Skip to main content

Deep Learning in Structure-Based Drug Design

  • Protocol
  • First Online:
Artificial Intelligence in Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2390))

Abstract

Computational methods play an increasingly important role in drug discovery. Structure-based drug design (SBDD), in particular, includes techniques that take into account the structure of the macromolecular target to predict compounds that are likely to establish optimal interactions with the binding site. The current interest in machine learning algorithms based on deep neural networks encouraged the application of deep learning to SBDD related problems. This chapter covers selected works in this active area of research.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Anderson AC (2003) The process of structure-based drug design. Chem Biol 10:787–797. https://doi.org/10.1016/j.chembiol.2003.09.002

    Article  CAS  PubMed  Google Scholar 

  2. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3:935–949. https://doi.org/10.1038/nrd1549

    Article  CAS  PubMed  Google Scholar 

  3. De Vivo M, Masetti M, Bottegoni G, Cavalli A (2016) Role of molecular dynamics and related methods in drug discovery. J Med Chem 59:4035–4061. https://doi.org/10.1021/acs.jmedchem.5b01684

    Article  CAS  PubMed  Google Scholar 

  4. Raha K, Peters MB, Wang B, Yu N, Wollacott AM, Westerhoff LM, Merz KM (2007) The role of quantum mechanics in structure-based drug design. Drug Discov Today 12:725–731. https://doi.org/10.1016/j.drudis.2007.07.006

    Article  CAS  PubMed  Google Scholar 

  5. LeCun Y, Bengio Y, Hinton G (2015) Deep learning. Nature 521:436–444. https://doi.org/10.1038/nature14539

    Article  CAS  PubMed  Google Scholar 

  6. Lo Y-C, Rensi SE, Torng W, Altman RB (2018) Machine learning in chemoinformatics and drug discovery. Drug Discov Today 23:1538–1546. https://doi.org/10.1016/j.drudis.2018.05.010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Elton DC, Boukouvalas Z, Fuge MD, Chung PW (2019) Deep learning for molecular design—a review of the state of the art. Mol Syst Des Eng 4:828–849. https://doi.org/10.1039/C9ME00039A

    Article  CAS  Google Scholar 

  8. Betzi S, Suhre K, Chétrit B, Guerlesquin F, Morelli X (2006) GFscore: a general nonlinear consensus scoring function for high-throughput docking. J Chem Inf Model 46:1704–1712. https://doi.org/10.1021/ci0600758

    Article  CAS  PubMed  Google Scholar 

  9. Artemenko N (2008) Distance dependent scoring function for describing protein−ligand intermolecular interactions. J Chem Inf Model 48:569–574. https://doi.org/10.1021/ci700224e

    Article  CAS  PubMed  Google Scholar 

  10. Adcock SA, McCammon JA (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106:1589–1615. https://doi.org/10.1021/cr040426m

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kim JT, Hamilton AD, Bailey CM, Domoal RA, Wang L, Anderson KS, Jorgensen WL (2006) FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Am Chem Soc 128:15372–15373. https://doi.org/10.1021/ja066472g

    Article  CAS  PubMed  Google Scholar 

  12. Ballester PJ, Mitchell JBO (2010) A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking. Bioinformatics 26:1169–1175. https://doi.org/10.1093/bioinformatics/btq112

    Article  CAS  PubMed  Google Scholar 

  13. Durrant JD, McCammon JA (2010) NNScore: a neural-network-based scoring function for the characterization of protein−ligand complexes. J Chem Inf Model 50:1865–1871. https://doi.org/10.1021/ci100244v

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Rawat W, Wang Z (2017) Deep convolutional neural networks for image classification: a comprehensive review. Neural Comput 29:2352–2449. https://doi.org/10.1162/neco_a_00990

    Article  PubMed  Google Scholar 

  15. LeCun Y, Boser BE, Denker JS, Henderson D, Howard RE, Hubbard WE, Jackel LD (1990) Handwritten digit recognition with a back-propagation network. Morgan Kaufmann, Burlington

    Google Scholar 

  16. LeCun Y, Boser B, Denker JS, Henderson D, Howard RE, Hubbard W, Jackel LD (1989) Backpropagation applied to handwritten zip code recognition. Neural Comput 1:541–551. https://doi.org/10.1162/neco.1989.1.4.541

    Article  Google Scholar 

  17. Krizhevsky A, Sutskever I, Hinton GE (2012) ImageNet classification with deep convolutional neural networks. Adv Neural Inf Process Syst 25:1097–1105

    Google Scholar 

  18. Russakovsky O, Deng J, Su H, Krause J, Satheesh S, Ma S, Huang Z, Karpathy A, Khosla A, Bernstein M, Berg AC, Fei-Fei L (2015) ImageNet large scale visual recognition challenge. Int J Comput Vis 115:211–252. https://doi.org/10.1007/s11263-015-0816-y

    Article  Google Scholar 

  19. Wallach I, Dzamba M, Heifets A (2015) AtomNet: a deep convolutional neural network for bioactivity prediction in structure-based drug discovery. ArXiv1510.02855

