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Li N, Zheng G, Fu L, Liu N, Chen T, Lu S. Designed dualsteric modulators: A novel route for drug discovery. Drug Discov Today 2024; 29:104141. [PMID: 39168404 DOI: 10.1016/j.drudis.2024.104141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
Orthosteric and allosteric modulators, which constitute the majority of current drugs, bind to the orthosteric and allosteric sites of target proteins, respectively. However, the clinical efficacy of these agents is frequently compromised by poor selectivity or reduced potency. Dualsteric modulators feature two linked pharmacophores that bind to orthosteric and allosteric sites of the target proteins simultaneously, thereby offering a promising avenue to achieve both potency and specificity. In this review, we summarize recent structures available for dualsteric modulators in complex with their target proteins, elucidating detailed drug-target interactions and dualsteric action patterns. Moreover, we provide a design and optimization strategy for dualsteric modulators based on structure-based drug design approaches.
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Affiliation(s)
- Nuan Li
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guodong Zheng
- Department of VIP Clinic, Changhai Hospital, Affiliated to Naval Medical University, Shanghai 200433, China
| | - Lili Fu
- Department of Nephrology, People's Hospital of Pudong New Area, Shanghai University of Medicine & Health Sciences, Shanghai 201299, China
| | - Ning Liu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai 200003, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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2
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Zhou Y, Kang J, Lu X. Targeting Solvent-Front Mutations for Kinase Drug Discovery: From Structural Basis to Design Strategies. J Med Chem 2024. [PMID: 39143914 DOI: 10.1021/acs.jmedchem.4c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Solvent-front mutations have emerged as a common mechanism leading to acquired resistance to kinase inhibitors, representing a major challenge in the clinic. Several new-generation kinase inhibitors targeting solvent-front mutations have either been approved or advanced to clinical trials. However, there remains a need to discover effective, new-generation inhibitors. In this Perspective, we systematically summarize the general types of solvent-front mutations across the kinome and describe the development of inhibitors targeting some key solvent-front mutations. Additionally, we highlight the challenges and opportunities for the next generation of kinase inhibitors directed toward overcoming solvent-front mutations.
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Affiliation(s)
- Yang Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Jibo Kang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaoyun Lu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
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3
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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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4
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Ferro A, Marinato GM, Mulargiu C, Marino M, Pasello G, Guarneri V, Bonanno L. The study of primary and acquired resistance to first-line osimertinib to improve the outcome of EGFR-mutated advanced Non-small cell lung cancer patients: the challenge is open for new therapeutic strategies. Crit Rev Oncol Hematol 2024; 196:104295. [PMID: 38382773 DOI: 10.1016/j.critrevonc.2024.104295] [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: 09/14/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
The development of targeted therapy in epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC) patients has radically changed their clinical perspectives. Current first-line standard treatment for advanced disease is commonly considered third-generation tyrosine kinase inhibitors (TKI), osimertinib. The study of primary and acquired resistance to front-line osimertinib is one of the main burning issues to further improve patients' outcome. Great heterogeneity has been depicted in terms of duration of clinical benefit and pattern of progression and this might be related to molecular factors including subtypes of EGFR mutations and concomitant genetic alterations. Acquired resistance can be categorized into two main classes: EGFR-dependent and EGFR-independent mechanisms and specific pattern of progression to first-line osimertinib have been demonstrated. The purpose of the manuscript is to provide a comprehensive overview of literature about molecular resistance mechanisms to first-line osimertinib, from a clinical perspective and therefore in relationship to emerging therapeutic approaches.
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Affiliation(s)
- Alessandra Ferro
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Gian Marco Marinato
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Cristiana Mulargiu
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Monica Marino
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Giulia Pasello
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Laura Bonanno
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy.
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5
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Wittlinger F, Ogboo BC, Shevchenko E, Damghani T, Pham CD, Schaeffner IK, Oligny BT, Chitnis SP, Beyett TS, Rasch A, Buckley B, Urul DA, Shaurova T, May EW, Schaefer EM, Eck MJ, Hershberger PA, Poso A, Laufer SA, Heppner DE. Linking ATP and allosteric sites to achieve superadditive binding with bivalent EGFR kinase inhibitors. Commun Chem 2024; 7:38. [PMID: 38378740 PMCID: PMC10879502 DOI: 10.1038/s42004-024-01108-3] [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: 09/06/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Bivalent molecules consisting of groups connected through bridging linkers often exhibit strong target binding and unique biological effects. However, developing bivalent inhibitors with the desired activity is challenging due to the dual motif architecture of these molecules and the variability that can be introduced through differing linker structures and geometries. We report a set of alternatively linked bivalent EGFR inhibitors that simultaneously occupy the ATP substrate and allosteric pockets. Crystal structures show that initial and redesigned linkers bridging a trisubstituted imidazole ATP-site inhibitor and dibenzodiazepinone allosteric-site inhibitor proved successful in spanning these sites. The re-engineered linker yielded a compound that exhibited significantly higher potency (~60 pM) against the drug-resistant EGFR L858R/T790M and L858R/T790M/C797S, which was superadditive as compared with the parent molecules. The enhanced potency is attributed to factors stemming from the linker connection to the allosteric-site group and informs strategies to engineer linkers in bivalent agent design.
