Non-immunoglobulin synthetic binding proteins for oncology
- Authors: David T.I1,2, Pestov N.B1,3,4, Korneenko T.V4, Barlev N.A1,3,5,6
-
Affiliations:
- Institute of Biomedical Chemistry
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- Institute of Cytology, Russian Academy of Sciences
- Nazarbayev University
- Issue: Vol 88, No 9 (2023)
- Pages: 1493-1512
- Section: Articles
- URL: https://journals.rcsi.science/0320-9725/article/view/141483
- DOI: https://doi.org/10.31857/S032097252309004X
- EDN: https://elibrary.ru/WTGRQC
- ID: 141483
Cite item
Abstract
Keywords
About the authors
T. I David
Institute of Biomedical Chemistry;Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology119121 Moscow, Russia;=141701 Dolgoprudny, Moscow Region, Russia
N. B Pestov
Institute of Biomedical Chemistry;Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
Email: nayeoff@yahoo.com
119121 Moscow, Russia;=108819 Moscow, Russia;=117997 Moscow, Russia
T. V Korneenko
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry=117997 Moscow, Russia
N. A Barlev
Institute of Biomedical Chemistry;Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences;Institute of Cytology, Russian Academy of Sciences;Nazarbayev University119121 Moscow, Russia;=108819 Moscow, Russia;=194064 St.-Petersburg, Russia;=010000 Astana, Kazakhstan
References
- Weidle, U. H., Auer, J., Brinkmann, U., Georges, G., and Tiefenthaler, G. (2013) The emerging role of new protein scaffold-based agents for treatment of cancer, Cancer Genomics Proteomics, 10, 155-168.
- Rabia, L. A., Desai, A. A., Jhajj, H. S., and Tessier, P. M. (2018) Understanding and overcoming trade-offs between antibody affinity, specificity, stability and solubility, Biochem. Eng. J., 137, 365-374, doi: 10.1016/j.bej.2018.06.003.
- Cunningham, O., Scott, M., Zhou, Z. S., and Finlay, W. J. J. (2021) Polyreactivity and polyspecificity in therapeutic antibody development: risk factors for failure in preclinical and clinical development campaigns, MAbs, 13, 1999195, doi: 10.1080/19420862.2021.1999195.
- Van Regenmortel, M. H. V. (2014) Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition, J. Mol. Recognit., 27, 627-639, doi: 10.1002/jmr.2394.
- Пестов Н. Б., Гусакова Т. В., Костина М. Б., Шахпаронов М. И. (1996) Фаговые мимотопы моноклональных антител к Ca2+-ATP-азе плазматических мембран, Биоорг. Хим., 22, 664.
- Rabia, L. A., Zhang, Y., Ludwig, S. D., Julian, M. C., and Tessier, P. M. (2018) Net charge of antibody complementarity-determining regions is a key predictor of specificity, Protein Eng. Des. Sel., 31, 409-418, doi: 10.1093/protein/gzz002.
- Gebauer, M., and Skerra, A. (2020) Engineered protein scaffolds as next-generation therapeutics, Annu. Rev. Pharmacol. Toxicol., 60, 391-415, doi: 10.1146/annurev-pharmtox-010818-021118.
- Aguilar, G., Vigano, M. A., Affolter, M., and Matsuda, S. (2019) Reflections on the use of protein binders to study protein function in developmental biology, Wiley Interdiscip. Rev. Dev. Biol., 8, e356, doi: 10.1002/wdev.356.
- Jenkins, T. P., Fryer, T., Dehli, R. I., Jürgensen, J. A., Fuglsang-Madsen, A., et al. (2019) Toxin neutralization using alternative binding proteins, Toxins (Basel), 11, E53, doi: 10.3390/toxins11010053.
- Olaleye, O., Govorukhina, N., van de Merbel, N. C., and Bischoff, R. (2021) Non-antibody-based binders for the enrichment of proteins for analysis by mass spectrometry, Biomolecules, 11, 1791, doi: 10.3390/biom11121791.
- Bondos, S. E., Dunker, A. K., and Uversky, V. N. (2022) Intrinsically disordered proteins play diverse roles in cell signaling, Cell Commun. Signal., 20, 20, doi: 10.1186/s12964-022-00821-7.
- Karlsson, O. A., Ramirez, J., Öberg, D., Malmqvist, T., Engström, Å., et al. (2015) Design of a PDZbody, a bivalent binder of the E6 protein from human papillomavirus, Sci. Rep., 5, 9382, doi: 10.1038/srep09382.
- Sha, F., Salzman, G., Gupta, A., and Koide, S. (2017) Monobodies and other synthetic binding proteins for expanding protein science, Protein Sci., 26, 910-924, doi: 10.1002/pro.3148.
