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Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning

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Article: 2168470 | Received 24 Jul 2022, Accepted 10 Jan 2023, Published online: 22 Jan 2023

References

  • Bateman A, Martin MJ, Orchard S, Magrane M, Agivetova R, Ahmad S, Alpi E, Bowler-Barnett EH, Britto R, Bursteinas B, et al. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49(D1):D480–11. doi:10.1093/nar/gkaa1100.
  • Packer MS, Liu DR. Methods for the directed evolution of proteins. Nat Rev Genet. 2015;16(7):379–94. doi:10.1038/nrg3927.
  • Wang YJ, Xue P, Cao MF, Yu TH, Lane ST, Zhao HM. Directed evolution: methodologies and applications. Chem Rev. 2021;121(20):12384–444. doi:10.1021/acs.chemrev.1c00260.
  • Qi H, Ma ML, Lai DY, Tao SC. Phage display: an ideal platform for coupling protein to nucleic acid. Acta Biochim Biophys Sin (Shanghai). 2021;53(4):389–99. doi:10.1093/abbs/gmab006.
  • Linciano S, Pluda S, Bacchin A, Angelini A. Molecular evolution of peptides by yeast surface display technology. Medchemcomm. 2019;10(9):1569–80. doi:10.1039/C9MD00252A.
  • Contreras-Llano LE, Tan CM. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Bio. 2018;3:1. doi:10.1093/synbio/ysy012.
  • Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev. 2021;50(16):9055–103. doi:10.1039/d1cs00160d.
  • Yan JR, Li GH, Hu YH, Ou WJ, Wan YK, Gajewski T, Wang Y, Wongchenko M, Choong N, Ribas A. Construction of a synthetic phage-displayed Nanobody library with CDR3 regions randomized by trinucleotide cassettes for diagnostic applications. J Transl Med. 2014;12(S1):12. doi:10.1186/1479-5876-12-S1-O12.
  • Saito Y, Oikawa M, Sato T, Nakazawa H, Ito T, Kameda T, Tsuda K, Umetsu M. Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration. ACS Catal. 2021;11(23):14615–24. doi:10.1021/acscatal.1c03753.
  • Yang KK, Wu Z, Arnold FH. Machine-learning-guided directed evolution for protein engineering. Nat Methods. 2019;16(8):687–94. doi:10.1038/s41592-019-0496-6.
  • Saito Y, Oikawa M, Nakazawa H, Niide T, Kameda T, Tsuda K. Machine-Learning-Guided UM. Mutagenesis for directed evolution of fluorescent proteins. ACS Synth Biol. 2018;7(9):2014–22. doi:10.1021/acssynbio.8b00155.
  • Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM. Unified rational protein engineering with sequence-based deep representation learning. Nat Methods. 2019;16(12):1315–22. doi:10.1038/s41592-019-0598-1.
  • Biswas S, Khimulya G, Alley EC, Esvelt KM, Church GM. Low-N protein engineering with data-efficient deep learning. Nat Methods. 2021;18(4):389–96. doi:10.1038/s41592-021-01100-y.
  • Liao J, Warmuth MK, Govindarajan S, Ness JE, Wang RP, Gustafsson C, Minshull J. Engineering proteinase K using machine learning and synthetic genes. BMC Biotechnol. 2007. 7.
  • Fox RJ, Davis SC, Mundorff EC, Newman LM, Gavrilovic V, Ma SK, Chung LM, Ching C, Tam S, Muley S, et al. Improving catalytic function by ProSAR-driven enzyme evolution. Nat Biotechnol. 2007;25(3):338–44. doi:10.1038/nbt1286.
  • Cadet F, Fontaine N, Li GY, Sanchis J, Chong MNF, Pandjaitan R, Vetrivel I, Offmann B, Reetz MT. A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes. Sci Rep. 2018. 8.
  • Wu Z, Kan SBJ, Lewis RD, Wittmann BJ, Arnold FH. Machine learning-assisted directed protein evolution with combinatorial libraries. Proceedings of the National Academy of Sciences. 2019;116(18):8852–58.
  • Giguere S, Laviolette F, Marchand M, Tremblay D, Moineau S, Liang XX, Biron E, Corbeil J, Kim PM. Machine learning assisted design of highly active peptides for drug discovery. PLoS Comp Biol. 2015;11:4. doi:10.1371/journal.pcbi.1004074.
  • Bedbrook CN, Yang KK, Robinson JE, Mackey ED, Gradinaru V, Arnold FH. Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics. Nat Methods. 2019;16(11):1176–84. doi:10.1038/s41592-019-0583-8.
  • Yoo DK, Lee SR, Jung Y, Han H, Lee HK, Han J, Kim S, Chae J, Ryu T, Chung J. Machine learning-guided prediction of antigen-reactive in silico clonotypes based on changes in clonal abundance through bio-panning. Biomolecules. 2020;10:3. doi:10.3390/biom10030421.