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Affiliation(s)
- Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Blessing C Ogboo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
| | - Tahereh Damghani
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Calvin D Pham
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, 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
| | - Brandon T Oligny
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Surbhi P Chitnis
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - 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
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 5119 Rollins Research Center, 1510 Clifton Rd, Atlanta, GA, 30322, USA
| | - Alexander Rasch
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Brian Buckley
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Daniel A Urul
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | - Tatiana Shaurova
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Earl W May
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | | | - 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
| | - Pamela A Hershberger
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany.
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany.
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
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6
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Lee JY, Gebauer E, Seeliger MA, Bahar I. Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments. Curr Opin Struct Biol 2024; 84:102770. [PMID: 38211377 PMCID: PMC11044982 DOI: 10.1016/j.sbi.2023.102770] [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: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
The eukaryotic protein kinase domain has been a broadly explored target for drug discovery, despite limitations imposed by its high sequence conservation as a shared modular domain and the development of resistance to drugs. One way of addressing those limitations has been to target its potential allosteric sites, shortly called allo-targeting, in conjunction with, or separately from, its conserved catalytic/orthosteric site that has been widely exploited. Allosteric regulation has gained importance as an alternative to overcome the drawbacks associated with the indiscriminate effect of targeting the active site, and it turned out to be particularly useful for these highly promiscuous and broadly shared kinase domains. Yet, allo-targeting often faces challenges as the allosteric sites are not as clearly defined as its orthosteric sites, and the effect on the protein function may not be unambiguously assessed. A robust understanding of the consequence of site-specific allo-targeting on the conformational dynamics of the target protein is essential to design effective allo-targeting strategies. Recent years have seen important advances in in silico identification of druggable sites and distinguishing among them those sites expected to allosterically mediate conformational switches essential to signal transmission. The present opinion underscores the utility of such computational approaches applied to the kinase domain, with the help of comparison between computational predictions and experimental observations.
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Affiliation(s)
- Ji Young Lee
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA
| | - Emma Gebauer
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA
| | - Markus A Seeliger
- Laufer Center for Physical & Quantitative Biology, Department of Pharmacological Sciences, School of Medicine, Stony Brook University, NY 11794, USA.
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, NY 11794, USA.
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7
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Hoyt KW, Urul DA, Ogboo BC, Wittlinger F, Laufer SA, Schaefer EM, May EW, Heppner DE. Pitfalls and Considerations in Determining the Potency and Mutant Selectivity of Covalent Epidermal Growth Factor Receptor Inhibitors. J Med Chem 2024; 67:2-16. [PMID: 38134304 DOI: 10.1021/acs.jmedchem.3c01502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Enzyme inhibitors that form covalent bonds with their targets are being increasingly pursued in drug development. Assessing their biochemical activity relies on time-dependent assays, which are distinct and more complex compared with methods commonly employed for reversible-binding inhibitors. To provide general guidance to the covalent inhibitor development community, we explored methods and reported kinetic values and experimental factors in determining the biochemical activity of various covalent epidermal growth factor receptor (EGFR) inhibitors. We showcase how liquid handling and assay reagents impact kinetic parameters and potency interpretations, which are critical for structure-kinetic relationships and covalent drug design. Additionally, we include benchmark kinetic values with reference inhibitors, which are imperative, as covalent EGFR inhibitor kinetic values are infrequently consistent in the literature. This overview seeks to inform best practices for developing new covalent inhibitors and highlight appropriate steps to address gaps in knowledge presently limiting assay reliability and reproducibility.
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Affiliation(s)
- Kristopher W Hoyt
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel A Urul
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - Blessing C Ogboo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Erik M Schaefer
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - Earl W May
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, United States
- Department of Structural Biology, The State University of New York, Buffalo, New York 14203, United States
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8
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Kim JJ, Schaeffner IK, Heppner DE, To C, Jänne PA, Beyett TS, Eck MJ. A Constitutive EGFR Kinase Dimer to Study Inhibitor Pharmacology. Mol Pharmacol 2024; 105:97-103. [PMID: 38164587 PMCID: PMC10794983 DOI: 10.1124/molpharm.123.000768] [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: 07/31/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Lung cancer is commonly caused by activating mutations in the epidermal growth factor receptor (EGFR). Allosteric kinase inhibitors are unaffected by common ATP-site resistance mutations and represent a promising therapeutic strategy for targeting drug-resistant EGFR variants. However, allosteric inhibitors are antagonized by kinase dimerization, and understanding this phenomenon has been limited to cellular experiments. To facilitate the study of allosteric inhibitor pharmacology, we designed and purified a constitutive EGFR kinase dimer harboring the clinically relevant L858R/T790M mutations. Kinetic characterization revealed that the EGFR kinase dimer is more active than monomeric EGFR(L858R/T790M) kinase and has the same Km,ATP Biochemical profiling of a large panel of ATP-competitive and allosteric EGFR inhibitors showed that allosteric inhibitor potency decreased by >500-fold in the kinase dimer compared with monomer, yielding IC50 values that correlate well with Ba/F3 cellular potencies. Thus, this readily purifiable constitutive asymmetric EGFR kinase dimer represents an attractive tool for biochemical evaluation of EGFR inhibitor pharmacology, in particular for allosteric inhibitors. SIGNIFICANCE STATEMENT: Drugs targeting epidermal growth factor receptor (EGFR) kinase are commonly used to treat lung cancers but are affected by receptor dimerization. Here, we describe a locked kinase dimer that can be used to study EGFR inhibitor pharmacology.
