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image of Exploring the Blueprint of Life: The Innovation in Antibody and Protein Design

Abstract

The innovation in antibody and protein design highlights the transformation from empirical approaches to sophisticated strategies integrating computational methods and artificial intelligence (AI). Key principles, such as combinatorial, structure-based, consensus, and computational designs, have been pivotal in predicting structures from sequences ( design). Advances in tools, like AlphaFold and Rosetta suite, enable accurate structure prediction, facilitating the development of functional proteins and antibodies. However, challenges remain, including improving prediction accuracy, modeling flexible regions, understanding structural dynamics, and designing catalytic and binding sites. Despite these, the field promises groundbreaking advancements in biomedical sciences, enriching our understanding and serving human health and scientific discovery.

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2025-02-20
2025-09-01
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References

  1. Barato A.C. Seifert U. Thermodynamic uncertainty relation for biomolecular processes. Phys. Rev. Lett. 2015 114 15 158101 10.1103/PhysRevLett.114.158101 25933341
    [Google Scholar]
  2. Guo J. Zhou H.X. Protein allostery and conformational dynamics. Chem. Rev. 2016 116 11 6503 6515 10.1021/acs.chemrev.5b00590 26876046
    [Google Scholar]
  3. Arnold F.H. Innovation by evolution: Bringing new chemistry to life (nobel lecture). Angew. Chem. Int. Ed. 2019 58 41 14420 14426 10.1002/anie.201907729 31433107
    [Google Scholar]
  4. Korendovych I.V. DeGrado W.F. De novo protein design, a retrospective. Q. Rev. Biophys. 2020 53 e3 10.1017/S0033583519000131 32041676
    [Google Scholar]
  5. Woolfson D.N. A brief history of de novo protein design: Minimal, rational, and computational. J. Mol. Biol. 2021 433 20 167160 10.1016/j.jmb.2021.167160 34298061
    [Google Scholar]
  6. Listov D. Opportunities and challenges in design and optimization of protein function Nat. Rev. Mol. Cell Biol. 2024 25 8 639 653 10.1038/s41580‑024‑00718‑y
    [Google Scholar]
  7. Saven J.G. Combinatorial protein design. Curr. Opin. Struct. Biol. 2002 12 4 453 458 10.1016/S0959‑440X(02)00347‑0 12163067
    [Google Scholar]
  8. Ovchinnikov S. Huang P.S. Structure-based protein design with deep learning. Curr. Opin. Chem. Biol. 2021 65 136 144 10.1016/j.cbpa.2021.08.004 34547592
    [Google Scholar]
  9. Porebski B.T. Buckle A.M. Consensus protein design. Protein Eng. Des. Sel. 2016 29 7 245 251 10.1093/protein/gzw015 27274091
    [Google Scholar]
  10. Yang W. Lai L.H. Computational design of proteins with novel structure and functions. Chin. Phys. B 2016 25 1 018702 10.1088/1674‑1056/25/1/018702
    [Google Scholar]
  11. Liu H. Chen Q. Computational protein design with data‐driven approaches: Recent developments and perspectives. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2023 13 3 e1646 10.1002/wcms.1646
    [Google Scholar]
  12. Notin P. Rollins N. Gal Y. Sander C. Marks D. Machine learning for functional protein design. Nat. Biotechnol. 2024 42 2 216 228 10.1038/s41587‑024‑02127‑0 38361074
    [Google Scholar]
  13. Kim J. McFee M. Fang Q. Abdin O. Kim P.M. Computational and artificial intelligence-based methods for antibody development. Trends Pharmacol. Sci. 2023 44 3 175 189 10.1016/j.tips.2022.12.005 36669976
    [Google Scholar]
