Abstract
Background: The artificial intelligence (AI)-assisted design of drug candidates with
novel structures and desired properties has received significant attention in the recent past, so related
areas of forward prediction that aim to discover chemical matters worth synthesizing and further
experimental investigation.
Objectives: The purpose behind developing AI-driven models is to explore the broader chemical
space and suggest new drug candidate scaffolds with promising therapeutic value. Moreover, it is
anticipated that such AI-based models may not only significantly reduce the cost and time but also
decrease the attrition rate of drug candidates that fail to reach the desirable endpoints at the final
stages of drug development. In an attempt to develop AI-based models for de novo drug design,
numerous methods have been proposed by various study groups by applying machine learning and
deep learning algorithms to chemical datasets. However, there are many challenges in obtaining accurate
predictions, and real breakthroughs in de novo drug design are still scarce.
Methods: In this review, we explore the recent trends in developing AI-based models for de novo
drug design to assess the current status, challenges, and opportunities in the field.
Conclusion: The consistently improved AI algorithms and the abundance of curated training chemical
data indicate that AI-based de novo drug design should perform better than the current models.
Improvements in the performance are warranted to obtain better outcomes in the form of potential
drug candidates, which can perform well in in vivo conditions, especially in the case of more complex
diseases.
Keywords:
Artificial intelligence, De novo drug design, Deep learning, Drug, Ligand, Machine learning.
Graphical Abstract
[42]
Jaques, N.; Gu, S.; Bahdanau, D.; Hernández-Lobato, J.M.; Turner, R.E.; Eck, D. Sequence tutor: conservative fine-tuning of sequence generation models with KL-control. Proc. Int. Conf. Machine Learn., 2017, 2017, 1645-1654.
[48]
Subramanian, A.; Narayan, R.; Corsello, S.M.; Peck, D.D.; Natoli, T.E.; Lu, X.; Gould, J.; Davis, J.F.; Tubelli, A.A.; Asiedu, J.K.; Lahr, D.L.; Hirschman, J.E.; Liu, Z.; Donahue, M.; Julian, B.; Khan, M.; Wadden, D.; Smith, I.C.; Lam, D.; Liberzon, A.; Toder, C.; Bagul, M.; Orzechowski, M.; Enache, O.M.; Piccioni, F.; Johnson, S.A.; Lyons, N.J.; Berger, A.H.; Shamji, A.F.; Brooks, A.N.; Vrcic, A.; Flynn, C.; Rosains, J.; Takeda, D.Y.; Hu, R.; Davison, D.; Lamb, J.; Ardlie, K.; Hogstrom, L.; Greenside, P.; Gray, N.S.; Clemons, P.A.; Silver, S.; Wu, X.; Zhao, W.N.; Read-Button, W.; Wu, X.; Haggarty, S.J.; Ronco, L.V.; Boehm, J.S.; Schreiber, S.L.; Doench, J.G.; Bittker, J.A.; Root, D.E.; Wong, B.; Golub, T.R. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles.
Cell, 2017,
171(6), 1437-1452.e17.
[
http://dx.doi.org/10.1016/j.cell.2017.10.049] [PMID:
29195078]
[55]
Kusner, M.J.; Paige, B.; Hernandez-Lobato, J.M. Grammar variational autoencoder. Proc. Int. Conf. Machine Learn., 2017, 2017, 1945-1954.
[58]
De Cao, N.; Kipf, T. MolGAN: An implicit generative model for small molecular graphs. arXiv, 2018, 2018, 1805.11973.
[59]
Jin, W.; Barzilay, R.; Jaakkola, T. Junction tree variational autoencoder for molecular graph generation. Int. Conf. Machine Learn., 2018, 2018, 2328-2337.
[62]
Liu, Q.; Allamanis, M.; Brockschmidt, M.; Gaunt, A. Constrained graph variational autoencoders for molecule design. Adv. Neural Inf. Process. Syst., 2018, 2018, 78067815.
[63]
You, J.; Liu, B.; Ying, R.; Pande, V.; Leskovec, J. Graph convolutional policy network for goal-directed molecular graph generation; Adv. Neural Inform. Proces. Sys, 2018, pp. 6410-6421.
[64]
You, J.; Ying, R.; Ren, X.; Hamilton, W.; Leskovec, J. Graphrnn: Generating realistic graphs with deep auto-regressive models. Int. Conf. Machine Learn., 2018, 2018, 5694-5703.