    Google Scholar 

  20. Da C, Kireev D (2014) Structural protein–ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study. J Chem Inf Model 54:2555–2561. https://doi.org/10.1021/ci500319f

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Deng Z, Chuaqui C, Singh J (2004) Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein−ligand binding interactions. J Med Chem 47:337–344. https://doi.org/10.1021/jm030331x

    Article  CAS  PubMed  Google Scholar 

  22. Pérez-Nueno VI, Rabal O, Borrell JI, Teixidó J (2009) APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening. J Chem Inf Model 49:1245–1260. https://doi.org/10.1021/ci900043r

    Article  CAS  PubMed  Google Scholar 

  23. Nair V, Hinton GE (2010) Rectified linear units improve restricted Boltzmann machines. In: Proceedings of the 27th international conference on international conference on machine learning. Omnipress, Madison, WI, USA, pp 807–814

    Google Scholar 

  24. Koes DR, Baumgartner MP, Camacho CJ (2013) Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. J Chem Inf Model 53:1893–1904. https://doi.org/10.1021/ci300604z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK (2012) Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 55:6582–6594. https://doi.org/10.1021/jm300687e

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100–D1107. https://doi.org/10.1093/nar/gkr777

    Article  CAS  PubMed  Google Scholar 

  27. Ragoza M, Hochuli J, Idrobo E, Sunseri J, Koes DR (2017) Protein–ligand scoring with convolutional neural networks. J Chem Inf Model 57:942–957. https://doi.org/10.1021/acs.jcim.6b00740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Dunbar JB, Smith RD, Yang C-Y, Ung PM-U, Lexa KW, Khazanov NA, Stuckey JA, Wang S, Carlson HA (2011) CSAR benchmark exercise of 2010: selection of the protein–ligand complexes. J Chem Inf Model 51:2036–2046. https://doi.org/10.1021/ci200082t

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang R, Fang X, Lu Y, Wang S (2004) The PDBbind database: collection of binding affinities for protein−ligand complexes with known three-dimensional structures. J Med Chem 47:2977–2980. https://doi.org/10.1021/jm030580l

    Article  CAS  PubMed  Google Scholar 

  30. Riniker S, Landrum GA (2013) Open-source platform to benchmark fingerprints for ligand-based virtual screening. J Cheminformatics 5:26. https://doi.org/10.1186/1758-2946-5-26

    Article  CAS  Google Scholar 

  31. Gomes J, Ramsundar B, Feinberg EN, Pande VS (2017) Atomic convolutional networks for predicting protein-ligand binding affinity. ArXiv1703.10603

    Google Scholar 

  32. Behler J, Parrinello M (2007) Generalized neural-network representation of high-dimensional potential-energy surfaces. Phys Rev Lett 98:146401. https://doi.org/10.1103/PhysRevLett.98.146401

    Article  CAS  PubMed  Google Scholar 

  33. Behler J (2011) Atom-centered symmetry functions for constructing high-dimensional neural network potentials. J Chem Phys 134:074106. https://doi.org/10.1063/1.3553717

    Article  CAS  PubMed  Google Scholar 

  34. Hassan-Harrirou H, Zhang C, Lemmin T (2020) RosENet: improving binding affinity prediction by leveraging molecular mechanics energies with an ensemble of 3D convolutional neural networks. J Chem Inf Model 60:2791–2802. https://doi.org/10.1021/acs.jcim.0c00075

    Article  CAS  PubMed  Google Scholar 

  35. Alford RF, Leaver-Fay A, Jeliazkov JR, O’Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ (2017) The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput 13:3031–3048. https://doi.org/10.1021/acs.jctc.7b00125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461. https://doi.org/10.1002/jcc.21334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. He K, Zhang X, Ren S, Sun J (2015) Deep residual learning for image recognition. ArXiv1512.03385

    Google Scholar 

  38. Cang Z, Wei G-W (2017) TopologyNet: topology based deep convolutional and multi-task neural networks for biomolecular property predictions. PLoS Comput Biol 13:e1005690. https://doi.org/10.1371/journal.pcbi.1005690

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Jiménez J, Škalič M, Martínez-Rosell G, De Fabritiis G (2018) KDEEP: protein–ligand absolute binding affinity prediction via 3D-convolutional neural networks. J Chem Inf Model 58:287–296. https://doi.org/10.1021/acs.jcim.7b00650