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Affiliation(s)
- Justin J Kim
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - Ilse K Schaeffner
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - David E Heppner
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - Ciric To
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - Pasi A Jänne
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - Tyler S Beyett
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
| | - Michael J Eck
- Department of Cancer Biology (J.J.K., I.K.S., T.S.B., M.J.E.), Lowe Center for Thoracic Oncology (C.T., P.A.J.), and Department of Medical Oncology (C.T., P.A.J.), Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology (J.J.K., I.K.S., T.S.B., M.J.E.) and Department of Medicine (C.T., P.A.J.), Harvard Medical School, Boston, Massachusetts; Department of Chemistry, University at Buffalo, Buffalo, New York (D.E.H.); Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York (D.E.H.)
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9
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Zhou Y, Takahashi JI, Sakurai H. New Directions for Advanced Targeting Strategies of EGFR Signaling in Cancer. Biol Pharm Bull 2024; 47:895-903. [PMID: 38692865 DOI: 10.1248/bpb.b23-00924] [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] [Indexed: 05/03/2024]
Abstract
Epidermal growth factor (EGF)-EGF receptor (EGFR) signaling studies paved the way for a basic understanding of growth factor and oncogene signaling pathways and the development of tyrosine kinase inhibitors (TKIs). Due to resistance mutations and the activation of alternative pathways when cancer cells escape TKIs, highly diverse cell populations form in recurrent tumors through mechanisms that have not yet been fully elucidated. In this review, we summarize recent advances in EGFR basic research on signaling networks and intracellular trafficking that may clarify the novel mechanisms of inhibitor resistance, discuss recent clinical developments in EGFR-targeted cancer therapy, and offer novel strategies for cancer drug development.
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Affiliation(s)
- Yue Zhou
- Department of Cancer Cell Biology, Faculty of Pharmaceutical Sciences, University of Toyama
| | - Jun-Ichiro Takahashi
- Department of Cancer Cell Biology, Faculty of Pharmaceutical Sciences, University of Toyama
| | - Hiroaki Sakurai
- Department of Cancer Cell Biology, Faculty of Pharmaceutical Sciences, University of Toyama
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10
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Bhanja KK, Sharma M, Patra N. Uncovering the Structural and Binding Insights of Dual Inhibitors Simultaneously Targeting Two Distinct Sites on EGFR Kinase. J Phys Chem B 2023; 127:10749-10765. [PMID: 38055900 DOI: 10.1021/acs.jpcb.3c04337] [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: 12/08/2023]
Abstract
Epidermal growth factor receptor (EGFR) is the first growth factor receptor identified in normal cells that is related to the receptor tyrosine kinase, which causes regular cell division. A point mutation in EGFR intracellular kinase domain forces the abnormal cell divisions throughout time, leading to non-small cell lung cancer (NSCLC) transformation. Thus, competitive inhibitors that bind to the ATP binding pocket have been developed as a targeted therapy for NSCLC. The third-generation kinase inhibitor Osimertinib is currently playing a very vital role in the treatment of NSCLC. However, it is not effective toward the C797S kinase domain mutation. For this reason, fourth-generation kinase noncompetitive inhibitors are introduced which work through binding to an allosteric pocket near the ATP binding region and act as a better binding agent for this mutated kinase domain. However, the problem is that these single fourth-generation kinase inhibitors may not be as effective as a single agent. The aim of this work was to apply combinations of these two inhibitors together in different binding regions of EGFR without overlapping the resistance mechanism to obtain the key direct and indirect interactions occurring between them. Moreover, the free energy of dissociation of an inhibitor from its binding sites in the presence of a second inhibitor immobilized in another binding site was also the focus of the study. To realize this aim, we performed conventional molecular dynamics simulations and principal component analysis and dynamic cross-correlation matrices along with umbrella sampling. Our results demonstrated that binding of dual inhibitors triggered conformational changes of the protein more toward the inactive state. Furthermore, allosteric inhibitors bound more strongly to protein kinase EGFR than the orthosteric inhibitors in the presence of dual inhibitors. Finally, the binding mechanism and important hydrogen-bonding residues during unbinding of the inhibitors were fully elucidated. This study provides insight into the binding of the receptor-orthosteric inhibitor-allosteric inhibitor, which can be helpful for further design of novel inhibitors that have a better inhibitory action.
