Skip to content
2000
Volume 5, Issue 1
  • ISSN: 2950-4023
  • E-ISSN: 2950-4031

Abstract

Introduction

Recent developments in artificial intelligence-driven tools are drastically changing drug research and developmental scenarios, especially in the area of structural protein predictions. This review aims to examine the impact that recent advancements (AI) in protein structure prediction have had on drug developmental processes, with an initial emphasis on studies related to cancer and other diseases.

Objective

The main objective of the article is how these technical advancements, such as AlphaFold2, as an example, are transforming our knowledge of the functional and structural changes in proteins that underlie cancer and enhance our defence against them.

Methods

The structured literature review, with its dependable and reproducible research process, allowed the authors to acquire 95 peer-reviewed publications from indexing databases, such as Scopus, ScienceDirect, Web of Science (WoS), PubMed, and EMBASE by utilizing PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) regulations. Numerous keyword combinations regarding AI tools and their role in structural biology were used to create the query syntax.

Results

Requests for search codes on five online archives served as the foundation for the review article selection procedure. The search request yielded 1,643 articles; however, only 1,553 articles remained when duplicates were removed, and 1,345 papers were excluded by the screening process. After screening 208 papers, we decided to focus our review study on 95 reputable publications.

Conclusion

AI applications in computational biology have reached a significant milestone with AF2, which initiated the process and has demonstrated exceptional performances in forecasting protein structures. By accurately predicting protein structures, these AI techniques can expedite the development process of new cancer treatments and medicines, and more efficiently detect and verify new targets for drugs, especially for those having no extensive structural knowledge.

Loading

Article metrics loading...

/content/journals/ctc/10.2174/0129504023345000250113104248
2025-01-01
2025-08-18
Loading full text...

Full text loading...