- Hantschel, O., Biancalana, M., and Koide, S. (2020) Monobodies as enabling tools for structural and mechanistic biology, Curr. Opin. Struct. Biol., 60, 167-174, doi: 10.1016/j.sbi.2020.01.015.
- McConnell, S. J., and Hoess, R. H. (1995) Tendamistat as a scaffold for conformationally constrained phage peptide libraries, J. Mol. Biol., 250, 460-470, doi: 10.1006/jmbi.1995.0390.
- Ciesiołkiewicz, A., Lizandra Perez, J., and Berlicki, Ł. (2022) Miniproteins in medicinal chemistry, Bioorg. Med. Chem. Lett., 71, 128806, doi: 10.1016/j.bmcl.2022.128806.
- Kolmar, H. (2008) Alternative binding proteins: biological activity and therapeutic potential of cystine-knot miniproteins, FEBS J., 275, 2684-2690, doi: 10.1111/j.1742-4658.2008.06440.x.
- Silverman, J., Liu, Q., Bakker, A., To, W., Duguay, A., et al. (2005) Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains, Nat. Biotechnol., 23, 1556-1561, doi: 10.1038/nbt1166.
- Tiede, C., Tang, A. A. S., Deacon, S. E., Mandal, U., Nettleship, J. E., et al. (2014) Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications, Protein Eng. Des. Sel., 27, 145-155, doi: 10.1093/protein/gzu007.
- Tiede, C., Bedford, R., Heseltine, S. J., Smith, G., Wijetunga, I., et al. (2017) Affimer proteins are versatile and renewable affinity reagents, Elife, 6, e24903, doi: 10.7554/eLife.24903.
- Shamsuddin, S. H., Jayne, D. G., Tomlinson, D. C., McPherson, M. J., and Millner, P. A. (2021) Selection and characterisation of Affimers specific for CEA recognition, Sci. Rep., 11, 744, doi: 10.1038/s41598-020-80354-6.
- Wicke, N., Bedford, M. R., and Howarth, M. (2021) Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid, Commun. Biol., 4, 960, doi: 10.1038/s42003-021-02487-2.
- Zoller, F., Markert, A., Barthe, P., Zhao, W., Weichert, W., et al. (2012) Combination of phage display and molecular grafting generates highly specific tumor-targeting miniproteins, Angew. Chem. Int. Ed. Engl., 51, 13136-13139, doi: 10.1002/anie.201203857.
- Cohen, I., Kayode, O., Hockla, A., Sankaran, B., Radisky, D. C., et al. (2016) Combinatorial protein engineering of proteolytically resistant mesotrypsin inhibitors as candidates for cancer therapy, Biochem. J., 473, 1329-1341, doi: 10.1042/BJ20151410.
- Sananes, A., Cohen, I., Shahar, A., Hockla, A., De Vita, E., et al. (2018) A potent, proteolysis-resistant inhibitor of kallikrein-related peptidase 6 (KLK6) for cancer therapy, developed by combinatorial engineering, J. Biol. Chem., 293, 12663-12680, doi: 10.1074/jbc.RA117.000871.
- Nishimiya, D., Kawaguchi, Y., Kodama, S., Nasu, H., Yano, H., et al. (2019) A protein scaffold, engineered SPINK2, for generation of inhibitors with high affinity and specificity against target proteases, Sci. Rep., 9, 11436, doi: 10.1038/s41598-019-47615-5.
- Jia, Z., Liu, Y., Ji, X., Zheng, Y., Li, Z., et al. (2021) DAKS1, a Kunitz scaffold peptide from the venom gland of Deinagkistrodon acutus prevents carotid-artery and middle-cerebral-artery thrombosis via targeting factor Xia, Pharmaceuticals (Basel), 14, 966, doi: 10.3390/ph14100966.
- Lee, S.-C., Park, K., Han, J., Lee, J., Kim, H. J., et al. (2012) Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering, Proc. Natl. Acad. Sci. USA, 109, 3299-3304, doi: 10.1073/pnas.1113193109.
- Hwang, D.-E., Ryou, J.-H., Oh, J. R., Han, J. W., Park, T. K., and Kim, H.-S. (2016) Anti-human VEGF repebody effectively suppresses choroidal neovascularization and vascular leakage, PLoS One, 11, e0152522, doi: 10.1371/journal.pone.0152522.
- Liu, H., Huang, H., Voss, C., Kaneko, T., Qin, W. T., et al. (2019) Surface loops in a single SH2 domain are capable of encoding the spectrum of specificity of the SH2 family, Mol. Cell. Proteomics, 18, 372-382, doi: 10.1074/mcp.RA118.001123.
- Schlatter, D., Brack, S., Banner, D. W., Batey, S., Benz, J., et al. (2012) Generation, characterization and structural data of chymase binding proteins based on the human Fyn kinase SH3 domain, MAbs, 4, 497-508, doi: 10.4161/mabs.20452.