  14. Kortemme T. De novo protein design—From new structures to programmable functions. Cell 2024 187 3 526 544 10.1016/j.cell.2023.12.028 38306980
    [Google Scholar]
  15. DeGrado W.F. Wasserman Z.R. Lear J.D. Protein design, a minimalist approach. Science 1989 243 4891 622 628 10.1126/science.2464850 2464850
    [Google Scholar]
  16. Koch I. Schäfer T. Protein super-secondary structure and quaternary structure topology: Theoretical description and application. Curr. Opin. Struct. Biol. 2018 50 134 143 10.1016/j.sbi.2018.02.005 29558676
    [Google Scholar]
  17. Nanda V. Koder R.L. Designing artificial enzymes by intuition and computation. Nat. Chem. 2010 2 1 15 24 10.1038/nchem.473 21124375
    [Google Scholar]
  18. O’Shea E.K. Klemm J.D. Kim P.S. Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991 254 5031 539 544 10.1126/science.1948029 1948029
    [Google Scholar]
  19. Pabo C.O. Peisach E. Grant R.A. Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem. 2001 70 1 313 340 10.1146/annurev.biochem.70.1.313 11395410
    [Google Scholar]
  20. Rhys G.G. Wood C.W. Lang E.J.M. Mulholland A.J. Brady R.L. Thomson A.R. Woolfson D.N. Maintaining and breaking symmetry in homomeric coiled-coil assemblies. Nat. Commun. 2018 9 1 4132 10.1038/s41467‑018‑06391‑y 30297707
    [Google Scholar]
  21. Magliery T.J. Protein stability: Computation, sequence statistics, and new experimental methods. Curr. Opin. Struct. Biol. 2015 33 161 168 10.1016/j.sbi.2015.09.002 26497286
    [Google Scholar]
  22. Huang P.S. Boyken S.E. Baker D. The coming of age of de novo protein design. Nature 2016 537 7620 320 327 10.1038/nature19946 27629638
    [Google Scholar]
  23. Goldenzweig A. Fleishman S.J. Principles of protein stability and their application in computational design. Annu. Rev. Biochem. 2018 87 105 129 10.1146/annurev‑biochem‑062917‑012102
    [Google Scholar]
  24. Warszawski S. Borenstein Katz A. Lipsh R. Khmelnitsky L. Ben Nissan G. Javitt G. Dym O. Unger T. Knop O. Albeck S. Diskin R. Fass D. Sharon M. Fleishman S.J. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLOS Comput. Biol. 2019 15 8 e1007207 10.1371/journal.pcbi.1007207 31442220
    [Google Scholar]
  25. Xu Y. Liu D. Gong H. Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy. Nat. Comput. Sci. 2024 4 11 840 850 10.1038/s43588‑024‑00716‑2 39455825
    [Google Scholar]
  26. Tu G. Fu T. Zheng G. Xu B. Gou R. Luo D. Wang P. Xue W. Computational chemistry in structure-based solute carrier transporter drug design: Recent advances and future perspectives. J. Chem. Inf. Model. 2024 64 5 1433 1455 10.1021/acs.jcim.3c01736 38294194
    [Google Scholar]
  27. Thomson A.R. Wood C.W. Burton A.J. Bartlett G.J. Sessions R.B. Brady R.L. Woolfson D.N. Computational design of water-soluble α-helical barrels. Science 2014 346 6208 485 488 10.1126/science.1257452 25342807
    [Google Scholar]
  28. Scott A.J. Niitsu A. Kratochvil H.T. Lang E.J.M. Sengel J.T. Dawson W.M. Mahendran K.R. Mravic M. Thomson A.R. Brady R.L. Liu L. Mulholland A.J. Bayley H. DeGrado W.F. Wallace M.I. Woolfson D.N. Constructing ion channels from water-soluble α-helical barrels. Nat. Chem. 2021 13 7 643 650 10.1038/s41557‑021‑00688‑0 33972753
    [Google Scholar]
  29. Dauparas J. Anishchenko I. Bennett N. Bai H. Ragotte R.J. Milles L.F. Wicky B.I.M. Courbet A. de Haas R.J. Bethel N. Leung P.J.Y. Huddy T.F. Pellock S. Tischer D. Chan F. Koepnick B. Nguyen H. Kang A. Sankaran B. Bera A.K. King N.P. Baker D. Robust deep learning–based protein sequence design using ProteinMPNN. Science 2022 378 6615 49 56 10.1126/science.add2187 36108050