References

  1. JumperJ. EvansR. PritzelA. GreenT. FigurnovM. RonnebergerO. TunyasuvunakoolK. BatesR. ŽídekA. PotapenkoA. BridglandA. MeyerC. KohlS.A.A. BallardA.J. CowieA. Romera-ParedesB. NikolovS. JainR. AdlerJ. BackT. PetersenS. ReimanD. ClancyE. ZielinskiM. SteineggerM. PacholskaM. BerghammerT. BodensteinS. SilverD. VinyalsO. SeniorA.W. KavukcuogluK. KohliP. HassabisD. Highly accurate protein structure prediction with AlphaFold.Nature2021596787358358910.1038/s41586‑021‑03819‑234265844
    [Google Scholar]
  2. TakkoucheA. QiuX. SedovaM. JaroszewskiL. GodzikA. Unusual structural and functional features of TpLRR/BspA-like LRR proteins.J. Struct. Biol.2023215310801110.1016/j.jsb.2023.10801137562586
    [Google Scholar]
  3. PakM.A. MarkhievaK.A. NovikovaM.S. PetrovD.S. VorobyevI.S. MaksimovaE.S. KondrashovF.A. IvankovD.N. Using AlphaFold to predict the impact of single mutations on protein stability and function.PLoS One2023183e028268910.1371/journal.pone.028268936928239
    [Google Scholar]
  4. NiaziS.K. MariamZ. ParachaR.Z. Limitations of protein structure prediction algorithms in therapeutic protein development.Bio Med Informatics2024419811210.3390/biomedinformatics4010007
    [Google Scholar]
  5. YamaguchiS. KanekoM. NarukawaM. Approval success rates of drug candidates based on target, action, modality, application, and their combinations.Clin. Transl. Sci.20211431113112210.1111/cts.1298033831276
    [Google Scholar]
  6. SchlanderM. Hernandez-VillafuerteK. ChengC.Y. Mestre-FerrandizJ. BaumannM. How much does it cost to research and develop a new drug? A systematic review and assessment.Pharmaco Economics202139111243126910.1007/s40273‑021‑01065‑y34368939
    [Google Scholar]
  7. MansooriB. MohammadiA. DavudianS. ShirjangS. BaradaranB. The different mechanisms of cancer drug resistance: A brief review.Adv. Pharm. Bull.20177333934810.15171/apb.2017.04129071215
    [Google Scholar]
  8. BaekM. DiMaioF. AnishchenkoI. DauparasJ. OvchinnikovS. LeeG.R. WangJ. CongQ. KinchL.N. SchaefferR.D. MillánC. ParkH. AdamsC. GlassmanC.R. DeGiovanniA. PereiraJ.H. RodriguesA.V. van DijkA.A. EbrechtA.C. OppermanD.J. SagmeisterT. BuhlhellerC. Pavkov-KellerT. RathinaswamyM.K. DalwadiU. YipC.K. BurkeJ.E. GarciaK.C. GrishinN.V. AdamsP.D. ReadR.J. BakerD. Accurate prediction of protein structures and interactions using a three-track neural network.Science2021373655787187610.1126/science.abj875434282049
    [Google Scholar]
  9. LinZ. AkinH. RaoR. HieB. ZhuZ. LuW. SmetaninN. VerkuilR. KabeliO. ShmueliY. dos Santos CostaA. Fazel-ZarandiM. SercuT. CandidoS. RivesA. Evolutionary-scale prediction of atomic-level protein structure with a language model.Science202337966371123113010.1126/science.ade257436927031
    [Google Scholar]
  10. AhdritzG. BouattaN. FloristeanC. KadyanS. XiaQ. GereckeW. O’DonnellT.J. BerenbergD. FiskI. ZanichelliN. ZhangB. NowaczynskiA. WangB. Stepniewska-DziubinskaM.M. ZhangS. OjewoleA. GuneyM.E. BidermanS. WatkinsA.M. RaS. LorenzoP.R. NivonL. WeitznerB. BanY.E.A. ChenS. ZhangM. LiC. SongS.L. HeY. SorgerP.K. MostaqueE. ZhangZ. BonneauR. AlQuraishiM. OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.Nat. Methods20242181514152410.1038/s41592‑024‑02272‑z38744917
    [Google Scholar]