- Garlich, J., Cinier, M., Chevrel, A., Perrocheau, A., Eyerman, D. J., et al. (2022) Discovery of APL-1030, a novel, high-affinity nanofitin inhibitor of C3-mediated complement activation, Biomolecules, 12, 432, doi: 10.3390/biom12030432.
- Gocha, T., Rao, B. M., and DasGupta, R. (2017) Identification and characterization of a novel Sso7d scaffold-based binder against Notch1, Sci. Rep., 7, 12021, doi: 10.1038/s41598-017-12246-1.
- Kalichuk, V., Renodon-Cornière, A., Béhar, G., Carrión, F., Obal, G., Maillasson, M., et al. (2018) A novel, smaller scaffold for Affitins: showcase with binders specific for EpCAM, Biotechnol. Bioeng., 115, 290-299, doi: 10.1002/bit.26463.
- Steemson, J. D., Baake, M., Rakonjac, J., Arcus, V. L., and Liddament, M. T. (2014) Tracking molecular recognition at the atomic level with a new protein scaffold based on the OB-fold, PLoS One, 9, e86050, doi: 10.1371/journal.pone.0086050.
- Napolitano, E. W., Villar, H. O., Kauvar, L. M., Higgins, D. L., Roberts, D., et al. (1996) Glubodies: randomized libraries of glutathione transferase enzymes, Chem. Biol., 3, 359-367, doi: 10.1016/s1074-5521(96)90119-2.
- Lorey, S., Fiedler, E., Kunert, A., Nerkamp, J., Lange, C., et al. (2014) Novel ubiquitin-derived high affinity binding proteins with tumor targeting properties, J. Biol. Chem., 289, 8493-8507, doi: 10.1074/jbc.M113.519884.
- Pham, P. N., Huličiak, M., Biedermannová, L., Černý, J., Charnavets, T., et al. (2021) Protein Binder (ProBi) as a new class of structurally robust non-antibody protein scaffold for directed evolution, Viruses, 13, 190, doi: 10.3390/v13020190.
- Pan, X., Thompson, M. C., Zhang, Y., Liu, L., Fraser, J. S., et al. (2020) Expanding the space of protein geometries by computational design of de novo fold families, Science, 369, 1132-1136, doi: 10.1126/science.abc0881.
- Desmet, J., Verstraete, K., Bloch, Y., Lorent, E., Wen, Y., et al. (2014) Structural basis of IL-23 antagonism by an Alphabody protein scaffold, Nat. Commun., 5, 5237, doi: 10.1038/ncomms6237.
- Koide, A., Bailey, C. W., Huang, X., and Koide, S. (1998) The fibronectin type III domain as a scaffold for novel binding proteins, J. Mol. Biol., 284, 1141-1151, doi: 10.1006/jmbi.1998.2238.
- Lipovsek, D. (2011) Adnectins: engineered target-binding protein therapeutics, Protein Eng. Des. Sel., 24, 3-9, doi: 10.1093/protein/gzq097.
- Sullivan, M. A., Brooks, L. R., Weidenborner, P., Domm, W., Mattiacio, J., et al. (2013) Anti-idiotypic monobodies derived from a fibronectin scaffold, Biochemistry, 52, 1802-1813, doi: 10.1021/bi3016668.
- Chandler, P. G., and Buckle, A. M. (2020) Development and differentiation in monobodies based on the fibronectin type 3 domain, Cells, 9, E610, doi: 10.3390/cells9030610.
- Akkapeddi, P., Teng, K. W., and Koide, S. (2021) Monobodies as tool biologics for accelerating target validation and druggable site discovery, RSC Med. Chem., 12, 1839-1853, doi: 10.1039/d1md00188d.
- Batori, V., Koide, A., and Koide, S. (2002) Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain, Protein Eng., 15, 1015-1020, doi: 10.1093/protein/15.12.1015.
- Kükenshöner, T., Schmit, N. E., Bouda, E., Sha, F., Pojer, F., et al. (2017) Selective targeting of SH2 domain-phosphotyrosine interactions of Src family tyrosine kinases with monobodies, J. Mol. Biol., 429, 1364-1380, doi: 10.1016/j.jmb.2017.03.023.
- Gross, G. G., Junge, J. A., Mora, R. J., Kwon, H.-B., Olson, C. A., et al. (2013) Recombinant probes for visualizing endogenous synaptic proteins in living neurons, Neuron, 78, 971-985, doi: 10.1016/j.neuron.2013.04.017.
- Porebski, B. T., Conroy, P. J., Drinkwater, N., Schofield, P., Vazquez-Lombardi, R., et al. (2016) Circumventing the stability-function trade-off in an engineered FN3 domain, Protein Eng. Des. Sel., 29, 541-550, doi: 10.1093/protein/gzw046.