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Affiliation(s)
- Kousik K Bhanja
- Department of Chemistry & Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Madhur Sharma
- Department of Chemistry & Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry & Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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11
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Abo Al-Hamd MG, Tawfik HO, Abdullah O, Yamaguchi K, Sugiura M, Mehany ABM, El-Hamamsy MH, El-Moselhy TF. Recruitment of hexahydroquinoline as anticancer scaffold targeting inhibition of wild and mutants EGFR (EGFR WT, EGFR T790M, and EGFR L858R). J Enzyme Inhib Med Chem 2023; 38:2241674. [PMID: 37548154 PMCID: PMC10408569 DOI: 10.1080/14756366.2023.2241674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/14/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023] Open
Abstract
Hexahydroquinoline (HHQ) scaffold was constructed and recruited for development of new series of anticancer agents. Thirty-two new compounds were synthesised where x-ray crystallography was performed to confirm enantiomerism. Thirteen compounds showed moderate to good activity against NCI 60 cancer cell lines, with GI % mean up to 74% for 10c. Expending erlotinib as a reference drug, target compounds were verified for their inhibiting activities against EGFRWT, EGFRT790M, and EGFRL858R where compound 10d was the best inhibitor with IC50 = 0.097, 0.280, and 0.051 µM, respectively, compared to erlotinib (IC50 = 0.082 µM, 0.342 µM, and 0.055 µM, respectively). Safety profile was validated using normal human lung (IMR-90) cells. 10c and 10d disrupted cell cycle at pre-G1 and G2/M phases in lung cancer, HOP-92, and cell line. Molecular docking study was achieved to understand the potential binding interactions and affinities in the active sites of three versions of EGFRs.
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Affiliation(s)
- Mahmoud G. Abo Al-Hamd
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Haytham O. Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Omeima Abdullah
- Pharmaceutical Chemistry Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Koki Yamaguchi
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Masaharu Sugiura
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Ahmed B. M. Mehany
- Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mervat H. El-Hamamsy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Tarek F. El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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12
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Zhang Y, Huang Q, Xu Q, Jia C, Xia Y. Pimavanserin tartrate induces apoptosis and cytoprotective autophagy and synergizes with chemotherapy on triple negative breast cancer. Biomed Pharmacother 2023; 168:115665. [PMID: 37832400 DOI: 10.1016/j.biopha.2023.115665] [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: 07/03/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Triple negative breast cancer (TNBC) poses a significant clinical challenge due to its lack of targeted therapy options and the frequent development of chemotherapy resistance. Metastasis remains a primary cause of mortality in late-stage TNBC patients, underscoring the urgent need for alternative treatments. Repurposing existing drugs offers a promising strategy for the discovery of novel therapies. In this study, we investigated the potential of pimavanserin tartrate (PVT) as a treatment for TNBC. While previous studies have highlighted PVT's anticancer effects in various cancer types, its activity in TNBC remains unclear. Our investigation aimed to elucidate the anticancer effects and underlying mechanisms of PVT in TNBC. We evaluated the impact of PVT and combination treatments involving PVT on TNBC cell viability, apoptosis, autophagy, and associated signaling pathways. Our findings revealed that PVT may induce mitochondria-dependent intrinsic apoptosis and caused cytoprotective autophagy via the PI3K/Akt/mTOR pathway in TNBC cells in vitro. Notably, our study demonstrated strong synergistic anti-TNBC effects when combining PVT with doxorubicin. We also found PVT showed some efficacies to inhibit TNBC tumor growth in vivo. These results provided valuable insights into the potential of PVT as an anti-TNBC therapeutic and a possible option for enhancing the sensitivity of TNBC cells to conventional chemotherapy drugs. Further studies are needed to determine the activity and mechanism of PVT in inhibiting TNBC.
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Affiliation(s)
- Yiqian Zhang
- Department of Rehabilitation Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qianrui Huang
- Department of Rehabilitation Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qisi Xu
- School of Food and Bioengineering, Xihua University, Chengdu 610041, China
| | - Chengsen Jia
- Department of Rehabilitation Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Xia
- Department of Rehabilitation Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Key Laboratory of Rehabilitation Medicine in Sichuan Province/Rehabilitation Medicine Research Institute, Chengdu 610041, China.
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13
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Elsebaie HA, El-Bastawissy EA, Elberembally KM, Khaleel EF, Badi RM, Shaldam MA, Eldehna WM, Tawfik HO, El-Moselhy TF. Novel 4-(2-arylidenehydrazineyl)thienopyrimidine derivatives as anticancer EGFR inhibitors: Design, synthesis, biological evaluation, kinome selectivity and in silico insights. Bioorg Chem 2023; 140:106799. [PMID: 37625210 DOI: 10.1016/j.bioorg.2023.106799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 08/27/2023]
Abstract
The current study discovered fifteen new thieno[2,3-d]pyrimidine derivatives with potential anticancer action, including 5a-l, 6, and 7a-b. Results from the NCI screening revealed that compounds 5f-i and 7a significantly inhibited the proliferation of MDA-MB-468 cells at mean GI% and GI50 levels. Compared to staurosporine, these compounds (5f-i and 7a) demonstrated better safety towards typical WI-38 cells. Compounds 5g and 7a demonstrated the highest inhibition (two-digit nanomolar) when compared to erlotinib when their potency was tested on EGFR kinase. Considering the outcomes above, 5g was examined for its ability to disrupt the cell cycle with trigger apoptosis in breast cancer MDA-MB-468 cell lines. The apoptosis markers Bax, Bcl-2, Caspase-8, and Caspase-9, were detected. In silico molecular docking and dynamic simulation were used to explainthe biological activities of the most potent compound.
