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Yao H, Ren Y, Wu F, Liu J, Li J, Cao L, Yan M, Li X. Discovery of new cyclopropane sulfonamide derivatives as EGFR inhibitors to overcome C797S-mediated resistance and EGFR double mutation. Eur J Med Chem 2024; 275:116590. [PMID: 38908104 DOI: 10.1016/j.ejmech.2024.116590] [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: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024]
Abstract
The C797S mutation of EGFR leads to Osimertinib resistance by blocking the covalent binding of Cys797. To develop new agents that can overcome EGFR mutation resistance, thirty seven new cyclopropane sulfonamide derivatives were synthesized and evaluated as EGFRL858R/T790M/C797S or EGFRDel19/T790M/C797S inhibitors by structure-based screening. Most of the synthesized compounds exhibit good to excellent anti proliferation activity against to BaF3-EGFR L858R/T790M/C797S and BaF3-C797S/Del19/T790M cancer cell lines. Representative compounds 8l showed inhibitory activity against the two cancer cell lines with the IC50 values of 0.0012 and 0.0013 μM, respectively. Another compound 8h, exhibited slightly lower activity (0.0042 and 0.0034 μM of the IC50 values) to both of the two tri-mutation cell lines, but excellent activities against H1975 and PC9 cells with IC50 values of 13 and 19 nM, respectively. Considering the acquired drug resistance of tumors is a gradual process, we chose 8h for further in vivo and mechanism study. 8h was demonstrated significantly inhibited tumor growth with 72.1 % of the TGI in the BaF3/EGFR-TM xenograft tumor model and 83.5 % in the H1975-DM xenograft tumor model. Compound 8h was confirmed to be safe with no significant side effects as showed by the results of in vitro assay of human normal cells and the sections of animals major organs. Mechanism studies showed that in addition to inhibiting EGFR mutations, 8h can also target the tumor microenvironment and induce tumor cell apoptosis. All these results indicate that 8h deserves further investigation as an EGFR inhibitor to overcome C797S-mediated resistance.
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Affiliation(s)
- Han Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyuan Ren
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, 510990, PR China
| | - Feng Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiadai Liu
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, 510990, PR China
| | - Jianheng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Longcai Cao
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, 510990, PR China
| | - Ming Yan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xingshu Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, 510990, PR China.
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2
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Beyett TS, Rana JK, Schaeffner IK, Heppner DE, Eck MJ. Structural Analysis of the Macrocyclic Inhibitor BI-4020 Binding to EGFR Kinase. ChemMedChem 2024; 19:e202300343. [PMID: 38523074 PMCID: PMC11212799 DOI: 10.1002/cmdc.202300343] [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: 07/04/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
A novel macrocyclic inhibitor of mutant EGFR (BI-4020) has shown promise in pre-clinical studies of T790M and C797S drug-resistant non-small cell lung cancer. To better understand the molecular basis for BI-4020 selectivity and potency, we have carried out biochemical activity assays and structural analysis with X-ray crystallography. Biochemical potencies agree with previous studies indicating that BI-4020 is uniquely potent against drug-resistant L858R/T790M and L858R/T790M/C797S variants. X-ray structures with wild-type (2.4 Å) and T790M/V948R (3.1 Å) EGFR kinase domains show that BI-4020 is likely rendered selective due to interactions with the kinase domain hinge region as well as T790M, akin to Osimertinib. Additionally, BI-4020 is also rendered more potent due to its constrained macrocycle geometry as well as additional H-bonds to conserved K745 and T845 residues in both active and inactive conformations. These findings taken together show how this novel macrocyclic inhibitor is both highly potent and selective for mutant EGFR in a reversible mechanism and motivate structure-inspired approaches to developing targeted therapies in medicinal oncology.