  11. MadaniA. KrauseB. GreeneE.R. SubramanianS. MohrB.P. HoltonJ.M. OlmosJ.L.Jr XiongC. SunZ.Z. SocherR. FraserJ.S. NaikN. Large language models generate functional protein sequences across diverse families.Nat. Biotechnol.20234181099110610.1038/s41587‑022‑01618‑236702895
    [Google Scholar]
  12. DauparasJ. AnishchenkoI. BennettN. BaiH. RagotteR.J. MillesL.F. WickyB.I.M. CourbetA. de HaasR.J. BethelN. LeungP.J.Y. HuddyT.F. PellockS. TischerD. ChanF. KoepnickB. NguyenH. KangA. SankaranB. BeraA.K. KingN.P. BakerD. Robust deep learning–based protein sequence design using ProteinMPNN.Science20223786615495610.1126/science.add218736108050
    [Google Scholar]
  13. AlamdariS. ThakkarT. BergR.V.D. Nicolo FusiA.X. AminiA.P. YangK.K. Protein generation with evolutionary diffusion: Sequence is all you need.bioRxiv202310.1101/2023.09.11.556673
    [Google Scholar]
  14. WatsonJ.L. JuergensD. BennettN.R. TrippeB.L. YimJ. EisenachH.E. AhernW. BorstA.J. RagotteR.J. MillesL.F. WickyB.I.M. HanikelN. PellockS.J. CourbetA. ShefflerW. WangJ. VenkateshP. SappingtonI. TorresS.V. LaukoA. De BortoliV. MathieuE. OvchinnikovS. BarzilayR. JaakkolaT.S. DiMaioF. BaekM. BakerD. De novo design of protein structure and function with RFdiffusion.Nature202362079761089110010.1038/s41586‑023‑06415‑837433327
    [Google Scholar]
  15. CorsoG. StärkH. JingB. BarzilayR. JaakkolaT. Diffdock: Diffusion steps, twists, and turns for molecular docking.arXiv2022
    [Google Scholar]
  16. SödingJ. BiegertA. LupasA.N. The HHpred interactive server for protein homology detection and structure prediction.Nucleic Acids Res.200533Web ServerSuppl. 2W244W24810.1093/nar/gki40815980461
    [Google Scholar]
  17. ZimmermannL. StephensA. NamS.Z. RauD. KüblerJ. LozajicM. GablerF. SödingJ. LupasA.N. AlvaV. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core.J. Mol. Biol.2018430152237224310.1016/j.jmb.2017.12.00729258817
    [Google Scholar]
  18. MarksD.S. ColwellL.J. SheridanR. HopfT.A. PagnaniA. ZecchinaR. SanderC. Protein 3D structure computed from evolutionary sequence variation.PLoS One2011612e2876610.1371/journal.pone.002876622163331
    [Google Scholar]
  19. WangS. SunS. LiZ. ZhangR. XuJ. Accurate de novo prediction of protein contact map by ultra-deep learning model.PLOS Comput. Biol.2017131e100532410.1371/journal.pcbi.100532428056090
    [Google Scholar]
  20. DuZ. SuH. WangW. YeL. WeiH. PengZ. AnishchenkoI. BakerD. YangJ. The trRosetta server for fast and accurate protein structure prediction.Nat. Protoc.202116125634565110.1038/s41596‑021‑00628‑934759384
    [Google Scholar]
  21. YangJ. ZhangY. Protein structure and function prediction using I-TASSER.201510.1002/0471250953.bi0508s52
    [Google Scholar]
  22. KryshtafovychA. SchwedeT. TopfM. FidelisK. MoultJ. Critical assessment of methods of protein structure prediction (CASP)—Round XIII.Proteins201987121011102010.1002/prot.2582331589781
    [Google Scholar]
  23. LaskowskiR. RullmannJ.A.C. MacArthurM. KapteinR. ThorntonJ. AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR.J. Biomol. NMR19968447748610.1007/BF002281489008363
    [Google Scholar]
  24. MeloF. DevosD. DepiereuxE. FeytmansE. ANOLEA: A www server to assess protein structures.Proc. Int. Conf. Intell. Syst. Mol. Biol.1997511871909322034
    [Google Scholar]
  25. BermanH.M. KleywegtG.J. NakamuraH. MarkleyJ.L. The protein data bank archive as an open data resource.J. Comput. Aided Mol. Des.201428101009101410.1007/s10822‑014‑9770‑y25062767