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Affiliation(s)
- Heba A Elsebaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527 Egypt.
| | - Eman A El-Bastawissy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527 Egypt.
| | - Kamel M Elberembally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527 Egypt.
| | - Eman F Khaleel
- Department of Medical Physiology, College of Medicine, King Khalid University, King Khalid University, Asir 61421, Saudi Arabia.
| | - Rehab Mustafa Badi
- Department of Medical Physiology, College of Medicine, King Khalid University, King Khalid University, Asir 61421, Saudi Arabia.
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; School of Biotechnology, Badr University in Cairo, Badr City 11829, Egypt.
| | - Haytham O Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527 Egypt.
| | - Tarek F El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527 Egypt.
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14
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Zhang Y. Targeting Epidermal Growth Factor Receptor for Cancer Treatment: Abolishing Both Kinase-Dependent and Kinase-Independent Functions of the Receptor. Pharmacol Rev 2023; 75:1218-1232. [PMID: 37339882 PMCID: PMC10595022 DOI: 10.1124/pharmrev.123.000906] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
Epidermal growth factor receptor (EGFR), a receptor tyrosine kinase, is activated by ligand binding, overexpression, or mutation. It is well known for its tyrosine kinase-dependent oncogenic activities in a variety of human cancers. A large number of EGFR inhibitors have been developed for cancer treatment, including monoclonal antibodies, tyrosine kinase inhibitors, and a vaccine. The EGFR inhibitors are aimed at inhibiting the activation or the activity of EGFR tyrosine kinase. However, these agents have shown efficacy in only a few types of cancers. Drug resistance, both intrinsic and acquired, is common even in cancers where the inhibitors have shown efficacy. The drug resistance mechanism is complex and not fully known. The key vulnerability of cancer cells that are resistant to EGFR inhibitors has not been identified. Nevertheless, it has been increasingly recognized in recent years that EGFR also possesses kinase-independent oncogenic functions and that these noncanonical functions may play a crucial role in cancer resistance to EGFR inhibitors. In this review, both kinase-dependent and -independent activities of EGFR are discussed. Also discussed are the mechanisms of actions and therapeutic activities of clinically used EGFR inhibitors and sustained EGFR overexpression and EGFR interaction with other receptor tyrosine kinases to counter the EGFR inhibitors. Moreover, this review discusses emerging experimental therapeutics that have shown potential for overcoming the limitation of the current EGFR inhibitors in preclinical studies. The findings underscore the importance and feasibility of targeting both kinase-dependent and -independent functions of EGFR to enhance therapeutic efficacy and minimize drug resistance. SIGNIFICANCE STATEMENT: EGFR is a major oncogenic driver and therapeutic target, but cancer resistance to current EGFR inhibitors remains a significant unmet clinical problem. This article reviews the cancer biology of EGFR as well as the mechanisms of actions and the therapeutic efficacies of current and emerging EGFR inhibitors. The findings could potentially lead to development of more effective treatments for EGFR-positive cancers.
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Affiliation(s)
- Yuesheng Zhang
- Department of Pharmacology and Toxicology, School of Medicine, and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
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15
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Rygiel KA, Elkins JM. Recent advances in the structural biology of tyrosine kinases. Curr Opin Struct Biol 2023; 82:102665. [PMID: 37562149 DOI: 10.1016/j.sbi.2023.102665] [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: 05/14/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
The past few years have seen exciting discoveries in the area of tyrosine kinase structural biology including the first high resolution models of full-length receptor tyrosine kinases and new mechanistic insights into the structural mechanisms of receptor tyrosine kinase activation. Despite being a mature area of research, the application of new technologies continues to advance our understanding. In this article we highlight a selection of recent studies that illustrate the current areas of research interest, focussing in particular on the exciting progress made possible by cryo-electron-microscopy. These new discoveries may herald a wave of new design ideas for therapeutics acting through novel mechanisms.