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Affiliation(s)
- Tyler S. Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jaimin K. Rana
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ilse K. Schaeffner
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - David E. Heppner
- Department of Chemistry, University at Buffalo, Buffalo, NY 14260, USA
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203
| | - Michael J. Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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3
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Laudadio E, Mangano L, Minnelli C. Chemical Scaffolds for the Clinical Development of Mutant-Selective and Reversible Fourth-Generation EGFR-TKIs in NSCLC. ACS Chem Biol 2024; 19:839-854. [PMID: 38552205 DOI: 10.1021/acschembio.4c00028] [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: 04/20/2024]
Abstract
In nonsmall cell lung cancer (NSCLC), as well as in other tumors, the targeted therapy is mainly represented by tyrosine kinase inhibitors (TKIs), small molecules able to target oncogenic driver alterations affecting the gene encoding the epidermal growth factor receptor (EGFR). Up to now, several different TKIs have been developed. However, cancer cells showed an incredible adaptive tumor response to the inhibition of the sequentially mutated EGFR (EGFRM+), triggering the need to explore novel pharmacochemical strategies. This Review summarizes the recent efforts in the development of new reversible next-generation EGFR TKIs to fight the resistance against T790M and C797S mutations. Specifically, after giving an overview of the role of the EGFR's signaling pathways in cancer progression, we are going to discuss the most relevant approved drugs and drug candidates in terms of chemical structure, binding modalities, and their potency and selectivity against the mutated EGFR over the wild-type form. This could provide important guidelines and rationale for the discovery and iterative development of new drugs.
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Affiliation(s)
- Emiliano Laudadio
- Department of Science and Engineering of Matter, Environment and Urban Planning, Marche Polytechnic University, 60131 Ancona, Italy
| | - Luca Mangano
- Roche Pharma Research and Early Development, Oncology Discovery, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Cristina Minnelli
- Department of Life and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
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4
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Chang H, Zhang Z, Tian J, Bai T, Xiao Z, Wang D, Qiao R, Li C. Machine Learning-Based Virtual Screening and Identification of the Fourth-Generation EGFR Inhibitors. ACS OMEGA 2024; 9:2314-2324. [PMID: 38250375 PMCID: PMC10795152 DOI: 10.1021/acsomega.3c06225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 01/23/2024]
Abstract
Epidermal growth factor receptor (EGFR) plays a pivotal regulatory role in treating patients with advanced nonsmall cell lung cancer (NSCLC). Following the emergence of the EGFR tertiary CIS C797S mutation, all types of inhibitors lose their inhibitory activity, necessitating the urgent development of new inhibitors. Computer systems employ machine learning methods to process substantial volumes of data and construct models that enable more accurate predictions of the outcomes of new inputs. The purpose of this article is to uncover innovative fourth-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) with the aid of machine learning techniques. The paper's data set was high-dimensional and sparse, encompassing both structured and unstructured descriptors. To address this considerable challenge, we introduced a fusion framework to select critical molecule descriptors by integrating the full quadratic effect model and the Lasso model. Based on structural descriptors obtained from the full quadratic effect model, we conceived and synthesized a variety of small-molecule inhibitors. These inhibitors demonstrated potent inhibitory effects on the two mutated kinases L858R/T790M/C797S and Del19/T790M/C797S. Moreover, we applied our model to virtual screening, successfully identifying four hit compounds. We have evaluated these hit ADME characteristics and look forward to conducting activity evaluations on them in the future to discover a new generation of EGFR-TKI.