- Porebski, B. T., Nickson, A. A., Hoke, D. E., Hunter, M. R., Zhu, L., et al. (2015) Structural and dynamic properties that govern the stability of an engineered fibronectin type III domain, Protein Eng. Des. Sel., 28, 67-78, doi: 10.1093/protein/gzv002.
- Chandler, P. G., Tan, L. L., Porebski, B. T., Green, J. S., Riley, B. T., et al. (2021) Mutational and biophysical robustness in a prestabilized monobody, J. Biol. Chem., 296, 100447, doi: 10.1016/j.jbc.2021.100447.
- Deuschle, F.-C., Ilyukhina, E., and Skerra, A. (2021) Anticalin® proteins: from bench to bedside, Expert Opin. Biol. Ther., 21, 509-518, doi: 10.1080/14712598.2021.1839046.
- Achatz, S., Jarasch, A., and Skerra, A. (2022) Structural plasticity in the loop region of engineered lipocalins with novel ligand specificities, so-called Anticalins, J. Struct. Biol., 6, 100054, doi: 10.1016/j.yjsbx.2021.100054.
- Gebauer, M., Schiefner, A., Matschiner, G., and Skerra, A. (2013) Combinatorial design of an anticalin directed against the extra-domain B for the specific targeting of oncofetal fibronectin, J. Mol. Biol., 425, 780-802, doi: 10.1016/j.jmb.2012.12.004.
- Chi, Y., Remsik, J., Kiseliovas, V., Derderian, C., Sener, U., et al. (2020) Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis, Science, 369, 276-282, doi: 10.1126/science.aaz2193.
- Yang, J., Bielenberg, D. R., Rodig, S. J., Doiron, R., Clifton, M. C., et al. (2009) Lipocalin 2 promotes breast cancer progression, Proc. Natl. Acad. Sci. USA, 106, 3913-3918, doi: 10.1073/pnas.0810617106.
- Chakraborty, S., Kaur, S., Guha, S., and Batra, S. K. (2012) The multifaceted roles of neutrophil gelatinase associated lipocalin (NGAL) in inflammation and cancer, Biochim. Biophys. Acta, 1826, 129-169, doi: 10.1016/j.bbcan.2012.03.008.
- Crescenzi, E., Leonardi, A., and Pacifico, F. (2021) NGAL as a potential target in tumor microenvironment, Int. J. Mol. Sci., 22, 12333, doi: 10.3390/ijms222212333.
- Xu, B., Zheng, W., Jin, D., Wang, D., Liu, X., and Qin, X. (2012) Treatment of pancreatic cancer using an oncolytic virus harboring the lipocalin-2 gene, Cancer, 118, 5217-5226, doi: 10.1002/cncr.27535.
- Xu, B., Zheng, W.-Y., Feng, J.-F., Huang, X.-Y., and Ge, H. (2013) One potential oncolytic adenovirus expressing Lipocalin-2 for colorectal cancer therapy, Cancer Biother. Radiopharm., 28, 415-422, doi: 10.1089/cbr.2012.1352.
- Nishimura, S., Yamamoto, Y., Sugimoto, A., Kushiyama, S., Togano, S., et al. (2022) Lipocalin-2 negatively regulates epithelial-mesenchymal transition through matrix metalloprotease-2 downregulation in gastric cancer, Gastric Cancer, 25, 850-861, doi: 10.1007/s10120-022-01305-w.
- Pinyopornpanish, K., Phrommintikul, A., Angkurawaranon, C., Kumfu, S., Angkurawaranon, S., et al. (2022) Circulating Lipocalin-2 level is positively associated with cognitive impairment in patients with metabolic syndrome, Sci. Rep., 12, 4635, doi: 10.1038/s41598-022-08286-x.
- Friedman, M., Lindström, S., Ekerljung, L., Andersson-Svahn, H., Carlsson, J., et al. (2009) Engineering and characterization of a bispecific HER2 x EGFR-binding affibody molecule, Biotechnol. Appl. Biochem., 54, 121-131, doi: 10.1042/BA20090096.
- Gorman, K., McGinnis, J., and Kay, B. (2018) Generating FN3-based affinity reagents through phage display, Curr. Protoc. Chem. Biol., 10, e39, doi: 10.1002/cpch.39.
- Давыдова Е. К. (2022) Белковая инженерия: достижения фагового дисплея в науке и медицине, Усп. Биол. Хим., 62, 319.
- Zhang, Y., Thangam, R., You, S.-H., Sultonova, R. D., Venu, A., et al. (2021) Engineering calreticulin-targeting monobodies to detect immunogenic cell death in cancer chemotherapy, Cancers (Basel), 13, 2801, doi: 10.3390/cancers13112801.