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Affiliation(s)
- Karolina A Rygiel
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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16
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Heppner D, Wittlinger F, Ogboo B, Shevchenko E, Damghani T, Pham C, Schaeffner I, Oligny B, Chitnis S, Beyett T, Rasch A, Buckley B, Urul D, Shaurova T, May E, Schaefer E, Eck M, Hershberger P, Poso A, Laufer S. Linking ATP and allosteric sites to achieve superadditive binding with bivalent EGFR kinase inhibitors. RESEARCH SQUARE 2023:rs.3.rs-3286949. [PMID: 37790373 PMCID: PMC10543509 DOI: 10.21203/rs.3.rs-3286949/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Bivalent molecules consisting of groups connected through bridging linkers often exhibit strong target binding and unique biological effects. However, developing bivalent inhibitors with the desired activity is challenging due to the dual motif architecture of these molecules and the variability that can be introduced through differing linker structures and geometries. We report a set of alternatively linked bivalent EGFR inhibitors that simultaneously occupy the ATP substrate and allosteric pockets. Crystal structures show that initial and redesigned linkers bridging a trisubstituted imidazole ATP-site inhibitor and dibenzodiazepinone allosteric-site inhibitor proved successful in spanning these sites. The reengineered linker yielded a compound that exhibited significantly higher potency (~60 pM) against the drug-resistant EGFR L858R/T790M and L858R/T790M/C797S, which was superadditive as compared with the parent molecules. The enhanced potency is attributed to factors stemming from the linker connection to the allosteric-site group and informs strategies to engineer linkers in bivalent agent design.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Eck
- Dana-Farber Cancer Institute & Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School
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17
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Nussinov R, Zhang M, Liu Y, Jang H. AlphaFold, allosteric, and orthosteric drug discovery: Ways forward. Drug Discov Today 2023; 28:103551. [PMID: 36907321 PMCID: PMC10238671 DOI: 10.1016/j.drudis.2023.103551] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Drug discovery is arguably a highly challenging and significant interdisciplinary aim. The stunning success of the artificial intelligence-powered AlphaFold, whose latest version is buttressed by an innovative machine-learning approach that integrates physical and biological knowledge about protein structures, raised drug discovery hopes that unsurprisingly, have not come to bear. Even though accurate, the models are rigid, including the drug pockets. AlphaFold's mixed performance poses the question of how its power can be harnessed in drug discovery. Here we discuss possible ways of going forward wielding its strengths, while bearing in mind what AlphaFold can and cannot do. For kinases and receptors, an input enriched in active (ON) state models can better AlphaFold's chance of rational drug design success.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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18
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Sato S, Yamamoto K, Ito M, Nishino K, Otsuka T, Irie K, Nagao M. Enhancement of Inhibitory Activity by Combining Allosteric Inhibitors Putatively Binding to Different Allosteric Sites on Cathepsin K. Molecules 2023; 28:molecules28104197. [PMID: 37241936 DOI: 10.3390/molecules28104197] [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: 03/28/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Cathepsin K, which is involved in bone resorption, is a good target for treating osteoporosis, but no clinically approved medicine has been developed. Recently, allosteric inhibitors with high specificity and few side effects have been attracting attention for use in new medicines. METHODS Cathepsin K inhibitors were isolated from the methanol extract of Chamaecrista nomame (Leguminosae) using cathepsin K inhibition activity-assisted multi-step chromatography. Standard kinetic analysis was employed to examine the mechanism of cathepsin K inhibition when an isolated inhibitor and its derivative were used. The allosteric binding of these cathepsin K inhibitors was supported by a docking study using AutoDock vina. Combinations of allosteric cathepsin K inhibitors expected to bind to different allosteric sites were examined by means of cathepsin K inhibition assay. RESULTS Two types of cathepsin K inhibitors were identified in the methanol extract of Chamaecrista nomame. One type consisted of cassiaoccidentalin B and torachrysone 8-β-gentiobioside, and inhibited both cathepsin K and B with similar inhibitory potential, while the other type of inhibitor consisted of pheophytin a, and inhibited cathepsin K but not cathepsin B, suggesting that pheophytin a binds to an allosteric site of cathepsin K. Kinetic analysis of inhibitory activity suggested that pheophytin a and its derivative, pheophorbide b, bind allosterically to cathepsin K. This possibility was supported by a docking study on cathepsin K. The cathepsin K inhibitory activity of pheophytin a and pheophorbide b was enhanced by combining them with the allosteric inhibitors NSC 13345 and NSC94914, which bind to other allosteric sites on cathepsin K. CONCLUSIONS Different allosteric inhibitors that bind to different sites in combination, as shown in this study, may be useful for designing new allosteric inhibitory drugs with high specificity and few side effects.
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Affiliation(s)
- Shun Sato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kana Yamamoto
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Moeno Ito
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Takanao Otsuka
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Okayama 700-0005, Japan
| | - Kazuhiro Irie
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masaya Nagao
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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19
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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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20
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Kim C, Ludewig H, Hadzipasic A, Kutter S, Nguyen V, Kern D. A biophysical framework for double-drugging kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533217. [PMID: 36993258 PMCID: PMC10055307 DOI: 10.1101/2023.03.17.533217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as "double-drugging", has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Förster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing this cooperative effect. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the doubledrugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe the first fully-closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light onto the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of doubledrugging strategies.
