Landscape of drug-resistance mutations in kinase regulatory hotspots

More than 48 kinase inhibitors (KIs) have been approved by Food and Drug Administration. However, drug-resistance (DR) eventually occurs, and secondary mutations have been found in the previously targeted primary-mutated cancer cells. Cancer and drug research communities recognize the importance of the kinase domain (KD) mutations for kinasopathies. So far, a systematic investigation of kinase mutations on DR hotspots has not been done yet. In this study, we systematically investigated four types of representative mutation hotspots (gatekeeper, G-loop, αC-helix and A-loop) associated with DR in 538 human protein kinases using large-scale cancer data sets (TCGA, ICGC, COSMIC and GDSC). Our results revealed 358 kinases harboring 3318 mutations that covered 702 drug resistance hotspot residues. Among them, 197 kinases had multiple genetic variants on each residue. We further computationally assessed and validated the epidermal growth factor receptor mutations on protein structure and drug-binding efficacy. This is the first study to provide a landscape view of DR-associated mutation hotspots in kinase's secondary structures, and its knowledge will help the development of effective next-generation KIs for better precision medicine.

[1]  F. Ciardiello,et al.  Mechanisms of resistance to EGFR-targeted drugs: lung cancer , 2016, ESMO Open.

[2]  M. Ladanyi,et al.  Acquired Resistance to Epidermal Growth Factor Receptor Kinase Inhibitors Associated with a Novel T854A Mutation in a Patient with EGFR-Mutant Lung Adenocarcinoma , 2008, Clinical Cancer Research.

[3]  Chris Sander,et al.  Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. , 2015, Cell systems.

[4]  M. Deininger,et al.  Bcr-Abl kinase domain mutations, drug resistance, and the road to a cure for chronic myeloid leukemia. , 2007, Blood.

[5]  G. Hoser,et al.  Mitochondrial mutagenesis in BCR-ABL1-expressing cells sensitive and resistant to imatinib. , 2016, Acta biochimica Polonica.

[6]  I. Zalcberg,et al.  Imatinib resistance: a review of alternative inhibitors in chronic myeloid leukemia , 2011, Revista brasileira de hematologia e hemoterapia.

[7]  Nikolas von Bubnoff,et al.  Differential Sensitivity of ERBB2 Kinase Domain Mutations towards Lapatinib , 2011, PloS one.

[8]  M. Tsao,et al.  Known and putative mechanisms of resistance to EGFR targeted therapies in NSCLC patients with EGFR mutations-a review. , 2015, Translational lung cancer research.

[9]  I. Rogozin,et al.  Theoretical analysis of mutation hotspots and their DNA sequence context specificity. , 2003, Mutation research.

[10]  R. Larson,et al.  BCR-ABL1 compound mutations combining key kinase domain positions confer clinical resistance to ponatinib in Ph chromosome-positive leukemia. , 2014, Cancer cell.

[11]  Gregory D. Hawkins,et al.  Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .

[12]  The Uniprot Consortium.  UniProt: the universal protein knowledgebase , 2018, Nucleic acids research.

[13]  Stefan Knapp,et al.  Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site , 2009, Structure.

[14]  K. Mori,et al.  Gilteritinib, a FLT3/AXL inhibitor, shows antileukemic activity in mouse models of FLT3 mutated acute myeloid leukemia , 2017, Investigational New Drugs.

[15]  B. Kuhn,et al.  Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.

[16]  K. Sharp,et al.  Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .

[17]  E. Avizienyte,et al.  Comparison of the EGFR resistance mutation profiles generated by EGFR-targeted tyrosine kinase inhibitors and the impact of drug combinations. , 2008, The Biochemical journal.

[18]  Qingxia Chen,et al.  MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis , 2014, Genome Biology.

[19]  Jaroslav Koca,et al.  Activation and inhibition of cyclin‐dependent kinase‐2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine‐rich loop , 2004, Protein science : a publication of the Protein Society.

[20]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[21]  A. Drilon,et al.  Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors , 2015, Proceedings of the National Academy of Sciences.

[22]  Nobuyoshi Shimizu,et al.  Presence of epidermal growth factor receptor gene T790M mutation as a minor clone in non-small cell lung cancer. , 2006, Cancer research.

[23]  Peilin Jia,et al.  Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study , 2016, Briefings Bioinform..