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Affiliation(s)
- Hao Chang
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Zeyu Zhang
- School
of Mathematics and Statistics, Beijing Institute
of Technology, Beijing 100081, P. R. China
| | - Jiaxin Tian
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Tian Bai
- School
of Mathematics and Statistics, Beijing Institute
of Technology, Beijing 100081, P. R. China
| | - Zijie Xiao
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Dianpeng Wang
- School
of Mathematics and Statistics, Beijing Institute
of Technology, Beijing 100081, P. R. China
| | - Renzhong Qiao
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Chao Li
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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5
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Grabe T, Jeyakumar K, Niggenaber J, Schulz T, Koska S, Kleinbölting S, Beck ME, Müller MP, Rauh D. Addressing the Osimertinib Resistance Mutation EGFR-L858R/C797S with Reversible Aminopyrimidines. ACS Med Chem Lett 2023; 14:591-598. [PMID: 37197473 PMCID: PMC10184309 DOI: 10.1021/acsmedchemlett.2c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
Drug resistance mutations emerging during the treatment of non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) inhibitors represent a major challenge in personalized cancer treatment and require constant development of new inhibitors. For the covalent irreversible EGFR inhibitor osimertinib, the predominant resistance mechanism is the acquired C797S mutation, which abolishes the covalent anchor point and thus results in a dramatic loss in potency. In this study, we present next-generation reversible EGFR inhibitors with the potential to overcome this EGFR-C797S resistance mutation. For this, we combined the reversible methylindole-aminopyrimidine scaffold known from osimertinib with the affinity driving isopropyl ester of mobocertinib. By occupying the hydrophobic back pocket, we were able to generate reversible inhibitors with subnanomolar activity against EGFR-L858R/C797S and EGFR-L858R/T790M/C797S with cellular activity on EGFR-L858R/C797S dependent Ba/F3 cells. Additionally, we were able to resolve cocrystal structures of these reversible aminopyrimidines, which will guide further inhibitor design toward C797S-mutated EGFR.
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Affiliation(s)
- Tobias Grabe
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | | | | | - Tom Schulz
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Sandra Koska
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Silke Kleinbölting
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | | | - Matthias P. Müller
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Daniel Rauh
- Department of Chemistry and
Chemical Biology, TU Dortmund University
and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte
Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Damghani T, Wittlinger F, Beyett TS, Eck MJ, Laufer SA, Heppner DE. Structural elements that enable specificity for mutant EGFR kinase domains with next-generation small-molecule inhibitors. Methods Enzymol 2023; 685:171-198. [PMID: 37245901 PMCID: PMC10445336 DOI: 10.1016/bs.mie.2023.03.013] [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] [Indexed: 05/30/2023]
Abstract
Specificity for a desired enzyme target is an essential property of small-molecule inhibitors. Molecules targeting oncogenic driver mutations in the epidermal growth factor receptor (EGFR) kinase domain have had a considerable clinical impact due to their selective binding to cancer-causing mutants compared to wild type. Despite the availability of clinically approved drugs for cancers driven by EGFR mutants, persistent challenges in drug resistance in the past decades have led to newer generations of drugs with divergent chemical structures. The current clinical challenges are mainly due to acquired resistance to third-generation inhibitors, including by the acquisition of the C797S mutation. Several diverse fourth-generation candidates and tool compounds that inhibit the C797S mutant have emerged, and their structural characterization has revealed molecular factors that allow for EGFR mutant selective binding. Here, we have reviewed all known structurally-characterized EGFR TKIs targeting clinically-relevant mutations to identify specific features that enable C797S inhibition. Newer generation EGFR inhibitors exhibit consistent and previously underutilized hydrogen bonding interactions with the conserved K745 and D855 residue side chains. We also consider binding modes and hydrogen bonding interactions of inhibitors targeting the classical ATP and the more unique allosteric sites.
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Affiliation(s)
- Tahereh Damghani
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls Universität Tübingen, Tübingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen, Germany
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.
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7
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Recent advances of novel fourth generation EGFR inhibitors in overcoming C797S mutation of lung cancer therapy. Eur J Med Chem 2022; 245:114900. [DOI: 10.1016/j.ejmech.2022.114900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/19/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
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8
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Zhao HY, Xi XX, Xin M, Zhang SQ. Overcoming C797S Mutation: The Challenges and Prospects of the Fourth-Generation EGFR-TKIs. Bioorg Chem 2022; 128:106057. [DOI: 10.1016/j.bioorg.2022.106057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/07/2023]
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