    [Google Scholar]
  26. VaradiM. AnyangoS. DeshpandeM. NairS. NatassiaC. YordanovaG. YuanD. StroeO. WoodG. LaydonA. ŽídekA. GreenT. TunyasuvunakoolK. PetersenS. JumperJ. ClancyE. GreenR. VoraA. LutfiM. FigurnovM. CowieA. HobbsN. KohliP. KleywegtG. BirneyE. HassabisD. VelankarS. AlphaFold protein structure database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models.Nucleic Acids Res.202250D1D439D44410.1093/nar/gkab106134791371
    [Google Scholar]
  27. VaradiM. BertoniD. MaganaP. ParamvalU. PidruchnaI. RadhakrishnanM. TsenkovM. NairS. MirditaM. YeoJ. KovalevskiyO. TunyasuvunakoolK. LaydonA. ŽídekA. TomlinsonH. HariharanD. AbrahamsonJ. GreenT. JumperJ. BirneyE. SteineggerM. HassabisD. VelankarS. AlphaFold protein structure database in 2024: Providing structure coverage for over 214 million protein sequences.Nucleic Acids Res.202452D1D368D37510.1093/nar/gkad101137933859
    [Google Scholar]
  28. BermanH.M. WestbrookJ. FengZ. GillilandG. BhatT.N. WeissigH. ShindyalovI.N. BourneP.E. The protein data bank.Nucleic Acids Res.200028123524210.1093/nar/28.1.23510592235
    [Google Scholar]
  29. KryshtafovychA. SchwedeT. TopfM. FidelisK. MoultJ. Critical assessment of methods of protein structure prediction (CASP)—Round XIV.Proteins202189121607161710.1002/prot.2623734533838
    [Google Scholar]
  30. BienertS. WaterhouseA. de BeerT.A.P. TaurielloG. StuderG. BordoliL. SchwedeT. The SWISS-MODEL repository: New features and functionality.Nucleic Acids Res.201745D1D313D31910.1093/nar/gkw113227899672
    [Google Scholar]
  31. Keskin KarakoyunH. YükselŞ.K. AmanogluI. NaserikhojastehL. YeşilyurtA. YakıcıerC. TimuçinE. AkyerliC.B. Evaluation of AlphaFold structure-based protein stability prediction on missense variations in cancer.Front. Genet.202314105238310.3389/fgene.2023.105238336896237
    [Google Scholar]
  32. AulakhS.S. BozelliJ.C.Jr EpandR.M. Exploring the alphafold predicted conformational properties of human diacylglycerol kinases.J. Phys. Chem. B2022126377172718310.1021/acs.jpcb.2c0453336041230
    [Google Scholar]
  33. NussinovR. ZhangM. LiuY. JangH. AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug Discov. Today202328610355110.1016/j.drudis.2023.10355136907321
    [Google Scholar]
  34. WengY. PanC. ShenZ. ChenS. XuL. DongX. ChenJ. Identification of potential WSB1 inhibitors by alphafold modeling, virtual screening, and molecular dynamics simulation studies.Evid. Based Complement. Alternat. Med.2022202211110.1155/2022/462939235600960
    [Google Scholar]
  35. ChengJ. NovatiG. PanJ. BycroftC. ŽemgulytėA. ApplebaumT. PritzelA. WongL.H. ZielinskiM. SargeantT. SchneiderR.G. SeniorA.W. JumperJ. HassabisD. KohliP. AvsecŽ. Accurate proteome-wide missense variant effect prediction with AlphaMissense.Science20233816664eadg749210.1126/science.adg749237733863
    [Google Scholar]
  36. BorkakotiN. ThorntonJ.M. AlphaFold2 protein structure prediction: Implications for drug discovery.Curr. Opin. Struct. Biol.20237810252610.1016/j.sbi.2022.10252636621153
    [Google Scholar]
  37. ZhangJ. PeiJ. DurhamJ. BosT. CongQ. Computed cancer interactome explains the effects of somatic mutations in cancers.Protein Sci.20223112e447910.1002/pro.447936261849
    [Google Scholar]