  • Saka K, Kakuzaki T, Metsugi S, Kashiwagi D, Yoshida K, Wada M, Tsunoda H, Teramoto R. Antibody design using LSTM based deep generative model from phage display library for affinity maturation. Sci Rep. 2021;11(1):1. doi:10.1038/s41598-021-85274-7.
  • Parkinson J, Hard R, Ainsworth RI, Li N, Wang W. Engineering a histone reader protein by combining directed evolution, sequencing, and neural network based ordinal regression. J Chem Inf Model. 2020;60(8):3992–4004. doi:10.1021/acs.jcim.0c00441.
  • Mason DM, Friedensohn S, Weber CR, Jordi C, Wagner B, Meng SM, Ehling RA, Bonati L, Dahinden J, Gainza P, et al. Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning. Nat Biomed Eng. 2021;5(6):600–12. doi:10.1038/s41551-021-00699-9.
  • Liu G, Zeng H, Mueller J, Carter B, Wang ZH, Schilz J, Horny G, Birnbaum ME, Ewert S, Gifford D. Antibody complementarity determining region design using high-capacity machine learning. Bioinformatics. 2020;36(7):2126–33. doi:10.1093/bioinformatics/btz895.
  • Thomas WD, Golomb M, Smith GP. Corruption of phage display libraries by target-unrelated clones: diagnosis and countermeasures. Anal Biochem. 2010;407(2):237–40. doi:10.1016/j.ab.2010.07.037.
  • Menendez A, Scott JK. The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal Biochem. 2005;336(2):145–57. doi:10.1016/j.ab.2004.09.048.
  • Gebauer M, Skerra A. Engineering of binding functions into proteins. Curr Opin Biotechnol. 2019;60:230–41. doi:10.1016/j.copbio.2019.05.007.
  • Vazquez-Lombardi R, Phan TG, Zimmermann C, Lowe D, Jermutus L, Christ D. Challenges and opportunities for non-antibody scaffold drugs. Drug Discov Today. 2015;20(10):1271–83. doi:10.1016/j.drudis.2015.09.004.
  • Yu XW, Yang YP, Dikici E, Deo SK, Daunert S. Beyond antibodies as binding partners: the role of antibody mimetics in bioanalysis. Annu Rev Anal Chem. 2017;10(1):293–320. doi:10.1146/annurev-anchem-061516-045205.
  • Skrlec K, Strukelj B, Berlec A. Non-immunoglobulin scaffolds: a focus on their targets. Trends Biotechnol. 2015;33(7):408–18. doi:10.1016/j.tibtech.2015.03.012.
  • Weidle UH, Auer J, Brinkmann U, Georges G, Tiefenthaler G. The emerging role of new protein scaffold-based agents for treatment of cancer. Cancer Genom Proteom. 2013;10:155–68.
  • Brinkmann U, Kontermann RE. The making of bispecific antibodies. Mabs. 2017;9(2):182–212. doi:10.1080/19420862.2016.1268307.
  • Fujii H, Tanaka Y, Nakazawa H, Sugiyama A, Manabe N, Shinoda A, Shimizu N, Hattori T, Hosokawa K, Sujino T, et al. Compact seahorse-shaped T cell-activating antibody for cancer therapy. Adv Therap. 2018;1(3):3. doi:10.1002/adtp.201700031.
  • Ito T, Nishi H, Kameda T, Yoshida M, Fukazawa R, Kawada S, Nakazawa H, Umetsu M. Combination informatic and experimental approach for selecting scaffold proteins for development as antibody mimetics. Chem Lett. 2021;50(11):1867–71. doi:10.1246/cl.210443.
  • Girard A, Magnani JL. Clinical trials and applications of galectin antagonists. Trends in Glycoscience and Glycotechnology. 2018;31(172):Se211–Se20.
  • Dong R, Zhang M, Hu QY, Zheng S, Soh A, Zheng YJ, Yuan H. Galectin-3 as a novel biomarker for disease diagnosis and a target for therapy. Int J Mol Med. 2018;41(2):599–614. doi:10.3892/ijmm.2017.3311.
  • Kruziki MA, Bhatnagar S, Woldring DR, Duong VT, Hackel BJ. A 45-amino-acid scaffold mined from the PDB for High-Affinity Ligand Engineering. Chem Biol. 2015;22(7):946–56. doi:10.1016/j.chembiol.2015.06.012.
  • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. doi:10.1093/nar/25.17.3389.
  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504. doi:10.1101/gr.1239303.
  • Hirano A, Kameda T. Aromaphilicity index of amino acids: molecular dynamics simulations of the protein binding affinity for carbon nanomaterials. Acs App Nano Mat. 2021;4(3):2486–95. doi:10.1021/acsanm.0c03047.
  • Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188–90. doi:10.1101/gr.849004.
  • Romero PA, Arnold FH. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol. 2009;10(12):866–76. doi:10.1038/nrm2805.