiliation(s)
- Zhihao Gu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Yan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hanwen Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Di Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hequan Yao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kejiang Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xuanyi Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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49
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Patel D, Huma ZE, Duncan D. Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action. ACS Chem Biol 2024; 19:824-838. [PMID: 38567529 PMCID: PMC11040609 DOI: 10.1021/acschembio.3c00805] [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: 12/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Covalent inhibition has seen a resurgence in the last several years. Although long-plagued by concerns of off-target effects due to nonspecific reactions leading to covalent adducts, there has been success in developing covalent inhibitors, especially within the field of anticancer therapy. Covalent inhibitors can have an advantage over noncovalent inhibitors since the formation of a covalent adduct may serve as an additional mode of selectivity due to the intrinsic reactivity of the target protein that is absent in many other proteins. Unfortunately, many covalent inhibitors form irreversible adducts with off-target proteins, which can lead to considerable side-effects. By designing the inhibitor to form reversible covalent adducts, one can leverage competing on/off kinetics in complex formation by taking advantage of the law of mass action. Although covalent adducts do form with off-target proteins, the reversible nature of inhibition prevents accumulation of the off-target adduct, thus limiting side-effects. In this perspective, we outline important characteristics of reversible covalent inhibitors, including examples and a guide for inhibitor development.
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Affiliation(s)
| | | | - Dustin Duncan
- Department of Chemistry, Brock
University, St. Catharines, Ontario L2S 3A1, Canada
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50
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Dickson P. DNA-Encoded Library Technology─A Catalyst for Covalent Ligand Discovery. ACS Chem Biol 2024; 19:802-808. [PMID: 38527941 DOI: 10.1021/acschembio.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The identification of novel covalent ligands for therapeutic purposes has long depended on serendipity, with dedicated hit finding techniques emerging only in the early 2000s. Advances in chemoproteomics have enabled robust characterization of putative drugs to derisk the unique liabilities associated with covalent hit molecules, leading to a renewed interest in this targeting modality. DNA-encoded library (DEL) technology has similarly emerged over the past two decades as a highly efficient method to identify new chemical equity toward protein targets of interest. A number of commercial and academic groups have reported methods in covalent DEL synthesis and hit identification; however, it is evident that there is still much to be done to fully realize the power of this technology for covalent ligand discovery. This perspective will explore the current approaches in covalent DEL technology and reflect on the next steps to advance this field.
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Affiliation(s)
- Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
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