    Article  CAS  PubMed  Google Scholar 

  40. Zheng L, Fan J, Mu Y (2019) OnionNet: a multiple-layer intermolecular-contact-based convolutional neural network for protein–ligand binding affinity prediction. ACS Omega 4:15956–15965. https://doi.org/10.1021/acsomega.9b01997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Stepniewska-Dziubinska MM, Zielenkiewicz P, Siedlecki P (2018) Development and evaluation of a deep learning model for protein–ligand binding affinity prediction. Bioinformatics 34:3666–3674. https://doi.org/10.1093/bioinformatics/bty374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Durrant JD, McCammon JA (2011) NNScore 2.0: a neural-network receptor–ligand scoring function. J Chem Inf Model 51:2897–2903. https://doi.org/10.1021/ci2003889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Durrant JD, McCammon JA (2011) BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model 29:888–893. https://doi.org/10.1016/j.jmgm.2011.01.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Hassan M, Mogollon DC, Fuentes O, Sirimulla S (2018) DLSCORE: a deep learning model for predicting protein-ligand binding affinities. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.6159143.v1

  45. Meli R, Anighoro A, Bodkin M, Morris G, Biggin P (2020) Learning protein-ligand binding affinity with atomic environment vectors. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.13469625.v1

  46. Smith JS, Isayev O, Roitberg AE (2017) ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost. Chem Sci 8:3192–3203. https://doi.org/10.1039/C6SC05720A

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Feinberg EN, Sur D, Wu Z, Husic BE, Mai H, Li Y, Sun S, Yang J, Ramsundar B, Pande VS (2018) PotentialNet for molecular property prediction. ACS Cent Sci 4:1520–1530. https://doi.org/10.1021/acscentsci.8b00507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Lim J, Ryu S, Park K, Choe YJ, Ham J, Kim WY (2019) Predicting drug–target interaction using a novel graph neural network with 3D structure-embedded graph representation. J Chem Inf Model 59:3981–3988. https://doi.org/10.1021/acs.jcim.9b00387

    Article  CAS  PubMed  Google Scholar 

  49. Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O’Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ (2019) Ultra-large library docking for discovering new chemotypes. Nature 566:224–229. https://doi.org/10.1038/s41586-019-0917-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Gorgulla C, Boeszoermenyi A, Wang Z-F, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H (2020) An open-source drug discovery platform enables ultra-large virtual screens. Nature 580:663–668. https://doi.org/10.1038/s41586-020-2117-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Gentile F, Agrawal V, Hsing M, Ton A-T, Ban F, Norinder U, Gleave ME, Cherkasov A (2020) Deep docking: a deep learning platform for augmentation of structure based drug discovery. ACS Cent Sci 6:939–949. https://doi.org/10.1021/acscentsci.0c00229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Jastrzębski S, Szymczak M, Pocha A, Mordalski S, Tabor J, Bojarski AJ, Podlewska S (2020) Emulating docking results using a deep neural network: a new perspective for virtual screening. J Chem Inf Model 60:4246–4262. https://doi.org/10.1021/acs.jcim.9b01202

    Article  CAS  PubMed  Google Scholar 

  53. Chupakhin V, Marcou G, Baskin I, Varnek A, Rognan D (2013) Predicting ligand binding modes from neural networks trained on protein–ligand interaction fingerprints. J Chem Inf Model 53:763–772. https://doi.org/10.1021/ci300200r

    Article  CAS  PubMed  Google Scholar 

  54. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242. https://doi.org/10.1093/nar/28.1.235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Chen L, Cruz A, Ramsey S, Dickson CJ, Duca JS, Hornak V, Koes DR, Kurtzman T (2019) Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. PLoS One 14:e0220113. https://doi.org/10.1371/journal.pone.0220113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Scantlebury J, Brown N, Von Delft F, Deane CM (2020) Data set augmentation allows deep learning-based virtual screening to better generalize to unseen target classes and highlight important binding interactions. J Chem Inf Model 60:3722–3730. https://doi.org/10.1021/acs.jcim.0c00263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Tran-Nguyen V-K, Rognan D (2020) Benchmarking data sets from PubChem BioAssay data: current scenario and room for improvement. Int J Mol Sci 21:4380. https://doi.org/10.3390/ijms21124380

    Article  CAS  PubMed Central  Google Scholar 

  58. Mansimov E, Mahmood O, Kang S, Cho K (2019) Molecular geometry prediction using a deep generative graph neural network. Sci Rep 9:20381. https://doi.org/10.1038/s41598-019-56773-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Žídek A, Nelson AWR, Bridgland A, Penedones H, Petersen S, Simonyan K, Crossan S, Kohli P, Jones DT, Silver D, Kavukcuoglu K, Hassabis D (2020) Improved protein structure prediction using potentials from deep learning. Nature 577:706–710. https://doi.org/10.1038/s41586-019-1923-7

    Article  CAS  PubMed  Google Scholar 

  60. Jiménez J, Doerr S, Martínez-Rosell G, Rose AS, De Fabritiis G (2017) DeepSite: protein-binding site predictor using 3D-convolutional neural networks. Bioinformatics 33:3036–3042. https://doi.org/10.1093/bioinformatics/btx350

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Anighoro, A. (2022). Deep Learning in Structure-Based Drug Design . In: Heifetz, A. (eds) Artificial Intelligence in Drug Design. Methods in Molecular Biology, vol 2390. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1787-8_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1787-8_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1786-1

  • Online ISBN: 978-1-0716-1787-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics