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Miniaturization of popular reactions from the medicinal chemists’ toolbox for ultrahigh-throughput experimentation

Nature Synthesis volume 2, pages 1082–1091 (2023)Cite this article

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Abstract

Miniaturization is a tactic employed in many technologies to accelerate discovery through parallelized data collection. The miniaturization of chemical synthesis to the limits of chemoanalytical and bioanalytical detection could accelerate drug discovery by increasing the amount of experimental data collected per milligram of material consumed. Here we demonstrate the miniaturization of popular reactions used in drug discovery such as reductive amination, N-alkylation, N-Boc (tert-butyloxycarbonyl) deprotection and Suzuki coupling for utilization in 1.2 µl reaction droplets. Reaction methods were evolved to perform in high-boiling solvents at room temperature, enabling the diversification of precious starting materials, such as the complex natural product staurosporine.

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Fig. 1: Popularity of common reactions in the synthesis of pharmaceuticals.
Fig. 2: Nanoscale ultraHTE Suzuki coupling reaction performance.
Fig. 3: Nanoscale reaction optimization for the reductive amination of staurosporine (36) with eight aldehydes, eight ketones and 48 reaction conditions.
Fig. 4: Nanoscale staurosporine analogue library synthesis via reductive amination.
Fig. 5: Two-step nanoscale synthesis of MK2-inhibitor analogues (56) and (57) via N-alkylation followed by Boc-deprotection.

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Data availability

The supporting information contains general information, experimental procedures, supplementary tables and images, and compound data and spectra. All raw high-throughput data can be accessed at https://github.com/cernaklab/medchem-reaction-miniaturization/tree/main.

References

  1. Roughley, S. D. & Jordan, A. M. The medicinal chemist’s toolbox: an analysis of reactions used in the pursuit of drug candidates. J. Med. Chem. 54, 3451–3479 (2011).

    Article  CAS  PubMed  Google Scholar 

  2. Faller, B., Ottaviani, G., Ertl, P., Berellini, G. & Collis, A. Evolution of the physicochemical properties of marketed drugs: can history foretell the future? Drug Discov. Today 16, 976–984 (2011).

    Article  CAS  PubMed  Google Scholar 

  3. Leeson, P. D. & Springthorpe, B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat. Rev. Drug Discov. 6, 881–890 (2007).

    Article  CAS  PubMed  Google Scholar 

  4. Campos, K. R. et al. The importance of synthetic chemistry in the pharmaceutical industry. Science 363, eaat0805 (2019).

    Article  CAS  PubMed  Google Scholar 

  5. Mahjour, B., Shen, Y., Liu, W. & Cernak, T. A map of the amine–carboxylic acid coupling system. Nature 580, 71–75 (2020).

    Article  CAS  PubMed  Google Scholar 

  6. Shen, Y. et al. Automation and computer-assisted planning for chemical synthesis. Nat. Rev. Methods Prim. 1, 23 (2021).

    Article  CAS  Google Scholar 

  7. Shim, E. et al. Predicting reaction conditions from limited data through active transfer learning. Chem. Sci. 13, 6655–6668 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Mahjour, B., Shen, Y. & Cernak, T. Ultrahigh-throughput experimentation for information-rich chemical synthesis. Acc. Chem. Res. 54, 2337–2346 (2021).

    Article  CAS  PubMed  Google Scholar 

  9. Moore, G. M. Cramming more components onto integrated circuits. Electronics 38, 114 (1965).

    Google Scholar 

  10. Krska, S. W., DiRocco, D. A., Dreher, S. D. & Shevlin, M. The evolution of chemical high-throughput experimentation to address challenging problems in pharmaceutical synthesis. Acc. Chem. Res. 50, 2976–2985 (2017).

    Article  CAS  PubMed  Google Scholar 

  11. Wong, H. & Cernak, T. Reaction miniaturization in eco-friendly solvents. Curr. Opin. Green Sustain. Chem. 11, 91–98 (2018).

    Article  Google Scholar 

  12. Cernak, T. et al. Microscale high-throughput experimentation as an enabling technology in drug discovery: application in the discovery of (piperidinyl)pyridinyl-1H-benzimidazole diacylglycerol acyltransferase 1 inhibitors. J. Med. Chem. 60, 3594–3605 (2017).