[24]  Jennifer L. Knight,et al.  Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. , 2015, Journal of the American Chemical Society.

[25]  A. Gazdar,et al.  Activating and resistance mutations of EGFR in non-small-cell lung cancer: role in clinical response to EGFR tyrosine kinase inhibitors , 2009, Oncogene.

[26]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[27]  Patricia L. Harris,et al.  Irreversible inhibitors of the EGF receptor may circumvent acquired resistance to gefitinib. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Federico Cappuzzo,et al.  Examining Treatment Outcomes with Erlotinib in Patients with Advanced Non–Small Cell Lung Cancer Whose Tumors Harbor Uncommon EGFR Mutations , 2016, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[29]  Yan Zhang,et al.  KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients , 2009, Proceedings of the National Academy of Sciences.

[30]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[31]  Susan S. Taylor,et al.  Evolution of the eukaryotic protein kinases as dynamic molecular switches , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[32]  S. Ou,et al.  ALK F1174V mutation confers sensitivity while ALK I1171 mutation confers resistance to alectinib. The importance of serial biopsy post progression. , 2016, Lung cancer.

[33]  Young Lim Choi,et al.  EML4-ALK mutations in lung cancer that confer resistance to ALK inhibitors. , 2010, The New England journal of medicine.

[34]  Niranjan Nagarajan,et al.  ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients. , 2018, Cancer research.

[35]  Jacob Kongsted,et al.  An improved method to predict the entropy term with the MM/PBSA approach , 2009, J. Comput. Aided Mol. Des..

[36]  M. Karplus,et al.  Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis , 2009, Proteins.

[37]  William Pao,et al.  Dual inhibition of EGFR with afatinib and cetuximab in kinase inhibitor-resistant EGFR-mutant lung cancer with and without T790M mutations. , 2014, Cancer discovery.

[38]  D. Alessi,et al.  The nuts and bolts of AGC protein kinases , 2010, Nature Reviews Molecular Cell Biology.

[39]  V. Miller,et al.  Mutation of MET Y1230 as an Acquired Mechanism of Crizotinib Resistance in NSCLC with MET Exon 14 Skipping. , 2017, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[40]  H. Scott,et al.  Sensitive detection of BCR-ABL1 mutations in patients with chronic myeloid leukemia after imatinib resistance is predictive of outcome during subsequent therapy. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  R. Corcoran,et al.  Strategies for monitoring and combating resistance to combination kinase inhibitors for cancer therapy , 2017, Genome Medicine.

[42]  Junmei Wang,et al.  Recent advances on aqueous solubility prediction. , 2011, Combinatorial chemistry & high throughput screening.

[43]  K. Sauer,et al.  Mechanisms of drug resistance in kinases , 2011, Expert opinion on investigational drugs.

[44]  Christopher L. McClendon,et al.  Dynamic architecture of a protein kinase , 2014, Proceedings of the National Academy of Sciences.

[45]  M. Meyerson,et al.  The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP , 2008, Proceedings of the National Academy of Sciences.

[46]  Zhongming Zhao,et al.  Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. , 2017, American journal of human genetics.

[47]  Nicolas Stransky,et al.  Targeting cancer with kinase inhibitors. , 2015, The Journal of clinical investigation.

[48]  P. Szankasi,et al.  BCR-ABL1 compound mutations in tyrosine kinase inhibitor-resistant CML: frequency and clonal relationships. , 2013, Blood.

[49]  R. Roskoski.  Properties of FDA-approved small molecule protein kinase inhibitors. , 2019, Pharmacological research.

[50]  T. Sim,et al.  Antitumor effects and molecular mechanisms of ponatinib on endometrial cancer cells harboring activating FGFR2 mutations , 2016, Cancer biology & therapy.

[51]  L. Ashman,et al.  Juxtamembrane mutant V560GKit is more sensitive to Imatinib (STI571) compared with wild-type c-kit whereas the kinase domain mutant D816VKit is resistant. , 2002, Molecular cancer therapeutics.

[52]  Wolfgang Jahnke,et al.  Solution Conformations and Dynamics of ABL Kinase-Inhibitor Complexes Determined by NMR Substantiate the Different Binding Modes of Imatinib/Nilotinib and Dasatinib*♦ , 2008, Journal of Biological Chemistry.