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Affiliation(s)
- C. Kim
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - H. Ludewig
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - A. Hadzipasic
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - S. Kutter
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - V. Nguyen
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - D. Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
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21
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Yang YC, Zhao CJ, Jin ZF, Zheng J, Ma LT. Targeted therapy based on ubiquitin-specific proteases, signalling pathways and E3 ligases in non-small-cell lung cancer. Front Oncol 2023; 13:1120828. [PMID: 36969062 PMCID: PMC10036052 DOI: 10.3389/fonc.2023.1120828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023] Open
Abstract
Lung cancer is one of the most common malignant tumours worldwide, with the highest mortality rate. Approximately 1.6 million deaths owing to lung cancer are reported annually; of which, 85% of deaths occur owing to non-small-cell lung cancer (NSCLC). At present, the conventional treatment methods for NSCLC include radiotherapy, chemotherapy, targeted therapy and surgery. However, drug resistance and tumour invasion or metastasis often lead to treatment failure. The ubiquitin–proteasome pathway (UPP) plays an important role in the occurrence and development of tumours. Upregulation or inhibition of proteins or enzymes involved in UPP can promote or inhibit the occurrence and development of tumours, respectively. As regulators of UPP, ubiquitin-specific proteases (USPs) primarily inhibit the degradation of target proteins by proteasomes through deubiquitination and hence play a carcinogenic or anticancer role. This review focuses on the role of USPs in the occurrence and development of NSCLC and the potential of corresponding targeted drugs, PROTACs and small-molecule inhibitors in the treatment of NSCLC.
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Affiliation(s)
- Yu-Chen Yang
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Can-Jun Zhao
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Zhao-Feng Jin
- School of Psychology, Weifang Medical University, Weifang, China
| | - Jin Zheng
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
| | - Li-Tian Ma
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
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Dou D, Wang J, Qiao Y, Wumaier G, Sha W, Li W, Mei W, Yang T, Zhang C, He H, Wang C, Chu L, Sun B, Su R, Ma X, Gong M, Xie L, Jiang W, Diao Y, Zhu L, Zhao Z, Chen Z, Xu Y, Li S, Li H. Discovery and optimization of 4-anilinoquinazoline derivatives spanning ATP binding site and allosteric site as effective EGFR-C797S inhibitors. Eur J Med Chem 2022; 244:114856. [DOI: 10.1016/j.ejmech.2022.114856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
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23
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OSW-1 induces apoptosis and cyto-protective autophagy, and synergizes with chemotherapy on triple negative breast cancer metastasis. Cell Oncol (Dordr) 2022; 45:1255-1275. [PMID: 36155886 DOI: 10.1007/s13402-022-00716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is the most malignant subtype of breast cancer. As yet, chemotherapy with drugs such as doxorubicin is the main treatment strategy. However, drug resistance and dose-dependent toxicities restrict their clinical use. Natural products are major sources of anti-tumor drugs. OSW-1 is a natural compound with strong anti-cancer effects in several types of cancer, but its effects on the efficacy of chemotherapy in TNBC and its underlying mechanism remain unclear. METHODS The inhibitory activities of OSW-1 and its combination with several chemotherapy drugs were tested using in vitro assays and in vivo subcutaneous and metastatic mouse TNBC models. The effects of the mono- and combination treatments on TNBC cell viability, apoptosis, autophagy and related signaling pathways were assessed using MTT, flow cytometry, RNA sequencing and immunology-based assays. In addition, the in vivo inhibitory effects of OSW-1 and (combined) chemotherapies were evaluated in subcutaneous and metastatic mouse tumor models. RESULTS We found that OSW-1 induces Ca2+-dependent mitochondria-dependent intrinsic apoptosis and cyto-protective autophagy through the PI3K-Akt-mTOR pathway in TNBC cells in vitro. We also found that OSW-1 and doxorubicin exhibited strong synergistic anti-TNBC capabilities both in vivo and in vitro. Combination treatment strongly inhibited spontaneous and experimental lung metastases in 4T1 mouse models. In addition, the combination strategy of OSW-1 + Carboplatin + Docetaxel showed an excellent anti-metastatic effect in vivo. CONCLUSIONS Our data revealed the mode of action and molecular mechanism underlying the effect of OSW-1 against TNBC, and provided a useful guidance for improving the sensitivity of TNBC cells to conventional chemotherapeutic drugs, which warrants further investigation.
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24
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Obst-Sander U, Ricci A, Kuhn B, Friess T, Koldewey P, Kuglstatter A, Hewings D, Goergler A, Steiner S, Rueher D, Imhoff MP, Raschetti N, Marty HP, Dietzig A, Rynn C, Ehler A, Burger D, Kornacker M, Schaffland JP, Herting F, Pao W, Bischoff JR, Martoglio B, Alice Nagel Y, Jaeschke G. Discovery of Novel Allosteric EGFR L858R Inhibitors for the Treatment of Non-Small-Cell Lung Cancer as a Single Agent or in Combination with Osimertinib. J Med Chem 2022; 65:13052-13073. [PMID: 36178776 DOI: 10.1021/acs.jmedchem.2c00893] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Addressing resistance to third-generation EGFR TKIs such as osimertinib via the EGFRC797S mutation remains a highly unmet need in EGFR-driven non-small-cell lung cancer (NSCLC). Herein, we present the discovery of the allosteric EGFR inhibitor 57, a novel fourth-generation inhibitor to overcome EGFRC797S-mediated resistance in patients harboring the activating EGFRL858R mutation. 57 exhibits an improved potency compared to previous allosteric EGFR inhibitors. To our knowledge, 57 is the first allosteric EGFR inhibitor that demonstrates robust tumor regression in a mutant EGFRL858R/C797S tumor model. Additionally, 57 is active in an H1975 EGFRL858R/T790M NSCLC xenograft model and shows superior efficacy in combination with osimertinib compared to the single agents. Our data highlight the potential of 57 as a single agent against EGFRL858R/C797S and EGFRL858R/T790M/C797S and as combination therapy for EGFRL858R- and EGFRL858R/T790M-driven NSCLC.