- Cetin, M., Evenson, W. E., Gross, G. G., Jalali-Yazdi, F., Krieger, D., et al. (2017) RasIns: genetically encoded intrabodies of activated Ras proteins, J. Mol. Biol., 429, 562-573, doi: 10.1016/j.jmb.2016.11.008.
- Olson, C. A., and Roberts, R. W. (2007) Design, expression, and stability of a diverse protein library based on the human fibronectin type III domain, Protein Sci., 16, 476-484, doi: 10.1110/ps.062498407
- Храмцов Ю. В., Уласов А. В., Лупанова Т. Н., Георгиев Г. П., Соболев А. С. (2022) Доставка антителоподобных молекул, монободи, способных связываться с нуклеокапсидным белком вируса SARS-COV-2, в клетки-мишени, Докл. РАН. Науки Жизни, 506, 68, doi: 10.31857/S2686738922050146.
- Lipovsek, D., Lippow, S. M., Hackel, B. J., Gregson, M. W., Cheng, P., et al. (2007) Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies, J. Mol. Biol., 368, 1024-1041, doi: 10.1016/j.jmb.2007.02.029.
- Riihimäki, T. A., Hiltunen, S., Rangl, M., Nordlund, H. R., Määttä, J. A. E., et al. (2011) Modification of the loops in the ligand-binding site turns avidin into a steroid-binding protein, BMC Biotechnol., 11, 64, doi: 10.1186/1472-6750-11-64.
- Hytönen, V. P. (2020) (Strept)avidin as a template for ligands other than biotin: An overview, Methods Enzymol., 633, 21-28, doi: 10.1016/bs.mie.2019.10.029.
- Kiss, C., Fisher, H., Pesavento, E., Dai, M., Valero, R., et al. (2006) Antibody binding loop insertions as diversity elements, Nucleic Acids Res., 34, e132, doi: 10.1093/nar/gkl681.
- Kadonosono, T., Yabe, E., Furuta, T., Yamano, A., Tsubaki, T., et al. (2014) A fluorescent protein scaffold for presenting structurally constrained peptides provides an effective screening system to identify high affinity target-binding peptides, PLoS One, 9, e103397, doi: 10.1371/journal.pone.0103397.
- Chee, S. M. Q., Wongsantichon, J., Yi, L. S., Sana, B., Frosi, Y., et al. (2021) Functional display of bioactive peptides on the vGFP scaffold, Sci. Rep., 11, 10127, doi: 10.1038/s41598-021-89421-y.
- Rinne, S. S., Yin, W., Borras, A. M., Abouzayed, A., Leitao, C. D., et al. (2022) Targeting tumor cells overexpressing the human epidermal growth factor receptor 3 with potent drug conjugates based on affibody molecules, Biomedicines, 10, 1293, doi: 10.3390/biomedicines10061293.
- Sokolova, E., Kutova, O., Grishina, A., Pospelov, A., Guryev, E., et al. (2019) Penetration efficiency of antitumor agents in ovarian cancer spheroids: the case of recombinant targeted toxin DARPin-LoPE and the chemotherapy drug, doxorubicin, Pharmaceutics, 11, 219, doi: 10.3390/pharmaceutics11050219.
- Sachdev, S., Cabalteja, C. C., and Cheloha, R. W. (2021) Strategies for targeting cell surface proteins using multivalent conjugates and chemical biology, Methods Cell Biol., 166, 205-222, doi: 10.1016/bs.mcb.2021.06.004.
- Шипунова В. О., Деев С. М. (2022) Распознающие cкаффолдовые полипептиды как инструмент для адресной доставки наноструктур in vitro и in vivo, Acta Naturae, 14, 54, doi: 10.32607/actanaturae.11545.
- Deyev, S., Proshkina, G., Baryshnikova, O., Ryabova, A., Avishai, G., et al. (2018) Selective staining and eradication of cancer cells by protein-carrying DARPin-functionalized liposomes, Eur. J. Pharm. Biopharm., 130, 296-305, doi: 10.1016/j.ejpb.2018.06.026.
- Nazari, M., Emamzadeh, R., Jahanpanah, M., Yazdani, E., and Radmanesh, R. (2022) A recombinant affitoxin derived from a HER3 affibody and diphteria-toxin has potent and selective antitumor activity, Int. J. Biol. Macromol., 219, 1122-1134, doi: 10.1016/j.ijbiomac.2022.08.150.
- Lipovšek, D., Carvajal, I., Allentoff, A. J., Barros, A., Brailsford, J., et al. (2018) Adnectin-drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors, Protein Eng. Des. Sel., 31, 159-171, doi: 10.1093/protein/gzy013.
- Karsten, L., Janson, N., Le Joncour, V., Alam, S., Müller, B., et al. (2022) Bivalent EGFR-targeting DARPin-MMAE conjugates, Int. J. Mol. Sci., 23, 2468, doi: 10.3390/ijms23052468.