[53]  Zhongming Zhao,et al.  Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes , 2016, Briefings Bioinform..

[54]  Junfeng Xia,et al.  Cancer Biology and Signal Transduction a Meta-analysis of Somatic Mutations from next Generation Sequencing of 241 Melanomas: a Road Map for the Study of Genes with Potential Clinical Relevance , 2022 .

[55]  G. Toyokawa,et al.  Updated Evidence on the Mechanisms of Resistance to ALK Inhibitors and Strategies to Overcome Such Resistance: Clinical and Preclinical Data , 2015, Oncology Research and Treatment.

[56]  Chuang Liu,et al.  A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types , 2015, PLoS Comput. Biol..

[57]  Zhongming Zhao,et al.  Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach , 2014, Genome Medicine.

[58]  Heiner Koch,et al.  The target landscape of clinical kinase drugs , 2017, Science.

[59]  Zhongming Zhao,et al.  Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy , 2014, Oncotarget.

[60]  T Darden,et al.  New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. , 1999, Structure.

[61]  H. Zou,et al.  A Phase I Pharmacologic Study of Necitumumab (imc-11f8), a Fully Human Igg1 Monoclonal Antibody the Alk/ros1 Inhibitor Pf-06463922 Overcomes Primary Resistance to Crizotinib in Alk-driven Neuroblastoma , 2022 .

[62]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[63]  Carol S. Lim,et al.  Resistant mutations in CML and Ph+ALL – role of ponatinib , 2014, Biologics : targets & therapy.

[64]  Tingjun Hou,et al.  Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking , 2011, J. Comput. Chem..

[65]  Doriano Fabbro,et al.  Ten things you should know about protein kinases: IUPHAR Review 14 , 2015, British journal of pharmacology.

[66]  G. Rastelli,et al.  αC helix displacement as a general approach for allosteric modulation of protein kinases. , 2013, Drug discovery today.

[67]  William Pao,et al.  Rational, biologically based treatment of EGFR-mutant non-small-cell lung cancer , 2010, Nature Reviews Cancer.

[68]  Thomas Simonson,et al.  Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases* , 2010, The Journal of Biological Chemistry.

[69]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[70]  B. Halmos,et al.  EGFR T790M: revealing the secrets of a gatekeeper , 2017, Lung Cancer.

[71]  R. Mannella,et al.  Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms. , 2007, The Journal of chemical physics.

[72]  Susan S. Taylor,et al.  Defining the Conserved Internal Architecture of a Protein Kinase , 2010, Biochimica et biophysica acta.

[73]  A. Sali,et al.  Novel TKI-resistant BCR-ABL1 gatekeeper residue mutations retain in vitro sensitivity to axitinib , 2016, Leukemia.

[74]  Tae Min Kim,et al.  Heterogeneity of Genetic Changes Associated with Acquired Crizotinib Resistance in ALK-Rearranged Lung Cancer , 2013, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[75]  Sonya M. Hanson,et al.  A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation , 2017, bioRxiv.

[76]  William Pao,et al.  Novel D761Y and Common Secondary T790M Mutations in Epidermal Growth Factor Receptor–Mutant Lung Adenocarcinomas with Acquired Resistance to Kinase Inhibitors , 2006, Clinical Cancer Research.

[77]  M. Warmuth,et al.  A conserved salt bridge in the G loop of multiple protein kinases is important for catalysis and for in vivo Lyn function. , 2009, Molecular cell.

[78]  Haidong Wang,et al.  A systematic profile of clinical inhibitors responsive to EGFR somatic amino acid mutations in lung cancer: implication for the molecular mechanism of drug resistance and sensitivity , 2014, Amino Acids.

[79]  Huang Gao,et al.  Database resources of the National Center for Biotechnology Information , 2015, Nucleic Acids Res..

[80]  Joost C. M. Uitdehaag,et al.  A guide to picking the most selective kinase inhibitor tool compounds for pharmacological validation of drug targets , 2012, British journal of pharmacology.

[81]  J. Radich,et al.  Chronic myeloid leukemia: an update of concepts and management recommendations of European LeukemiaNet. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[82]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[83]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[84]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[85]  Tingjun Hou,et al.  Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations , 2012, J. Chem. Inf. Model..

[86]  Junfeng Xia,et al.  Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance , 2013, Genome research.