  38. SakamotoK. AsanoS. AgoY. HirokawaT. AlphaFold version 2.0 elucidates the binding mechanism between VIPR2 and KS-133, and reveals an S–S bond (Cys25−Cys192) formation of functional significance for VIPR2.Biochem. Biophys. Res. Commun.2022636Pt 1101610.1016/j.bbrc.2022.10.07136332470
    [Google Scholar]
  39. RenF. DingX. ZhengM. KorzinkinM. CaiX. ZhuW. MantsyzovA. AliperA. AladinskiyV. CaoZ. KongS. LongX. Man LiuB.H. LiuY. NaumovV. ShneydermanA. OzerovI.V. WangJ. PunF.W. PolykovskiyD.A. SunC. LevittM. Aspuru-GuzikA. ZhavoronkovA. AlphaFold accelerates artificial intelligence powered drug discovery: Efficient discovery of a novel CDK20 small molecule inhibitor.Chem. Sci. (Camb.)20231461443145210.1039/D2SC05709C36794205
    [Google Scholar]
  40. RichardsonL. AllenB. BaldiG. BeracocheaM. BileschiM.L. BurdettT. BurginJ. Caballero-PérezJ. CochraneG. ColwellL.J. CurtisT. Escobar-ZepedaA. GurbichT.A. KaleV. KorobeynikovA. RajS. RogersA.B. SakharovaE. SanchezS. WilkinsonD.J. FinnR.D. MGnify: the microbiome sequence data analysis resource in 2023.Nucleic Acids Res.202351D1D753D75910.1093/nar/gkac108036477304
    [Google Scholar]
  41. KrishnaR. WangJ. AhernW. SturmfelsP. VenkateshP. KalvetI. LeeG.R. Morey-BurrowsF.S. AnishchenkoI. HumphreysI.R. McHughR. VafeadosD. LiX. SutherlandG.A. HitchcockA. HunterC.N. KangA. BrackenbroughE. BeraA.K. BaekM. DiMaioF. BakerD. Generalized biomolecular modeling and design with RoseTTAFold All-Atom.Science20243846693eadl252810.1126/science.adl252838452047
    [Google Scholar]
  42. BaekM. AnishchenkoC. Humphreys,I.R. CongQ. BakerB. DiMaioF. Efficient and accurate prediction of protein structure using RoseTTAFold2.bioRxiv202310.1101/2023.05.24.542179
    [Google Scholar]
  43. WangJ. LisanzaS. JuergensD. TischerD. WatsonJ.L. CastroK.M. RagotteR. SaragoviA. MillesL.F. BaekM. AnishchenkoI. YangW. HicksD.R. ExpòsitM. SchlichthaerleT. ChunJ.H. DauparasJ. BennettN. WickyB.I.M. MuenksA. DiMaioF. CorreiaB. OvchinnikovS. BakerD. Scaffolding protein functional sites using deep learning.Science2022377660438739410.1126/science.abn210035862514
    [Google Scholar]
  44. GentileF. YaacoubJ.C. GleaveJ. FernandezM. TonA.T. BanF. SternA. CherkasovA. Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking.Nat. Protoc.202217367269710.1038/s41596‑021‑00659‑235121854
    [Google Scholar]
  45. GuptaR. SrivastavaD. SahuM. TiwariS. AmbastaR.K. KumarP. Artificial intelligence to deep learning: Machine intelligence approach for drug discovery.Mol. Divers.20212531315136010.1007/s11030‑021‑10217‑333844136
    [Google Scholar]
  46. SavageN. Tapping into the drug discovery potential of AI.Nature BioPharma Dealmakers2021B37B3910.1038/d43747‑021‑00045‑7
    [Google Scholar]
  47. AnishchenkoI. PellockS.J. ChidyausikuT.M. RamelotT.A. OvchinnikovS. HaoJ. BafnaK. NornC. KangA. BeraA.K. DiMaioF. CarterL. ChowC.M. MontelioneG.T. BakerD. De novo protein design by deep network hallucination.Nature2021600788954755210.1038/s41586‑021‑04184‑w34853475
    [Google Scholar]
  48. YimJ. TrippeB.L. BortoliW.D. Mathieu,E. DouceA. BarzilayR. Diffusion model with application to protein backbone generation.arXiv2023
    [Google Scholar]
  49. CallawayE. How generative AI is building better antibodies.Nature202361723510.103810.1038/d41586‑023‑01516‑w
    [Google Scholar]