- Sharma, R., Suman, S. K., and Mukherjee, A. (2022) Antibody-based radiopharmaceuticals as theranostic agents: an overview, Curr. Med. Chem., 29, 5979, doi: 10.2174/0929867329666220607160559.
- Luo, R., Liu, H., and Cheng, Z. (2022) Protein scaffolds: antibody alternatives for cancer diagnosis and therapy, RSC Chem. Biol., 3, 830-847, doi: 10.1039/d2cb00094f.
- Klont, F., Hadderingh, M., Horvatovich, P., Ten Hacken, N. H. T., and Bischoff, R. (2018) Affimers as an alternative to antibodies in an affinity LC-MS assay for quantification of the soluble receptor of advanced glycation end-products (sRAGE) in human serum, J. Proteome Res., 17, 2892-2899, doi: 10.1021/acs.jproteome.8b00414.
- Mayoral-Peña, K., González Peña, O. I., Orrantia Clark, A. M., Flores-Vallejo, R. D. C., Oza, G., et al. (2022) Biorecognition engineering technologies for cancer diagnosis: a systematic literature review of non-conventional and plausible sensor development methods, Cancers (Basel), 14, 1867, doi: 10.3390/cancers14081867.
- Шилова О. Н., Деев С. М. (2019) Дарпины - перспективные адресные белки для тераностики, Acta Naturae, 11, 42, doi: 10.32607/20758251-2019-11-4-42-53.
- Shipunova, V. O., Kolesnikova, O. A., Kotelnikova, P. A., Soloviev, V. D., Popov, A. A., et al. (2021) Comparative evaluation of engineered polypeptide scaffolds in HER2-targeting magnetic nanocarrier delivery, ACS Omega, 6, 16000, doi: 10.1021/acsomega.1c01811.
- Mamluk, R., Carvajal, I. M., Morse, B. A., Wong, H., Abramowitz, J., et al. (2010) Anti-tumor effect of CT-322 as an adnectin inhibitor of vascular endothelial growth factor receptor-2, MAbs, 2, 199-208, doi: 10.4161/mabs.2.2.11304.
- Tolmachev, V., and Orlova, A. (2020) Affibody molecules as targeting vectors for PET imaging, Cancers (Basel), 12, E651, doi: 10.3390/cancers12030651.
- Deyev, S., Vorobyeva, A., Schulga, A., Proshkina, G., Güler, R., et al. (2019) Comparative evaluation of two DARPin variants: effect of affinity, size, and label on tumor targeting properties, Mol. Pharm., 16, 995-1008, doi: 10.1021/acs.molpharmaceut.8b00922.
- Wang, Y., Ballou, B., Schmidt, B. F., Andreko, S., St Croix, C. M., et al. (2017) Affibody-targeted fluorogen activating protein for in vivo tumor imaging, Chem. Commun. (Camb.), 53, 2001, doi: 10.1039/c6cc09137g.
- Yun, M., Kim, D.-Y., Lee, J.-J., Kim, H.-S., Kim, H.-S., et al. (2017) A high-affinity repebody for molecular imaging of EGFR-expressing malignant tumors, Theranostics, 7, 2620-2633, doi: 10.7150/thno.18096.
- Mączyńska, J., Raes, F., Da Pieve, C., Turnock, S., Boult, J. K. R., et al. (2022) Triggering anti-GBM immune response with EGFR-mediated photoimmunotherapy, BMC Med., 20, 16, doi: 10.1186/s12916-021-02213-z.
- Lui, B. G., Salomon, N., Wüstehube-Lausch, J., Daneschdar, M., Schmoldt, H.-U., et al. (2020) Targeting the tumor vasculature with engineered cystine-knot miniproteins, Nat. Commun., 11, 295, doi: 10.1038/s41467-019-13948-y.
- Балалаева И. В., Крылова Л. В., Карпова М. А., Шульга А. А., Коновалова Е. В. (2023) Синергический эффект комбинированного действия таргетной и фотодинамической терапии в отношении HER2-положительного рака молочной железы, Докл. РАН. Науки Жизни, 508, 48, doi: 10.31857/S268673892270007X.
- Proshkina, G. M., Shramova, E. I., Shilova, M. V., Zelepukin, I. V., Shipunova, V. O., et al. (2021) DARPin_9-29-targeted gold nanorods selectively suppress HER2-positive tumor growth in mice, Cancers (Basel), 13, 5235, doi: 10.3390/cancers1320523.
- Shramova, E., Proshkina, G., Shipunova, V., Ryabova, A., Kamyshinsky, R., et al. (2020) Dual targeting of cancer cells with DARPin-based toxins for overcoming tumor escape, Cancers (Basel), 12, E3014, doi: 10.3390/cancers12103014.
