journal article·2021-06Open access

Computationally guided high-throughput design of self-assembling drug nanoparticles

Daniel Reker, Yulia Rybakova, Ameya R. Kirtane, Ruonan Cao, Jee Won Yang, Natsuda Navamajiti, Apolonia Gardner, Rosanna M. Zhang, Tina Esfandiary, Johanna L’Heureux, Thomas von Erlach, Elena M. Smekalova, Dominique Leboeuf, Kaitlyn Hess, Aaron Lopes, Jaimie Rogner, Joy Collins, Siddartha M. Tamang, Keiko Ishida, Paul Chamberlain, DongSoo Yun, Abigail Lytton-Jean, Christian K. Soule, Jaime H. Cheah, Alison M. Hayward, Robert Langer, Giovanni Traverso

Nature Nanotechnology· Volume 16· Issue 6

Abstract

Nanoformulations of therapeutic drugs are transforming our ability to effectively deliver and treat a myriad of conditions. Often, however, they are complex to produce and exhibit low drug loading, except for nanoparticles formed via co-assembly of drugs and small molecular dyes, which display drug-loading capacities of up to 95%. There is currently no understanding of which of the millions of small-molecule combinations can result in the formation of these nanoparticles. Here we report the integration of machine learning with high-throughput experimentation to enable the rapid and large-scale identification of such nanoformulations. We identified 100 self-assembling drug nanoparticles from 2.1 million pairings, each including one of 788 candidate drugs and one of 2,686 approved excipients. We further characterized two nanoparticles, sorafenib-glycyrrhizin and terbinafine-taurocholic acid both ex vivo and in vivo. We anticipate that our platform can accelerate the development of safer and more efficacious nanoformulations with high drug-loading capacities for a wide range of therapeutics.
Source: europepmc · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: Nanoparticle-Based Drug Delivery · Computational Drug Discovery Methods · Nanoparticles: synthesis and applications

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (48)