    Article  CAS  PubMed  Google Scholar 

  13. Uehling, M. R., King, R. P., Krska, S. W., Cernak, T. & Buchwald, S. L. Organic chemistry: pharmaceutical diversification via palladium oxidative addition complexes. Science 363, 405–408 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Gesmundo, N. J. et al. Nanoscale synthesis and affinity ranking. Nature 557, 228–232 (2018).

    Article  CAS  PubMed  Google Scholar 

  15. Lin, S. et al. Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS. Science 361, eaar6236 (2018).

    Article  PubMed  Google Scholar 

  16. Santanilla, A. B. et al. Nanomole-scale high-throughput chemistry for the synthesis of complex molecules. Science 347, 49–53 (2015).

    Article  Google Scholar 

  17. Brown, D. G. & Boström, J. Analysis of past and present synthetic methodologies on medicinal chemistry: where have all the new reactions gone? J. Med. Chem. 59, 4443–4458 (2016).

    Article  CAS  PubMed  Google Scholar 

  18. Boström, J., Brown, D. G., Young, R. J. & Keserü, G. M. Expanding the medicinal chemistry synthetic toolbox. Nat. Rev. Drug Discov. 17, 709–727 (2018).

    Article  PubMed  Google Scholar 

  19. Dombrowski, A. W., Aguirre, A. L., Shrestha, A., Sarris, K. A. & Wang, Y. The chosen few: parallel library reaction methodologies for drug discovery. J. Org. Chem. 87, 1880–1897 (2022).

    Article  CAS  PubMed  Google Scholar 

  20. Cooper, T. W. J., Campbell, I. B. & MacDonald, S. J. F. Factors determining the selection of organic reactions by medicinal chemists and the use of these reactions in arrays (small focused libraries). Angew. Chem. Int. Ed. 49, 8082–8091 (2010).

    Article  CAS  Google Scholar 

  21. Yu, Y. et al. Accelerating the discovery of DGAT1 inhibitors through the application of parallel medicinal chemistry (PMC). Bioorganic Med. Chem. Lett. 29, 1380–1385 (2019).

    Article  CAS  Google Scholar 

  22. Richardson, P. & Abdiaj, I. in Flow Chemistry in Drug Discovery (eds Alcazar, J. et al.) 421–479 (Springer, 2021).

  23. Gioiello, A., Piccinno, A., Lozza, A. M. & Cerra, B. The medicinal chemistry in the era of machines and automation: recent advances in continuous flow technology. J. Med. Chem. 63, 6624–6647 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Bogdan, A. R. & Organ, M. G. in Flow Chemistry for the Synthesis of Heterocycles (eds Sharma, U. K. & Van der Eycken, E. V.) 319–341 (Springer, 2018).

  25. Perera, D. et al. A platform for automated nanomole-scale reaction screening and micromole-scale synthesis in flow. Science 359, 429–434 (2018).

    Article  CAS  PubMed  Google Scholar 

  26. Koppmann, R. Volatile Organic Compounds in the Atmosphere (Blackwell Publishing Ltd, 2007).

  27. Alder, C. M. et al. Updating and further expanding GSK’s solvent sustainability guide. Green Chem. 18, 3879–3890 (2016).

    Article  CAS  Google Scholar 

  28. Tu, N. P. et al. High-throughput reaction screening with nanomoles of solid reagents coated on glass beads. Angew. Chem. Int. Ed. 58, 7987–7991 (2019).

    Article  CAS  Google Scholar 

  29. Hendershot, D. C. & Sarafin, A. Safe chemical reaction scale up. Chem. Health Saf. 12, 29–35 (2005).

    Article  CAS  Google Scholar 

  30. Logsdon, D. L. et al. High-throughput screening of reductive amination reactions using desorption electrospray ionization mass spectrometry. Org. Process Res. Dev. 24, 1647–1657 (2020).

    Article  CAS  Google Scholar 

  31. Mahjour, B. et al. Rapid planning and analysis of high-throughput experiment arrays for reaction discovery. Preprint at ChemRxiv https://doi.org/10.26434/chemrxiv-2022-hcnng (2022).

  32. Buitrago Santanilla, A., Christensen, M., Campeau, L. C., Davies, I. W. & Dreher, S. D. P2Et phosphazene: a mild, functional group tolerant base for soluble, room temperature Pd-catalyzed C-N, C-O, and C-C cross-coupling reactions. Org. Lett. 17, 3370–3373 (2015).

