A recent update on small-molecule kinase inhibitors for targeted cancer therapy and their therapeutic insights from mass spectrometry-based proteomic analysis.


Journal

The FEBS journal
ISSN: 1742-4658
Titre abrégé: FEBS J
Pays: England
ID NLM: 101229646

Informations de publication

Date de publication:
06 2023
Historique:
revised: 21 02 2022
received: 16 12 2021
accepted: 18 03 2022
medline: 8 6 2023
pubmed: 22 3 2022
entrez: 21 3 2022
Statut: ppublish

Résumé

Kinases are key regulatory signalling proteins governing numerous essential biological processes and cellular functions. Dysregulation of many protein kinases is associated with cancer initiation and progression. Given their crucial roles, there has been increasing interest in harnessing kinases as prospective drug targets for cancer. In recent decades, numerous small-molecule kinase inhibitors have been developed and revolutionized the cancer treatment landscape. Despite their great potential, challenges remain in developing highly selective and effective kinase inhibitors, with toxicity and resistance issues frequently arising. In this review, we first provide an overview of the role of kinases in carcinogenesis and describe the current progress with small-molecule kinase inhibitors that have been approved for clinical use. We then discuss the application of mass spectrometry (MS)-based proteomics strategies to help in the design of kinase inhibitors. Finally, we discuss the challenges and outlook concerning MS-based proteomics techniques for kinase drug research.

Identifiants

pubmed: 35313089
doi: 10.1111/febs.16442
doi:

Substances chimiques

Protein Kinase Inhibitors 0
Protein Kinases EC 2.7.-

Types de publication

Journal Article Review Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2845-2864

Informations de copyright

© 2022 Federation of European Biochemical Societies.

Références

Adam K, Hunter T. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. Lab Investig. 2018;98:233-47.
Cieśla J, Fraczyk T, Rode W. Phosphorylation of basic amino acid residues in proteins: important but easily missed. Acta Biochim Pol. 2011;58:137-48.
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002;298:1912-34.
Ardito F, Giuliani M, Perrone D, Troiano G, Lo ML. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (review). Int J Mol Med. 2017;40:271-80.
Hanks SK, Quinn AM, Hunter T. The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science. 1988;241:42-52.
Hanks SK, Hunter T. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J. 1995;9:576-96.
Miranda-Saavedra D, Diego Barton GJ. Classification and functional annotation of eukaryotic protein kinases. Proteins. 2007;68:893-914.
Martin DMA, Miranda-Saavedra D, Barton GJ. Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res. 2009;37:244-50.
Martin J, Anamika K, Srinivasan N. Classification of protein kinases on the basis of both kinase and non-kinase regions. PLoS One. 2010;5:e12460.
Johnson L, Lewis R. Structural basis for control by phosphorylation. Chem Rev. 2001;101:2209-42.
Cheng H, Qi R, Paudel H, Zhu H. Regulation and function of protein kinases and phosphatases. Enzyme Res. 2011;2011:794089.
Kannaiyan R, Mahadevan D. A comprehensive review of protein kinase inhibitors for cancer therapy. Expert Rev Anticancer Ther. 2018;18:1249-70.
Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature. 2001;411:355-65.
Dankner M, Rose AAN, Rajkumar S, Siegel PM, Watson IR. Classifying BRAF alterations in cancer: new rational therapeutic strategies for actionable mutations. Oncogene. 2018;37:3183-99.
Śmiech M, Leszczyński P, Kono H, Wardell C, Taniguchi H. Emerging braf mutations in cancer progression and their possible effects on transcriptional networks. Genes (Basel). 2020;11:1342.
Thomas R, Weihua Z. Rethink of EGFR in cancer with its kinase independent function on board. Front Oncol. 2019;9:800.
Knapp S. New opportunities for kinase drug repurposing and target discovery. Br J Cancer. 2018;118:936-7.
Druker B, Sawyers C, Kantarjian H, Resta D, Reese S, Ford J, et al. Activity of a specific inhibitor of the BCR-ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome. N Engl J Med. 2001;344:1038-42.
Bhullar KS, Lagarón NO, Mcgowan EM, Parmar I, Jha A, Hubbard BP, et al. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer. 2018;17:48.
Roskoski RJ. Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes. Pharmacol Res. 2016;103:26-48.
Roskoski RJ. Properties of FDA-approved small molecule protein kinase inhibitors. Pharmacol Res. 2019;144:19-50.
Roskoski RJ. Properties of FDA-approved small molecule protein kinase inhibitors: a 2022 update. Pharmacol Res. 2022;175:106037.
Zuccotto F, Ardini E, Casale E, Angiolini M. Through the ‘gatekeeper door’: exploiting the active kinase conformation. J Med Chem. 2010;53:2681-94.
Kufareva I, Abagyan R. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem. 2008;51:7921-32.
Liu Y, Gray N. Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol. 2006;2:358-64.
Gavrin L, Saiah E. Approaches to discover non-ATP site kinase inhibitors. Med Chem Comm. 2013;4:41-51.
Lamba V, Ghosh I. New directions in targeting protein kinases: focusing upon true allosteric and bivalent inhibitors. Curr Pharm Des. 2012;18:2936-45.
Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, et al. The target landscape of clinical kinase drugs. Science. 2017;358:eaan4368.
Johnson TK, Soellner MB. Bivalent inhibitors of c-Src tyrosine kinase that bind a regulatory domain. Bioconjug Chem. 2016;27:1745-9.
Roskoski R. Small molecule inhibitors targeting the EGFR/ErbB family of protein-tyrosine kinases in human cancers. Pharmacol Res. 2019;139:395-411.
Rabindran S, Discafani C, Rosfjord E, Baxter M, Floyd M, Golas J, et al. Antitumor activity of HKI-272, an orally active, irreversible inhibitor of the HER-2 tyrosine kinase. Cancer Res. 2004;64:3958-65.
Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, et al. Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of fgf receptor signaling. Cancer Cell. 2013;23:489-501.
Grither WR, Longmore GD. Inhibition of tumor-microenvironment interaction and tumor invasion by small-molecule allosteric inhibitor of DDR2 extracellular domain. Proc Natl Acad Sci USA. 2018;115:E7786-94.
Hochhaus A, Saussele S, Rosti G, Mahon F-X, Janssen J, Hjorth-Hansen H, et al. Chronic myeloid leukaemia: ESMO clinical practice guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2017;28(Suppl 4):iv41-51.
Barouch-Bentov R, Sauer K. Mechanisms of drug resistance in kinases. Expert Opin Investig Drugs. 2011;20:153-208.
O'Hare T, Shakespeare W, Zhu X, Eide C, Rivera V, Wang F, et al. AP24534, a pan-BCR-ABL inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance. Cancer Cell. 2009;16:401-12.
Gainor J, Chabner B. Ponatinib: accelerated disapproval. Oncologist. 2015;20:847-8.
Roskoski R Jr. The ErbB/HER family of protein-tyrosine kinases and cancer. Pharmacol Res. 2014;79:34-74.
Riely G, Politi K, Miller V, Pao W. Update on epidermal growth factor receptor mutations in non-small cell lung cancer. Clin Cancer Res. 2006;12:7232-41.
Hirsh V. Next-generation covalent irreversible kinase inhibitors in NSCLC: focus on afatinib. BioDrugs. 2015;29:167-83.