    [Google Scholar]
  30. Watson J.L. Juergens D. Bennett N.R. Trippe B.L. Yim J. Eisenach H.E. Ahern W. Borst A.J. Ragotte R.J. Milles L.F. Wicky B.I.M. Hanikel N. Pellock S.J. Courbet A. Sheffler W. Wang J. Venkatesh P. Sappington I. Torres S.V. Lauko A. De Bortoli V. Mathieu E. Ovchinnikov S. Barzilay R. Jaakkola T.S. DiMaio F. Baek M. Baker D. De novo design of protein structure and function with RFdiffusion. Nature 2023 620 7976 1089 1100 10.1038/s41586‑023‑06415‑8 37433327
    [Google Scholar]
  31. Albanese K.I. Petrenas R. Pirro F. Naudin E.A. Borucu U. Dawson W.M. Scott D.A. Leggett G.J. Weiner O.D. Oliver T.A.A. Woolfson D.N. Rationally seeded computational protein design of ɑ-helical barrels. Nat. Chem. Biol. 2024 20 8 991 999 10.1038/s41589‑024‑01642‑0 38902458
    [Google Scholar]
  32. Jumper J. Evans R. Pritzel A. Green T. Figurnov M. Ronneberger O. Tunyasuvunakool K. Bates R. Žídek A. Potapenko A. Bridgland A. Meyer C. Kohl S.A.A. Ballard A.J. Cowie A. Romera-Paredes B. Nikolov S. Jain R. Adler J. Back T. Petersen S. Reiman D. Clancy E. Zielinski M. Steinegger M. Pacholska M. Berghammer T. Bodenstein S. Silver D. Vinyals O. Senior A.W. Kavukcuoglu K. Kohli P. Hassabis D. Highly accurate protein structure prediction with AlphaFold. Nature 2021 596 7873 583 589 10.1038/s41586‑021‑03819‑2 34265844
    [Google Scholar]
  33. Abramson J. Adler J. Dunger J. Evans R. Green T. Pritzel A. Ronneberger O. Willmore L. Ballard A.J. Bambrick J. Bodenstein S.W. Evans D.A. Hung C.C. O’Neill M. Reiman D. Tunyasuvunakool K. Wu Z. Žemgulytė A. Arvaniti E. Beattie C. Bertolli O. Bridgland A. Cherepanov A. Congreve M. Cowen-Rivers A.I. Cowie A. Figurnov M. Fuchs F.B. Gladman H. Jain R. Khan Y.A. Low C.M.R. Perlin K. Potapenko A. Savy P. Singh S. Stecula A. Thillaisundaram A. Tong C. Yakneen S. Zhong E.D. Zielinski M. Žídek A. Bapst V. Kohli P. Jaderberg M. Hassabis D. Jumper J.M. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 2024 630 8016 493 500 10.1038/s41586‑024‑07487‑w 38718835
    [Google Scholar]
  34. Adams P.D. Advances, interactions, and future developments in the CNS, phenix, and rosetta structural biology software systems. Annu. Rev. Biophys. 2013 42 265 287 10.1146/annurev‑biophys‑083012‑130253
    [Google Scholar]
  35. Krishna R. Generalized biomolecular modeling and design with RoseTTAFold all-atom. Science 2024 384 6693 eadl2528 10.1126/science.adl2528
    [Google Scholar]
  36. Gainza P. OSPREY: Protein design with ensembles, flexibility, and provable algorithms. Methods in Protein Design. Keating A.E. 2013 87 107 10.1016/B978‑0‑12‑394292‑0.00005‑9
    [Google Scholar]
  37. Wood C.W. Heal J.W. Thomson A.R. Bartlett G.J. Ibarra A.Á. Brady R.L. Sessions R.B. Woolfson D.N. ISAMBARD: An open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics 2017 33 19 3043 3050 10.1093/bioinformatics/btx352 28582565
    [Google Scholar]
  38. Winnifrith A. Outeiral C. Hie B.L. Generative artificial intelligence for de novo protein design. Curr. Opin. Struct. Biol. 2024 86 102794 10.1016/j.sbi.2024.102794 38663170
    [Google Scholar]
  39. Chungyoun M.F. Gray J.J. AI models for protein design are driving antibody engineering. Curr. Opin. Biomed. Eng. 2023 28 100473 10.1016/j.cobme.2023.100473 37484815
    [Google Scholar]
  40. Vázquez Torres S. Leung P.J.Y. Venkatesh P. Lutz I.D. Hink F. Huynh H.H. Becker J. Yeh A.H.W. Juergens D. Bennett N.R. Hoofnagle A.N. Huang E. MacCoss M.J. Expòsit M. Lee G.R. Bera A.K. Kang A. De La Cruz J. Levine P.M. Li X. Lamb M. Gerben S.R. Murray A. Heine P. Korkmaz E.N. Nivala J. Stewart L. Watson J.L. Rogers J.M. Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature 2024 626 7998 435 442 10.1038/s41586‑023‑06953‑1 38109936