Show source-provided references
1. Hopkins, A. L., Keserü, G. M., Leeson, P. D., Rees, D. C. & Reynolds, C. H. The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discov. 13, 105–121 (2014).10.1038/nrd4163 ↗
2. Irwin, J. J. et al. An aggregation advisor for ligand discovery. J. Med. Chem. 58, 7076–7087 (2015).10.1021/acs.jmedchem.5b01105 ↗
3. Reker, D., Bernardes, G. J. L. & Rodrigues, T. Computational advances in combating colloidal aggregation in drug discovery. Nat. Chem. 11, 402–418 (2019).10.1038/s41557-019-0234-9 ↗
4. Owen, S. C., Doak, A. K., Wassam, P., Shoichet, M. S. & Shoichet, B. K. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem. Biol. 7, 1429–1435 (2012).10.1021/cb300189b ↗
5. Kipp, J. E. The role of solid nanoparticle technology in the parenteral delivery of poorly water-soluble drugs. Int. J. Pharm. 284, 109–122 (2004).10.1016/j.ijpharm.2004.07.019 ↗
6. Mcdonald, T. O. et al. Antiretroviral solid drug nanoparticles with enhanced oral bioavailability: production, characterization, and in vitro-in vivo correlation. Adv. Healthc. Mater. 3, 400–411 (2014).10.1002/adhm.201300280 ↗
7. Govender, T., Stolnik, S., Garnett, M. C., Illum, L. & Davis, S. S. PLGA nanoparticles prepared by nanoprecipitation: drug loading and release studies of a water soluble drug. J. Control. Release 57, 171–185 (1999).10.1016/S0168-3659(98)00116-3 ↗
8. Westesen, K., Bunjes, H. & Koch, M. H. Physicochemical characterization of lipid nanoparticles and evaluation of their drug loading capacity and sustained release potential. J. Control. Release 48, 223–236 (1997).10.1016/S0168-3659(97)00046-1 ↗
9. Reker, D. et al. ‘Inactive’ ingredients in oral medications. Sci. Transl. Med. 11, eaau6753 (2019).10.1126/scitranslmed.aau6753 ↗
10. McLaughlin, C. K. et al. Stable colloidal drug aggregates catch and release active enzymes. ACS Chem. Biol. 11, 992–1000 (2016).10.1021/acschembio.5b00806 ↗
11. Shamay, Y. et al. Quantitative self-assembly prediction yields targeted nanomedicines. Nat. Mater. 17, 361–368 (2018).10.1038/s41563-017-0007-z ↗
12. Inactive Ingredient Search for Approved Drug Products (FDA, 2016); https://www.accessdata.fda.gov/scripts/cder/iig/
13. Feng, B. Y., Shelat, A., Dorman, T. N., Guy, R. K. & Shoichet, B. K. High-throughput assays for promiscuous inhibitors. Nat. Chem. Biol. 1, 146–148 (2005).10.1038/nchembio718 ↗
14. SCOGS (Select Committee on GRAS Substances) (FDA, 2016); https://www.accessdata.fda.gov/scripts/fdcc/?set=SCOGS
15. Wishart, D. S. et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 46, D1074–D1082 (2018).10.1093/nar/gkx1037 ↗
16. Reker, D. et al. Machine learning uncovers food- and excipient-drug interactions. Cell Rep. 30, 3710–3716.e4 (2020).10.1016/j.celrep.2020.02.094 ↗
17. Reker, D., Schneider, P. & Schneider, G. Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors. Chem. Sci. 7, 3919–3927 (2016).10.1039/C5SC04272K ↗
18. Gregori-Puigjane, E. & Mestres, J. A ligand-based approach to mining the chemogenomic space of drugs. Comb. Chem. High T. Scr. 11, 669–676 (2008).
19. Wildman, S. A. & Crippen, G. M. Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comp. Sci. 39, 868–873 (1999).10.1021/ci990307l ↗
20. Chuang, K. V. & Keiser, M. J. Adversarial controls for scientific machine learning. ACS Chem. Biol. 13, 2819–2821 (2018).10.1021/acschembio.8b00881 ↗
21. Test no. 318: dispersion stability of nanomaterials in simulated environmental media. OECD Guidelines for the Testing of Chemicals, Section 3 https://doi.org/10.1787/9789264284142-en (2017).10.1787/9789264284142-en ↗
22. Lipner, S. R. & Scher, R. K. Onychomycosis: treatment and prevention of recurrence. J. Am. Acad. Dermatol. 80, 853–867 (2019).10.1016/j.jaad.2018.05.1260 ↗
23. McClellan, K. J., Wiseman, L. R. & Markham, A. Terbinafine. Drugs 58, 179–202 (1999).10.2165/00003495-199958010-00018 ↗
24. Matteucci, M. E., Hotze, M. A., Johnston, K. P. & Williams, R. O. Drug nanoparticles by antisolvent precipitation: mixing energy versus surfactant stabilization. Langmuir 22, 8951–8959 (2006).10.1021/la061122t ↗
25. Ganesh, A. N. et al. Colloidal drug aggregate stability in high serum conditions and pharmacokinetic consequence. ACS Chem. Biol. 14, 751–757 (2019).10.1021/acschembio.9b00032 ↗
26. Jayatilake, J. A. M. S., Tilakaratne, W. M. & Panagoda, G. J. Candidal onychomycosis: a mini-review. Mycopathologia 168, 165–173 (2009).10.1007/s11046-009-9212-x ↗
27. Cabral, H. et al. Accumulation of sub-100 nm polymeric micelles in poorly permeable tumours depends on size. Nat. Nanotechnol. 6, 815–823 (2011).10.1038/nnano.2011.166 ↗
28. Wong, C. et al. Multistage nanoparticle delivery system for deep penetration into tumor tissue. Proc. Natl Acad. Sci. USA 108, 2426–2431 (2011).10.1073/pnas.1018382108 ↗
29. Pavlović, N. et al. Bile acids and their derivatives as potential modifiers of drug release and pharmacokinetic profiles. Front. Pharmacol. 9, 1283 (2018).10.3389/fphar.2018.01283 ↗
30. Villanueva, A. Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019).10.1056/NEJMra1713263 ↗
31. El-Serag, H. B. & Mason, A. C. Rising incidence of hepatocellular carcinoma in the United States. N. Engl. J. Med. 340, 745–750 (1999).10.1056/NEJM199903113401001 ↗
32. Isbrucker, R. A. A. & Burdock, G. A. A. Risk and safety assessment on the consumption of Licorice root (Glycyrrhiza sp.), its extract and powder as a food ingredient, with emphasis on the pharmacology and toxicology of glycyrrhizin. Regul. Toxicol. Pharm. 46, 167–192 (2006).10.1016/j.yrtph.2006.06.002 ↗
33. Basso, U., Brunello, A., Bertuzzi, A. & Santoro, A. Sorafenib is active on lung metastases from synovial sarcoma. Ann. Oncol. 20, 386–387 (2009).10.1093/annonc/mdn685 ↗
34. Chaparro, M., González Moreno, L., Trapero-Marugán, M., Medina, J. & Moreno-Otero, R. Review article: pharmacological therapy for hepatocellular carcinoma with sorafenib and other oral agents. Aliment. Pharm. Ther. 28, 1269–1277 (2008).10.1111/j.1365-2036.2008.03857.x ↗
35. Zhong, J. et al. Meloxicam combined with sorafenib synergistically inhibits tumor growth of human hepatocellular carcinoma cells via ER stress-related apoptosis. Oncol. Rep. 34, 2142–2150 (2015).10.3892/or.2015.4181 ↗
36. Auffan, M. et al. Towards a definition of inorganic nanoparticles from an environmental, health and safety perspective. Nat. Nanotechnol. https://doi.org/10.1038/nnano.2009.242 (2009).10.1038/nnano.2009.242 ↗
37. Lin, A. et al. Glycyrrhizin surface-modified chitosan nanoparticles for hepatocyte-targeted delivery. Int. J. Pharm. 359, 247–253 (2008).10.1016/j.ijpharm.2008.03.039 ↗
38. Tward, A. D. et al. Distinct pathways of genomic progression to benign and malignant tumors of the liver. Proc. Natl Acad. Sci. USA 104, 14771–14776 (2007).10.1073/pnas.0706578104 ↗
39. Bogorad, R. L. et al. Nanoparticle-formulated siRNA targeting integrins inhibits hepatocellular carcinoma progression in mice. Nat. Commun. 5, 3869 (2014).10.1038/ncomms4869 ↗
40. Lee, J. et al. Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell 9, 391–403 (2006).10.1016/j.ccr.2006.03.030 ↗
41. Sharpless, N. E. & DePinho, R. A. The mighty mouse: genetically engineered mouse models in cancer drug development. Nat. Rev. Drug Discov. 5, 741–754 (2006).10.1038/nrd2110 ↗
42. Waidely, E., Al-Yuobi, A. R. O., Bashammakh, A. S., El-Shahawi, M. S. & Leblanc, R. M. Serum protein biomarkers relevant to hepatocellular carcinoma and their detection. Analyst 141, 36–44 (2016).10.1039/C5AN01884F ↗
43. Lee, C. H. et al. Protective mechanism of glycyrrhizin on acute liver injury induced by carbon tetrachloride in mice. Biol. Pharm. Bull. 30, 1898–1904 (2007).10.1248/bpb.30.1898 ↗
44. Gelderblom, H., Verweij, J., Nooter, K., Sparreboom, A. & Cremophor, E. L. The drawbacks and advantages of vehicle selection for drug formulation. Eur. J. Cancer 37, 1590–1598 (2001).10.1016/S0959-8049(01)00171-X ↗
45. Singh, A., Iyer, A. K. & Amiji, M. M. in Handbook of Nanobiomedical Research (ed. Torchilin, V.) 199–233 (World Scientific Publishing Company, 2014); https://doi.org/10.1142/9789814520652_000610.1142/9789814520652_0006 ↗
46. Pohjala, L., Tammela, P., Pohjala, L. & Tammela, P. Aggregating behavior of phenolic compounds—a source of false bioassay results? Molecules 17, 10774–10790 (2012).10.3390/molecules170910774 ↗
47. Traverso, G. & Langer, R. Perspective: special delivery for the gut. Nature 519, S19 (2015).10.1038/519S19a ↗
48. Cheng, C. J. & Saltzman, W. M. Nanomedicine: downsizing tumour therapeutics. Nat. Nanotechnol. 7, 346–347 (2012).10.1038/nnano.2012.89 ↗