Ou S, Soo R. Dacomitinib in lung cancer: a ‘lost generation’ EGFR tyrosine-kinase inhibitor from a bygone era? Drug Des Devel Ther. 2015;9:5641-53.
Finlay MRV, Anderton M, Ashton S, Ballard P, Bethel PA, Box MR, et al. Discovery of a potent and selective EGFR inhibitor (AZD9291) of both sensitizing and T790M resistance mutations that spares the wild type form of the receptor. J Med Chem. 2014;57:8249-67.
Burotto M, Chiou V, Lee J, Kohn E. The MAPK pathway across different malignancies: a new perspective. Cancer. 2014;120:3446-56.
Savoia P, Fava P, Casoni F, Cremona O. Targeting the ERK signaling pathway in melanoma. Int J Mol Sci. 2019;20:1483.
Yang H, Higgins B, Kolinsky K, Packman K, Go Z, Iyer R, et al. RG7204 (PLX4032), a selective BRAFV600E inhibitor, displays potent antitumor activity in preclinical melanoma models. Cancer Res. 2010;70:5518-27.
Gentilcore G, Madonna G, Mozzillo N, Ribas A, Cossu A, Palmieri G, et al. Effect of dabrafenib on melanoma cell lines harbouring the BRAF(V600D/R) mutations. BMC Cancer. 2013;13:17.
Koelblinger P, Thuerigen O, Dummer R. Development of encorafenib for BRAF-mutated advanced melanoma. Curr Opin Oncol. 2018;30:125-33.
Daud A, Tsai K. Management of treatment-related adverse events with agents targeting the MAPK pathway in patients with metastatic melanoma. Oncologist. 2017;22:823-33.
Pal Singh S, Dammeijer F, Hendriks RW. Role of Bruton's tyrosine kinase in B cells and malignancies. Mol Cancer. 2018;17:57.
Honigberg LA, Smith AM, Sirisawad M, Verner E, Loury D, Chang B, et al. The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy. Proc Natl Acad Sci USA. 2010;107:13075-80.
Wu J, Zhang M, Liu D. Acalabrutinib (ACP-196): a selective secondgeneration BTK inhibitor. J Hematol Oncol. 2016;9:21.
Tam C, Opat S, D'Sa S, Jurczak W, Lee H, Cull G, et al. A randomized phase 3 trial of zanubrutinib versus ibrutinib in symptomatic waldenström macroglobulinemia: the ASPEN study. Blood. 2020;136:2038-50.
Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. Widening the bottleneck of phosphoproteomics: evolving strategies for phosphopeptide enrichment. Mass Spectrom Rev. 2021;40:309-33.
Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, et al. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal. 2013;6:rs6.
Drake JM, Graham NA, Stoyanova T, Sedghi A, Goldstein AS, Cai H, et al. Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci USA. 2012;109:1643-8.
Xue L, Wang W, Iliuk A, Hu L, Galan J, Yu S, et al. Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates. Proc Natl Acad Sci USA. 2012;109:5615-20.
Beltran L, Casado P, Rodriguez-Prados JC, Cutillas PR. Global profiling of protein kinase activities in cancer cells by mass spectrometry. J Proteome. 2012;77:492-503.
Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, et al. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell. 2007;131:1190-203.
Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534:55-62.
Drake J, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, et al. Phosphoproteome integration reveals patient specific networks in prostate cancer. Cell. 2016;166:1041-54.
Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, et al. Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma. Nature. 2019;567:257-61.
Mun DG, Bhin J, Kim S, Kim H, Jung JH, Jung Y, et al. Proteogenomic characterization of human early-onset gastric cancer. Cancer Cell. 2019;35:111-24.e10.
Tong M, Yu C, Shen L, Tong M, Yu C, Shi J, et al. Phosphoproteomics enables molecular subtyping and nomination of kinase candidates for individual patients of diffuse-type gastric cancer. iScience. 22:44-57.
Fleuren EDG, Vlenterie M, Van Der Graaf WTA, Hillebrandt-Roeffen MHS, Blackburn J, Ma X, et al. Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. Cancer Res. 2017;77:4279-92.
Lescarbeau R, Lei L, Bakken K, Sims P, Sarkaria J, Canoll P, et al. Quantitative phosphoproteomics reveals Wee1 kinase as a therapeutic target in a model of proneural glioblastoma. Mol Cancer Ther. 2016;15:1332-43.
Tactacan CM, Phua YW, Liu L, Zhang L, Humphrey ES, Cowley M, et al. The pseudokinase SgK223 promotes invasion of pancreatic ductal epithelial cells through JAK1/Stat3 signaling. Mol Cancer. 2015;14:139.
Muellner MK, Mair B, Ibrahim Y, Kerzendorfer C, Lechtermann H, Trefzer C, et al. Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol. 2015;11:789.
Yu S, Huang H, Iliuk A, Wang WH, Jayasundera KB, Tao WA, et al. Syk inhibits the activity of protein kinase A by phosphorylating tyrosine 330 of the catalytic subunit. J Biol Chem. 2013;288:10870-81.
Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, et al. Identification of mediator kinase substrates in human cells using cortistatin A and quantitative phosphoproteomics. Cell Rep. 2016;15:436-50.
Braun T, Eide C, Druker B. Response and resistance to BCR-ABL1-targeted therapies. Cancer Cell. 2020;37:530-42.
Massicotte M, Brassard M, Claude-Desroches M, Borget I, Bonichon F, Giraudet A, et al. Tyrosine kinase inhibitor treatments in patients with metastatic thyroid carcinomas: a retrospective study of the TUTHYREF network. Eur J Endocrinol. 2014;170:575-82.
Haley J, White F. Adaptive protein and phosphoprotein networks which promote therapeutic sensitivity or acquired resistance. Biochem Soc Trans. 2014;42:758-64.