  50. CuiH. WangC. MaanH. PangK. LuoF. DuanN. WangB. scGPT: Toward building a foundation model for single-cell multi-omics using generative AI.Nat. Methods20242181470148010.1038/s41592‑024‑02201‑038409223
    [Google Scholar]
  51. BenegasG. BatraS.S. SongY.S. DNA language models are powerful predictors of genome-wide variant effects.Proc. Natl. Acad. Sci. USA202312044e231121912010.1073/pnas.231121912037883436
    [Google Scholar]
  52. YamadaK. HamadaM. Prediction of RNA–protein interactions using a nucleotide language model.Bioinform. Adv.202221vbac02310.1093/bioadv/vbac02336699410
    [Google Scholar]
  53. ZvyaginM. BraceA. HippeK. DengY. ZhangB. BohorquezC.O. ClydeA. KaleB. Perez-RiveraD. MaH. MannC.M. IrvinM. OzgulbasD.G. VassilievaN. PauloskiJ.G. WardL. Hayot-SassonV. EmaniM. ForemanS. XieZ. LinD. ShuklaM. NieW. RomeroJ. DallagoC. VahdatA. XiaoC. GibbsT. FosterI. DavisJ.J. PapkaM.E. BrettinT. StevensR. AnandkumarA. VishwanathV. RamanathanA. GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.Int. J. High Perform. Comput. Appl.202337668370510.1177/10943420231201154
    [Google Scholar]
  54. KatherJ.N. Ghaffari LalehN. FoerschS. TruhnD. Medical domain knowledge in domain-agnostic generative AI.NPJ Digit. Med.2022519010.1038/s41746‑022‑00634‑535817798
    [Google Scholar]
  55. KhaderF. Müller-FranzesG. Tayebi ArastehS. HanT. HaarburgerC. Schulze-HagenM. SchadP. EngelhardtS. BaeßlerB. FoerschS. StegmaierJ. KuhlC. NebelungS. KatherJ.N. TruhnD. Denoising diffusion probabilistic models for 3D medical image generation.Sci. Rep.2023131730310.1038/s41598‑023‑34341‑237147413
    [Google Scholar]
  56. StokesJ.M. YangK. SwansonK. JinW. Cubillos-RuizA. DonghiaN.M. MacNairC.R. FrenchS. CarfraeL.A. Bloom-AckermannZ. TranV.M. Chiappino-PepeA. BadranA.H. AndrewsI.W. ChoryE.J. ChurchG.M. BrownE.D. JaakkolaT.S. BarzilayR. CollinsJ.J. A deep learning approach to antibiotic discovery.Cell20201804688702.e1310.1016/j.cell.2020.01.02132084340
    [Google Scholar]
  57. BurkiT. A new paradigm for drug development.Lancet Digit. Health202025e226e22710.1016/S2589‑7500(20)30088‑132373787
    [Google Scholar]
  58. Blanco-GonzálezA. CabezónA. Seco-GonzálezA. Conde-TorresD. Antelo-RiveiroP. PiñeiroÁ. Garcia-FandinoR. The role of AI in drug discovery: Challenges, opportunities, and strategies.Pharmaceuticals202316689110.3390/ph1606089137375838
    [Google Scholar]
  59. KhanB. FatimaH. QureshiA. KumarS. HananA. HussainJ. AbdullahS. Drawbacks of artificial intelligence and their potential solutions in the healthcare sector.Biomed Mater Devices20231810.1007/s44174‑023‑00063‑2
    [Google Scholar]
  60. FernándezA. Artificial intelligence teaches drugs to target proteins by tackling the induced folding problem.Mol. Pharm.20201782761276710.1021/acs.molpharmaceut.0c0047032551659
    [Google Scholar]
  61. GershensonA. GosaviS. FaccioliP. WintrodeP.L. Successes and challenges in simulating the folding of large proteins.J. Biol. Chem.20202951153310.1074/jbc.REV119.00679431712314
    [Google Scholar]
/content/journals/ctc/10.2174/0129504023345000250113104248
Loading
/content/journals/ctc/10.2174/0129504023345000250113104248
Loading

Data & Media loading...

Supplements

PRISMA checklist is available as supplementary material on the publisher’s website along with the published article.

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test