[87]  Paul A. Bates,et al.  Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors? , 2006, J. Comput. Chem..

[88]  Tingjun Hou,et al.  Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations , 2011, J. Chem. Inf. Model..

[89]  Narasimhan P. Agaram,et al.  Mechanisms of Sunitinib Resistance in Gastrointestinal Stromal Tumors Harboring KITAY502-3ins Mutation: An In vitro Mutagenesis Screen for Drug Resistance , 2009, Clinical Cancer Research.

[90]  Arlo Z. Randall,et al.  Prediction of protein stability changes for single‐site mutations using support vector machines , 2005, Proteins.

[91]  P. Kollman,et al.  Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. , 2001, Journal of the American Chemical Society.

[92]  Matthew Meyerson,et al.  Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity. , 2007, Cancer cell.

[93]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[94]  H. Scott,et al.  Poor response to second-line kinase inhibitors in chronic myeloid leukemia patients with multiple low-level mutations, irrespective of their resistance profile. , 2012, Blood.

[95]  H. Kantarjian,et al.  Mutation profile of JAK2 transcripts in patients with chronic myeloproliferative neoplasias. , 2009, The Journal of molecular diagnostics : JMD.

[96]  C. Klein,et al.  Target Binding Properties and Cellular Activity of Afatinib (BIBW 2992), an Irreversible ErbB Family Blocker , 2012, Journal of Pharmacology and Experimental Therapeutics.

[97]  J. Kuriyan,et al.  Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia. , 2002, Cancer cell.

[98]  P. Kollman,et al.  Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.

[99]  J. Verweij,et al.  A phase I dose escalation study of BIBW 2992, an irreversible dual inhibitor of epidermal growth factor receptor 1 (EGFR) and 2 (HER2) tyrosine kinase in a 2-week on, 2-week off schedule in patients with advanced solid tumours , 2007, British Journal of Cancer.

[100]  R. Rosell,et al.  The impact of rare EGFR mutations on the treatment response of patients with non-small cell lung cancer , 2015, Expert review of respiratory medicine.

[101]  Zhongming Zhao,et al.  Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach* , 2015, Molecular & Cellular Proteomics.

[102]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[103]  William H. Bisson,et al.  Crizotinib-Resistant NPM-ALK Mutants Confer Differential Sensitivity to Unrelated Alk Inhibitors , 2012, Molecular Cancer Research.

[104]  Geoffrey R. Oxnard,et al.  Structural, Biochemical, and Clinical Characterization of Epidermal Growth Factor Receptor (EGFR) Exon 20 Insertion Mutations in Lung Cancer , 2013, Science Translational Medicine.

[105]  R. Palmer,et al.  The role of the ALK receptor in cancer biology. , 2016, Annals of oncology : official journal of the European Society for Medical Oncology.

[106]  P. Savagner,et al.  Potential Advantages of CUDC-101, a Multitargeted HDAC, EGFR, and HER2 Inhibitor, in Treating Drug Resistance and Preventing Cancer Cell Migration and Invasion , 2013, Molecular Cancer Therapeutics.

[107]  S. Hwang,et al.  Compound EGFR mutation is frequently detected with co-mutations of actionable genes and associated with poor clinical outcome in lung adenocarcinoma , 2016, Cancer biology & therapy.

[108]  Renate Griffith,et al.  Therapeutic targeting of c-KIT in cancer , 2013, Expert opinion on investigational drugs.

[109]  P. Jänne,et al.  Noninvasive Detection of EGFR T790M in Gefitinib or Erlotinib Resistant Non–Small Cell Lung Cancer , 2009, Clinical Cancer Research.

[110]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[111]  J. Shih,et al.  Effectiveness of Tyrosine Kinase Inhibitors on “Uncommon” Epidermal Growth Factor Receptor Mutations of Unknown Clinical Significance in Non–Small Cell Lung Cancer , 2011, Clinical Cancer Research.

[112]  S. Digumarthy,et al.  Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors , 2011, Science Translational Medicine.

[113]  Krystal J Alligood,et al.  A Unique Structure for Epidermal Growth Factor Receptor Bound to GW572016 (Lapatinib) , 2004, Cancer Research.

[114]  Zhongming Zhao,et al.  Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer , 2010, Nucleic acids research.