- Eijkenboom, L., Palacio-Castañeda, V., Groenman, F., Braat, D., Beerendonk, C., et al. (2021) Assessing the use of tumor-specific DARPin-toxin fusion proteins for ex vivo purging of cancer metastases from human ovarian cortex before autotransplantation, F. S. Sci., 2, 330-344, doi: 10.1016/j.xfss.2021.09.004.
- Xu, T., Schulga, A., Konovalova, E., Rinne, S. S., Zhang, H., et al. (2023) Feasibility of co-targeting HER3 and EpCAM using seribantumab and DARPin-toxin fusion in a pancreatic cancer xenograft model, Int. J. Mol. Sci., 24, 2838, doi: 10.3390/ijms24032838.
- Hanauer, J. R. H., Koch, V., Lauer, U. M., and Mühlebach, M. D. (2019) High-affinity DARPin allows targeting of MeV to glioblastoma multiforme in combination with protease targeting without loss of potency, Mol. Ther. Oncolytics, 15, 186-200, doi: 10.1016/j.omto.2019.10.004.
- Lal, S., and Raffel, C. (2017) Using cystine knot proteins as a novel approach to retarget oncolytic measles virus, Mol. Ther. Oncolytics, 7, 57-66, doi: 10.1016/j.omto.2017.09.005.
- Strecker, M. I., Wlotzka, K., Strassheimer, F., Roller, B., Ludmirski, G., et al. (2022) AAV-mediated gene transfer of a checkpoint inhibitor in combination with HER2-targeted CAR-NK cells as experimental therapy for glioblastoma, Oncoimmunology, 11, 2127508, doi: 10.1080/2162402X.2022.2127508.
- Zajc, C. U., Salzer, B., Taft, J. M., Reddy, S. T., Lehner, M., and Traxlmayr, M. W. (2021) Driving CARs with alternative navigation tools - the potential of engineered binding scaffolds, FEBS J., 288, 2103-2118, doi: 10.1111/febs.15523.
- Stepanov, A. V., Kalinin, R. S., Shipunova, V. O., Zhang, D., Xie, J., et al. (2022) Switchable targeting of solid tumors by BsCAR T cells, Proc. Natl. Acad. Sci. USA, 119, e2210562119, doi: 10.1073/pnas.2210562119.
- Parfenyev, S., Singh, A., Fedorova, O., Daks, A., Kulshreshtha, R., and Barlev, N. A. (2021) Interplay between p53 and non-coding RNAs in the regulation of EMT in breast cancer, Cell Death Dis., 12, 17, doi: 10.1038/s41419-020-03327-7.
- Lezina, L., Aksenova, V., Fedorova, O., Malikova, D., Shuvalov, O., Antonov, A. V., et al. (2015) KMT Set7/9 affects genotoxic stress response via the Mdm2 axis, Oncotarget, 6, 25843-25855, doi: 10.18632/oncotarget.4584.
- Davidovich, P., Aksenova, V., Petrova, V., Tentler, D., Orlova, D., et al. (2015) Discovery of novel isatin-based p53 inducers, ACS Med. Chem. Lett., 6, 856-860, doi: 10.1021/acsmedchemlett.5b00011.
- Bulatov, E., Sayarova, R., Mingaleeva, R., Miftakhova, R., Gomzikova, M., et al. (2018) Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors, Cell Death Discov., 4, 103, doi: 10.1038/s41420-018-0120-z.
- Lau, S.-Y., Siau, J. W., Sobota, R. M., Wang, C.-I., Zhong, P., et al. (2018) Synthetic 10FN3-based mono- and bivalent inhibitors of MDM2/X function, Protein Eng. Des. Sel., 31, 301-312, doi: 10.1093/protein/gzy018.
- Spencer-Smith, R., Koide, A., Zhou, Y., Eguchi, R. R., Sha, F., et al. (2017) Inhibition of RAS function through targeting an allosteric regulatory site, Nat. Chem. Biol., 13, 62-68, doi: 10.1038/nchembio.2231.
- Teng, K. W., Tsai, S. T., Hattori, T., Fedele, C., Koide, A., et al. (2021) Selective and noncovalent targeting of RAS mutants for inhibition and degradation, Nat. Commun., 12, 2656, doi: 10.1038/s41467-021-22969-5.
- Khan, I., Koide, A., Zuberi, M., Ketavarapu, G., Denbaum, E., et al. (2022) Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants, Cell Rep., 38, 110322, doi: 10.1016/j.celrep.2022.110322.
- Wallon, L., Khan, I., Teng, K. W., Koide, A., Zuberi, M., et al. (2022) Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket, Proc. Natl. Acad. Sci. USA, 119, e2204481119, doi: 10.1073/pnas.2204481119.