    [Google Scholar]
  41. Khakzad H. Igashov I. Schneuing A. Goverde C. Bronstein M. Correia B. A new age in protein design empowered by deep learning. Cell Syst. 2023 14 11 925 939 10.1016/j.cels.2023.10.006 37972559
    [Google Scholar]
  42. Tan P. Chen X. Zhang H. Wei Q. Luo K. Artificial intelligence aids in development of nanomedicines for cancer management. Semin. Cancer Biol. 2023 89 61 75 10.1016/j.semcancer.2023.01.005 36682438
    [Google Scholar]
  43. Marques L. Costa B. Pereira M. Silva A. Santos J. Saldanha L. Silva I. Magalhães P. Schmidt S. Vale N. Advancing precision medicine: A review of innovative in silico approaches for drug development, clinical pharmacology and personalized healthcare. Pharmaceutics 2024 16 3 332 10.3390/pharmaceutics16030332 38543226
    [Google Scholar]
  44. Lee C. Su B.H. Tseng Y.J. Comparative studies of AlphaFold, RoseTTAFold and Modeller: A case study involving the use of G-protein-coupled receptors. Brief. Bioinform. 2022 23 5 bbac308 10.1093/bib/bbac308 35945035
    [Google Scholar]
  45. da Silva G.M. High-throughput prediction of protein conformational distributions with subsampled AlphaFold2. Nat. Commun. 2024 15 1
    [Google Scholar]
  46. Hegedűs T. Geisler M. Lukács G.L. Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell. Mol. Life Sci. 2022 79 1 73 10.1007/s00018‑021‑04112‑1 35034173
    [Google Scholar]
  47. Buyanov I. Popov P. Characterizing conformational states in GPCR structures using machine learning. Sci. Rep. 2024 14 1 1098 10.1038/s41598‑023‑47698‑1 38212515
    [Google Scholar]
  48. Fraser J.S. Murcko M.A. Structure is beauty, but not always truth. Cell 2024 187 3 517 520 10.1016/j.cell.2024.01.003 38306978
    [Google Scholar]
  49. Wei G. Xi W. Nussinov R. Ma B. Protein ensembles: How does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell. Chem. Rev. 2016 116 11 6516 6551 10.1021/acs.chemrev.5b00562 26807783
    [Google Scholar]
  50. Yang Z. Accounting receptor’s dynamic behavior into structure-based design. Comb. Chem. High Throughput Screen. 2021 24 7 1005 1006 10.2174/138620732407210504100334 34259135
    [Google Scholar]
  51. Baek M. Baker D. Deep learning and protein structure modeling. Nat. Methods 2022 19 1 13 14 10.1038/s41592‑021‑01360‑8 35017724
    [Google Scholar]
  52. Yang Z. Ye Q. Zhao Y. Li X. Zhao Y. Fu X. Zhang S. Zhang L. Accounting conformational dynamics into structural modeling reflected by Cryo-EM with deep learning. Comb. Chem. High Throughput Screen. 2023 26 3 449 458 10.2174/1386207325666220514143909 35570549
    [Google Scholar]
  53. Polizzi N.F. DeGrado W.F. A defined structural unit enables de novo design of small-molecule–binding proteins. Science 2020 369 6508 1227 1233 10.1126/science.abb8330 32883865
    [Google Scholar]
  54. Gainza P. Wehrle S. Van Hall-Beauvais A. Marchand A. Scheck A. Harteveld Z. Buckley S. Ni D. Tan S. Sverrisson F. Goverde C. Turelli P. Raclot C. Teslenko A. Pacesa M. Rosset S. Georgeon S. Marsden J. Petruzzella A. Liu K. Xu Z. Chai Y. Han P. Gao G.F. Oricchio E. Fierz B. Trono D. Stahlberg H. Bronstein M. Correia B.E. De novo design of protein interactions with learned surface fingerprints. Nature 2023 617 7959 176 184 10.1038/s41586‑023‑05993‑x 37100904
    [Google Scholar]
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