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Affiliation(s)
- Ulrike Obst-Sander
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Antonio Ricci
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Thomas Friess
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg82377, Germany
| | - Philipp Koldewey
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - David Hewings
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Annick Goergler
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Sandra Steiner
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Daniel Rueher
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Marie-Paule Imhoff
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Noemi Raschetti
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Hans-Peter Marty
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Aline Dietzig
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Caroline Rynn
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Andreas Ehler
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Dominique Burger
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Martin Kornacker
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Clinical Development Oncology, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Jeannine Petrig Schaffland
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Frank Herting
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Discovery Oncology, Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg82377, Germany
| | - William Pao
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - James R Bischoff
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Bruno Martoglio
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Yvonne Alice Nagel
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Cancer Targeted Therapies, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
| | - Georg Jaeschke
- F. Hoffmann-La Roche Ltd, Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel4070, Switzerland
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25
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López-Cade I, García-Barberán V, Cabañas Morafraile E, Díaz-Tejeiro C, Saiz-Ladera C, Sanvicente A, Pérez Segura P, Pandiella A, Győrffy B, Ocaña A. Genomic mapping of copy number variations influencing immune response in breast cancer. Front Oncol 2022; 12:975437. [PMID: 36119512 PMCID: PMC9476651 DOI: 10.3389/fonc.2022.975437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype.
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Affiliation(s)
- Igor López-Cade
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Esther Cabañas Morafraile
- Center for Biological Research, Margarita Salas Centro de Investigaciones Biologicas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Spanish National Research Council, Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Cristina Saiz-Ladera
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Pedro Pérez Segura
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer [IBMCC-Centro de Investigacion del Cancer (CIC)], Instituto de Investigación Biomédica de Salamanca (IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2Department of Pediatrics, Semmelweis University, Budapest, Hungary
- Termeszettudomanyi Kutatokozpont (TTK) Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Alberto Ocaña
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
- Translational Oncology Laboratory, Translational Research Unit, Albacete University Hospital, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
- *Correspondence: Alberto Ocaña,
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26
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Koulouris A, Tsagkaris C, Corriero AC, Metro G, Mountzios G. Resistance to TKIs in EGFR-Mutated Non-Small Cell Lung Cancer: From Mechanisms to New Therapeutic Strategies. Cancers (Basel) 2022; 14:3337. [PMID: 35884398 PMCID: PMC9320011 DOI: 10.3390/cancers14143337] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/25/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Resistance to tyrosine kinase inhibitors (TKIs) of the epidermal growth factor receptor (EGFR) in advanced mutant Non-Small Cell Lung Cancer (NSCLC) constitutes a therapeutic challenge. This review intends to summarize the existing knowledge about the mechanisms of resistance to TKIs in the context of EGFR mutant NSCLC and discuss its clinical and therapeutic implications. EGFR-dependent and independent molecular pathways have the potential to overcome or circumvent the activity of EGFR-targeted agents including the third-generation TKI, osimertinib, negatively impacting clinical outcomes. CNS metastases occur frequently in patients on EGFR-TKIs, due to the inability of first and second-generation agents to overcome both the BBB and the acquired resistance of cancer cells in the CNS. Newer-generation TKIs, TKIs targeting EGFR-independent resistance mechanisms, bispecific antibodies and antibody-drug conjugates or combinations of TKIs with other TKIs or chemotherapy, immunotherapy and Anti-Vascular Endothelial Growth Factors (anti-VEGFs) are currently in use or under investigation in EGFR mutant NSCLC. Liquid biopsies detecting mutant cell-free DNA (cfDNA) provide a window of opportunity to attack mutant clones before they become clinically apparent. Overall, EGFR TKIs-resistant NSCLC constitutes a multifaceted therapeutic challenge. Mapping its underlying mutational landscape, accelerating the detection of resistance mechanisms and diversifying treatment strategies are essential for the management of the disease.
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Affiliation(s)
- Andreas Koulouris
- Thoracic Oncology Center, Theme Cancer, Karolinska University Hospital, 17177 Stockholm, Sweden;
- Faculty of Medicine, University of Crete, 70013 Heraklion, Greece;
| | | | - Anna Chiara Corriero
- School of Medicine, Faculty of Health, Education, Medicine & Social Care, Anglia Ruskin University, Bishop Hall Lane, Chelmsford CM1 1SQ, UK;
| | - Giulio Metro
- Giulio Metro, Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, 06132 Perugia, Italy;
| | - Giannis Mountzios
- Clinical Trials Unit, Fourth Department of Medical Oncology, Henry Dunant Hospital Center, 11526 Athens, Greece
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