- Guillard, S., Kolasinska-Zwierz, P., Debreczeni, J., Breed, J., Zhang, J., et al. (2017) Structural and functional characterization of a DARPin which inhibits Ras nucleotide exchange, Nat. Commun., 8, 16111, doi: 10.1038/ncomms16111.
- Bery, N., Legg, S., Debreczeni, J., Breed, J., Embrey, K., et al. (2019) KRAS-specific inhibition using a DARPin binding to a site in the allosteric lobe, Nat. Commun., 10, 2607, doi: 10.1038/s41467-019-10419-2.
- McGee, J. H., Shim, S. Y., Lee, S.-J., Swanson, P. K., Jiang, S. Y., et al. (2018) Exceptionally high-affinity Ras binders that remodel its effector domain, J. Biol. Chem., 293, 3265-3280, doi: 10.1074/jbc.M117.816348.
- Jung, Y. H., Choi, Y., Seo, H.-D., Seo, M.-H., and Kim, H.-S. (2023) A conformation-selective protein binder for a KRAS mutant inhibits the interaction between RAS and RAF, Biochem. Biophys. Res. Commun., 645, 110-117, doi: 10.1016/j.bbrc.2023.01.019.
- Schmit, N. E., Neopane, K., and Hantschel, O. (2019) Targeted protein degradation through cytosolic delivery of monobody binders using bacterial toxins, ACS Chem. Biol., 14, 916-924, doi: 10.1021/acschembio.9b00113.
- Röth, S., Macartney, T. J., Konopacka, A., Chan, K.-H., Zhou, H., et al. (2020) Targeting endogenous K-RAS for degradation through the affinity-directed protein missile system, Cell. Chem. Biol., 27, 1151-1163.e6, doi: 10.1016/j.chembiol.2020.06.012.
- Kim, J. W., Cochran, F. V., and Cochran, J. R. (2015) A chemically cross-linked knottin dimer binds integrins with picomolar affinity and inhibits tumor cell migration and proliferation, J. Am. Chem. Soc., 137, 6-9, doi: 10.1021/ja508416e.
- Gad, S., and Ayakar, S. (2021) Protein scaffolds: A tool for multi-enzyme assembly, Biotechnol. Rep. (Amst.), 32, e00670, doi: 10.1016/j.btre.2021.e00670.
- Islam, M., Kehoe, H. P., Lissoos, J. B., Huang, M., Ghadban, C. E., et al. (2021) Chemical diversification of simple synthetic antibodies, ACS Chem. Biol., 16, 344-359, doi: 10.1021/acschembio.0c00865.
- Rabe von Pappenheim, F., Wensien, M., Ye, J., Uranga, J., Irisarri, I., et al. (2022) Widespread occurrence of covalent lysine-cysteine redox switches in proteins, Nat. Chem. Biol., 18, 368-375, doi: 10.1038/s41589-021-00966-5.
- Maggi, M., Pessino, G., Guardamagna, I., Lonati, L., Pulimeno, C., and Scotti, C. (2021) A targeted catalytic nanobody (T-CAN) with asparaginolytic activity, Cancers (Basel), 13, 5637, doi: 10.3390/cancers13225637.
- Fellouse, F. A., Barthelemy, P. A., Kelley, R. F., and Sidhu, S. S. (2006) Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code, J. Mol. Biol., 357, 100-114, doi: 10.1016/j.jmb.2005.11.092.
- Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer, G., and Sidhu, S. S. (2008) The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies, J. Mol. Biol., 377, 1518-1528, doi: 10.1016/j.jmb.2008.01.093.
- Gilbreth, R. N., Esaki, K., Koide, A., Sidhu, S. S., and Koide, S. (2008) A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces, J. Mol. Biol., 381, 407-418, doi: 10.1016/j.jmb.2008.06.014.
- Bonvin, P., Venet, S., Fontaine, G., Ravn, U., Gueneau, F., Kosco-Vilbois, M., et al. (2015) De novo isolation of antibodies with pH-dependent binding properties, MAbs, 7, 294-302, doi: 10.1080/19420862.2015.1006993.
- Hackel, B. J., and Wittrup, K. D. (2010) The full amino acid repertoire is superior to serine/tyrosine for selection of high affinity immunoglobulin G binders from the fibronectin scaffold, Protein Eng. Des. Sel., 23, 211-219, doi: 10.1093/protein/gzp083.
- Svilenov, H. L., Sacherl, J., Protzer, U., Zacharias, M., and Buchner, J. (2021) Mechanistic principles of an ultra-long bovine CDR reveal strategies for antibody design, Nat. Commun., 12, 6737, doi: 10.1038/s41467-021-27103-z.
- Schilling, J., Schöppe, J., and Plückthun, A. (2014) From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display, J. Mol. Biol., 426, 691-721, doi: 10.1016/j.jmb.2013.10.026.
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