Casado P, Alcolea M, Iorio F, Rodríguez-Prados J, Vanhaesebroeck B, Saez-Rodriguez J, et al. Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors. Genome Biol. 2013;14:R37.
Zhang X, Maity T, Kashyap M, Bansal M, Venugopalan A, Singh S, et al. Quantitative tyrosine phosphoproteomics of epidermal growth factor receptor (egfr) tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response. Mol Cell Proteom. 2017;16:891-910.
Yeoh Y, Low TY, Abu N, Lee PY. Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ. 2021;9:e12338.
Dazert E, Colombi M, Boldanova T, Moes S, Adametz D, Quagliata L, et al. Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient. Proc Natl Acad Sci USA. 2016;113:1381-6.
Chen C, Liao L, Lu C, Huang Y, Lin Y, Lin J, et al. Quantitative phosphoproteomic analysis identifies the potential therapeutic target EphA2 for overcoming sorafenib resistance in hepatocellular carcinoma cells. Exp Mol Med. 2020;52:497-513.
Liu W, Chang J, Liu M, Yuan J, Zhang J, Qin J, et al. Quantitative proteomics profiling reveals activation of mtor pathway in trastuzumab resistance. Oncotarget. 2017;8:45793-806.
Low TY, Syafruddin SE, Mohtar MA, Vellaichamy A, Rahman NSA, Pung Y-F, et al. Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions. Cell Mol Life Sci. 2021;78:5325-39.
Miao Q, Zhang CC, Kast J. Chemical proteomics and its impact on the drug discovery process. Expert Rev Proteomics. 2012;9:281-91.
Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol. 2007;25:1035-44.
Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, et al. Optimized chemical proteomics assay for kinase inhibitor profiling. J Proteome Res. 2015;14:1574-86.
Niu S, Wang Z, Ge D, Zhang G, Li Y. Prediction of functional phosphorylation sites by incorporating evolutionary information. Protein Cell. 2012;3:675-90.
Golkowski M, Lau HT, Chan M, Kenerson H, Vidadala VN, Shoemaker A, et al. Pharmacoproteomics identifies kinase pathways that drive the epithelial-mesenchymal transition and drug resistance in hepatocellular carcinoma. Cell Syst. 2020;11:196-207.e7.
Linley AJ, Karydis LI, Mondru AK, D'Avola A, Al Shmrany H, Cicconi S, et al. Kinobead profiling reveals reprogramming of BCR signaling in response to therapy within primary CLL cells. Clin Cancer Res. 2021;27:5647-59.
Savitski MM, Reinhard FBM, Franken H, Werner T, Savitski MF, Eberhard D, et al. Tracking cancer drugs in living cells by thermal profiling of the proteome. Science. 2014;346:1255784.
Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, et al. Thermal proteome profiling for interrogating protein interactions. Mol Syst Biol. 2020;16:e9232.
Becher I, Werner T, Doce C, Zaal EA, Tögel I, Khan CA, et al. Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nat Chem Biol. 2016;12:908-10.
Xia ZK, Wang W, Qiu JG, Shi XN, Li HJ, Chen R, et al. Discovery of a new CDK4/6 and PI3K/AKT multiple kinase inhibitor aminoquinol for the treatment of hepatocellular carcinoma. Front Pharmacol. 2021;12:691769.
Azimi A, Caramuta S, Seashore-ludlow B, Boström J, Robinson JL, Edfors F, et al. Targeting CDK 2 overcomes melanoma resistance against BRAF and Hsp 90 inhibitors. Mol Syst Biol. 2018;14:e7858.
Huang JX, Lee G, Cavanaugh KE, Chang JW, Gardel ML, Moellering RE. High throughput discovery of functional protein modifications by hotspot thermal profiling. Nat Methods. 2019;16:894-901.
Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski SM. Impact of phosphorylation on thermal stability of proteins. Nat Methods. 2021;18:757-9.
Angel T, Aryal U, Hengel S, Baker E, Kelly R, Robinson E, et al. Mass spectrometry-based proteomics: existing capabilities and future directions. Chem Soc Rev. 2012;41:3912-28.
Bekker-Jensen D, Bernhardt O, Hogrebe A, Martinez-Val A, Verbeke L, Gandhi T, et al. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat Commun. 2020;11:787.
Lienhard G. Non-functional phosphorylations? Trends Biochem Sci. 2008;33:351.
Beltrao P, Albanèse V, Kenner L, Swaney D, Burlingame A, Villén J, et al. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012;150:413-25.
Thorsness P, Koshland D. Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate. J Biol Chem. 1987;262:10422-5.
Venne A, Kollipara L, Zahedi R. The next level of complexity: crosstalk of posttranslational modifications. Proteomics. 2014;14:513-24.
Nguyen L, Kolch W, Kholodenko B. When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun Signal. 2013;11:52.
Leney A, Atmioui D, Wu W, Ovaa H, Heck A. Elucidating crosstalk mechanisms between phosphorylation and O-GlcNAcylation. Proc Natl Acad Sci USA. 2017;114:E7255-61.
Doll S, Burlingame A. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol. 2015;10:63-71.
Reinhard FBM, Eberhard D, Werner T, Franken H, Childs D, Doce C, et al. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Nat Methods. 2015;12:1129-31.
Kalxdorf M, Günthner I, Becher I, Kurzawa N, Knecht S, Savitski MM, et al. Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane. Nat Methods. 2021;18:84-91.
Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, et al. Pervasive protein thermal stability variation during the cell cycle. Cell. 2018;173:1495-507.

Auteurs

Pey Yee Lee (PY)

UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.

Yeelon Yeoh (Y)

UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.

Teck Yew Low (TY)

UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH