Generative AI for designing and validating easily synthesizable and structurally novel antibiotics – Nature.com
Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629655 (2022).
Article CAS Google Scholar
Rice, L. B. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: No ESKAPE. J. Infect. Dis. 197, 10791081 (2008).
Article PubMed Google Scholar
Ma, Y. et al. Considerations and caveats in combating ESKAPE pathogens against nosocomial infections. Adv. Sci. 7, 1901872 (2020).
Article CAS Google Scholar
Tacconelli, E. et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318327 (2018).
Article PubMed Google Scholar
Lee, C. R. et al. Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options. Front. Cell. Infect. Microbiol. 7, 55 (2017).
Article PubMed PubMed Central Google Scholar
Carracedo-Reboredo, P. et al. A review on machine learning approaches and trends in drug discovery. Comput. Struct. Biotechnol. J. 19, 45384558 (2021).
Article CAS PubMed PubMed Central Google Scholar
Gaudelet, T. et al. Utilizing graph machine learning within drug discovery and development. Brief. Bioinform. 22, bbab159 (2021).
Article PubMed PubMed Central Google Scholar
Stokes, J. M. et al. A deep learning approach to antibiotic discovery. Cell 180, 688702.e13 (2020).
Article CAS PubMed PubMed Central Google Scholar
Rahman, A. S. M. Z. et al. A machine learning model trained on a high-throughput antibacterial screen increases the hit rate of drug discovery. PLoS Comput. Biol. 18, e1010613 (2022).
Article CAS PubMed PubMed Central Google Scholar
Zeng, X. et al. Deep generative molecular design reshapes drug discovery. Cell Rep. Med. 3, 100794 (2022).
Article CAS PubMed PubMed Central Google Scholar
Bilodeau, C., Jin, W., Jaakkola, T., Barzilay, R. & Jensen, K. F. Generative models for molecular discovery: recent advances and challenges. WIREs Comput. Mol. Sci. 12, e1608 (2022).
Article Google Scholar
Bian, Y. & Xie, X. Q. Generative chemistry: drug discovery with deep learning generative models. J. Mol. Model. 27, 71 (2021).
Article CAS PubMed Google Scholar
Liu, G. & Stokes, J. M. A brief guide to machine learning for antibiotic discovery. Curr. Opin. Microbiol. 69, 102190 (2022).
Article CAS PubMed Google Scholar
Gao, W. & Coley, C. W. The synthesizability of molecules proposed by generative models. J. Chem. Inf. Model. 60, 57145723 (2020).
Article CAS PubMed Google Scholar
Bradshaw, J., Paige, B., Kusner, M. J., Segler, M. H. S. & Hernndez-Lobato, J. M. A model to search for synthesizable molecules. In Proc. 33rd International Conference on Neural Information Processing Systems (eds Wallach, H. M., Larochelle, H., Beygelzimer, A., d'Alch-Buc, F. & Fox, E. B.) 79377949 (Curran Associates Inc., 2019).
Bradshaw, J., Paige, B., Kusner, M. J., Segler, M. H. S. & Hernndez-Lobato, J. M. Barking up the right tree: an approach to search over molecule synthesis DAGs. In Proc. 34th International Conference on Neural Information Processing Systems (eds Larochelle, H., Ranzato, M., Hadsell, R., Balcan, M. F. & Lin, H.) 68526866 (Curran Associates Inc., 2020).
Gottipati, S. K. et al. Learning to navigate the synthetically accessible chemical space using reinforcement learning. In Proc. 37th International Conference on Machine Learning (eds Daum III, H. & Singh, A.) 36683679 (PMLR, 2020).
Gao, W., Mercado, R. & Coley, C. W. Amortized tree generation for bottom-up synthesis planning and synthesizable molecular design. In Proc. 10th International Conference on Learning Representations (2022); https://openreview.net/forum?id=FRxhHdnxt1
Pedawi, A., Gniewek, P., Chang, C., Anderson, B. M. & Bedem, H. van den. An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries. In Proc. 36th International Conference on Neural Information Processing Systems (eds Oh, A. H., Agarwal. A., Belgrave, D. & Cho, K.) (2022); https://openreview.net/forum?id=VBbxHvbJd94
Kocsis, L. & Szepesvri, C. Bandit based Monte-Carlo planning. In Proc. European Conference on Machine Learning, ECML 2006 Vol. 4212 (eds Furnkranz, J. et al.) 282293 (Springer, 2006).
Coulom, R. Efficient selectivity and backup operators in Monte-Carlo tree search. In Proc. International Conference on Computers and Games, CG 2006 Vol. 4630 (eds van den Herik, H. J. et al.) 7283 (Springer, 2007).
Grygorenko, O. O. et al. Generating multibillion chemical space of readily accessible screening compounds. iScience 23, 101681 (2020).
Article CAS PubMed PubMed Central Google Scholar
Stokes, J. M., Davis, J. H., Mangat, C. S., Williamson, J. R. & Brown, E. D. Discovery of a small molecule that inhibits bacterial ribosome biogenesis. eLife 3, e03574 (2014).
Article PubMed PubMed Central Google Scholar
van der Maaten, L. & Hinton, G. Visualizing data using t-SNE. J. Mach. Learn. Res. 9, 25792605 (2008).
Google Scholar
Mendez, D. et al. ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res. 47, D930D940 (2019).
Article CAS PubMed Google Scholar
Yang, K. et al. Analyzing learned molecular representations for property prediction. J. Chem. Inf. Model. 59, 33703388 (2019).
Article CAS PubMed PubMed Central Google Scholar
RDKit: open-source cheminformatics. RDKit https://www.rdkit.org/. Accessed 28 Mar 2022.
Breiman, L. Random forests. Mach. Learn. 45, 532 (2001).
Article Google Scholar
Silver, D. et al. Mastering the game of Go with deep neural networks and tree search. Nature 529, 484489 (2016).
Article CAS PubMed Google Scholar
Tversky, A. Features of similarity. Psychol. Rev. 84, 327352 (1977).
Article Google Scholar
Rogers, D. & Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Model. 50, 742754 (2010).
Article CAS PubMed Google Scholar
Arthur, D. & Vassilvitskii, S. K-Means++: the advantages of careful seeding. In Proc. Eighteenth Annu. ACM-SIAM Symp. Discrete Algorithms 10271035 (SIAM, 2007).
Maggiora, G., Vogt, M., Stumpfe, D. & Bajorath, J. Molecular similarity in medicinal chemistry: miniperspective. J. Med. Chem. 57, 31863204 (2014).
Article CAS PubMed Google Scholar
Tanimoto, T. T. IBM Internal Report (IBM, 1957).
Nikaido, H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol. Mol. Biol. Rev. 67, 593656 (2003).
Article CAS PubMed PubMed Central Google Scholar
Zurawski, D. V. et al. SPR741, an antibiotic adjuvant, potentiates the in vitro and in vivo activity of rifampin against clinically relevant extensively drug-resistant Acinetobacter baumannii. Antimicrob. Agents Chemother. 61, e01239-17 (2017).
Article PubMed PubMed Central Google Scholar
Eckburg, P. B. et al. Safety, tolerability, pharmacokinetics, and drug interaction potential of SPR741, an intravenous potentiator, after single and multiple ascending doses and when combined with -lactam antibiotics in healthy subjects. Antimicrob. Agents Chemother. 63, e00892-19 (2019).
Article PubMed PubMed Central Google Scholar
Moffatt, J. H. et al. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob. Agents Chemother. 54, 49714977 (2010).
Article CAS PubMed PubMed Central Google Scholar
ONeill, A. J., Cove, J. H. & Chopra, I. Mutation frequencies for resistance to fusidic acid and rifampicin in Staphylococcus aureus. J. Antimicrob. Chemother. 47, 647650 (2001).
Article PubMed Google Scholar
Bjrkholm, B. et al. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc. Natl Acad. Sci. USA 98, 1460714612 (2001).
Article PubMed PubMed Central Google Scholar
Nicholson, W. L. & Maughan, H. The spectrum of spontaneous rifampin resistance mutations in the rpoB Gene of Bacillussubtilis 168 spores differs from that of vegetative cells and resembles that of Mycobacterium tuberculosis. J. Bacteriol. 184, 49364940 (2002).
Article CAS PubMed PubMed Central Google Scholar
Wu, Z. et al. MoleculeNet: a benchmark for molecular machine learning. Chem. Sci. 9, 513530 (2018).
Article CAS PubMed Google Scholar
Melo, M. C. R., Maasch, J. R. M. A. & de la Fuente-Nunez, C. Accelerating antibiotic discovery through artificial intelligence. Commun. Biol. 4, 1050 (2021).
Article CAS PubMed PubMed Central Google Scholar
Yan, J. et al. Recent progress in the discovery and design of antimicrobial peptides using traditional machine learning and deep learning. Antibiotics 11, 1451 (2022).
Article CAS PubMed PubMed Central Google Scholar
Mahlapuu, M., Hkansson, J., Ringstad, L. & Bjrn, C. Antimicrobial peptides: an emerging category of therapeutic agents. Front. Cell. Infect. Microbiol. 6, 194 (2016).
Article PubMed PubMed Central Google Scholar
Mahlapuu, M., Bjrn, C. & Ekblom, J. Antimicrobial peptides as therapeutic agents: opportunities and challenges. Crit. Rev. Biotechnol. 40, 978992 (2020).
Article CAS PubMed Google Scholar
Gmez-Bombarelli, R. et al. Automatic chemical design using a data-driven continuous representation of molecules. ACS Cent. Sci. 4, 268276 (2018).
Article PubMed PubMed Central Google Scholar
Kang, S. & Cho, K. Conditional molecular design with deep generative models. J. Chem. Inf. Model. 59, 4352 (2019).
Article CAS PubMed Google Scholar
Krenn, M., Hse, F., Nigam, A., Friederich, P. & Aspuru-Guzik, A. Self-referencing embedded strings (SELFIES): a 100% robust molecular string representation. Mach. Learn. Sci. Technol. 1, 045024 (2020).
Article Google Scholar
Liu, Q., Allamanis, M., Brockschmidt, M. & Gaunt, A. L. Constrained graph variational autoencoders for molecule design. In Proc. 32nd International Conference on Neural Information Processing Systems (eds Wallach, H. M., Larochelle, H., Grauman, K. & Cesa-Bianchi, N.) 78067815 (Curran Associates Inc., 2018).
You, J., Liu, B., Ying, R., Pande, V. & Leskovec, J. Graph convolutional policy network for goal-directed molecular graph generation. In Proc. 32nd International Conference on Neural Information Processing Systems (eds Wallach, H. M., Larochelle, H., Grauman, K. & Cesa-Bianchi, N.) 64126422 (Curran Associates Inc., 2018).
Jin, W., Barzilay, R. & Jaakkola, T. Junction tree variational autoencoder for molecular graph generation. ICML 80, 23232332 (2018).
Google Scholar
Jin, W., Barzilay, R. & Jaakkola, T. Hierarchical generation of molecular graphs using structural motifs. ICML 119, 48394848 (2020).
Google Scholar
Bilodeau, C. et al. Generating molecules with optimized aqueous solubility using iterative graph translation. React. Chem. Eng. 7, 297309 (2022).
Article CAS Google Scholar
Sadybekov, A. A. et al. Synthon-based ligand discovery in virtual libraries of over 11 billion compounds. Nature 601, 452459 (2022).
Article CAS PubMed Google Scholar
Yang, X., Zhang, J., Yoshizoe, K., Terayama, K. & Tsuda, K. ChemTS: an efficient python library for de novo molecular generation. Sci. Technol. Adv. Mater. 18, 972976 (2017).
Article CAS PubMed PubMed Central Google Scholar
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