    Article  CAS  PubMed  Google Scholar 

  33. Bruno, N. C., Tudge, M. T. & Buchwald, S. L. Design and preparation of new palladium precatalysts for C-C and C-N cross-coupling reactions. Chem. Sci. 4, 916–920 (2013).

    Article  CAS  PubMed  Google Scholar 

  34. Thomas, A. A. & Denmark, S. E. Pre-transmetalation intermediates in the Suzuki-Miyaura reaction revealed: the missing link. Science 352, 329–332 (2016).

    Article  CAS  PubMed  Google Scholar 

  35. Kutchukian, P. S. et al. Chemistry informer libraries: a chemoinformatics enabled approach to evaluate and advance synthetic methods. Chem. Sci. 7, 2604–2613 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dreher, S. D. & Krska, S. W. Chemistry informer libraries: conception, early experience, and role in the future of cheminformatics. Acc. Chem. Res. 54, 1586–1596 (2021).

    Article  CAS  PubMed  Google Scholar 

  37. Abdel-Magid, A. F. & Mehrman, S. J. A review on the use of sodium triacetoxyborohydride in the reductive amination of ketones and aldehydes. Org. Process Res. Dev. 10, 971–1031 (2006).

    Article  CAS  Google Scholar 

  38. Abdel-Magid, A. F., Carson, K. G., Harris, B. D., Maryanoff, C. A. & Shah, R. D. Reductive amination of aldehydes and ketones with sodium triacetoxyborohydride. Studies on direct and indirect reductive amination procedures. J. Org. Chem. 61, 3849–3862 (1996).

    Article  CAS  PubMed  Google Scholar 

  39. Afanasyev, O. I., Kuchuk, E., Usanov, D. L. & Chusov, D. Reductive amination in the synthesis of pharmaceuticals. Chem. Rev. 119, 11857–11911 (2019).

    Article  CAS  PubMed  Google Scholar 

  40. Pels, K. & Kodadek, T. Solid-phase synthesis of diverse peptide tertiary amides by reductive amination. ACS Comb. Sci. 17, 152–155 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Bhattacharyya, S. Titanium(IV) isopropoxide and sodium borohydride: a reagent of choice for reductive amination. Tetrahedron Lett. 35, 2401–2404 (1994).

    Article  CAS  Google Scholar 

  42. Mattson, R. J., Pham, K. M., Leuck, D. J. & Cowen, K. A. An improved method for reductive alkylation of amines using titanium(IV) isopropoxide and sodium cyanoborohydride. J. Org. Chem. 55, 2552–2554 (1990).

    Article  CAS  Google Scholar 

  43. Neidigh, K. A., Avery, M. A., Williamson, J. S. & Bhattacharyya, S. Facile preparation of N-methyl secondary amines by titanium(IV) isopropoxide-mediated reductive animation of carbonyl compounds. J. Chem. Soc., Perkin Trans. 1 16, 2527–2531 (1998).

    Article  Google Scholar 

  44. Huang, X. et al. Discovery and hit-to-lead optimization of non-ATP competitive MK2 (MAPKAPK2) inhibitors. ACS Med. Chem. Lett. 2, 632–637 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Huang, X. et al. A three-step protocol for lead optimization: quick identification of key conformational features and functional groups in the SAR studies of non-ATP competitive MK2 (MAPKAPK2) inhibitors. Bioorg. Med. Chem. Lett. 22, 65–70 (2012).

    Article  PubMed  Google Scholar 

  46. Fiore, M., Forli, S. & Manetti, F. Targeting mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2, MK2): medicinal chemistry efforts to lead small molecule inhibitors to clinical trials. J. Med. Chem. 59, 3609–3634 (2016).

    Article  CAS  PubMed  Google Scholar 

  47. Weis, E., Johansson, M., Korsgren, P., Martín-Matute, B. & Johansson, M. J. Merging directed C-H activations with high-throughput experimentation: development of iridium-catalyzed C-H aminations applicable to late-stage functionalization. JACS Au 2, 906–916 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank S. Krska (Merck & Co., Inc.) for helpful discussions. This study was supported by the University of Michigan College of Pharmacy (start-up funds to T.C.), NIH (R01GM144471 to T.C.), the American Chemical Society MEDI Division (predoctoral fellowship to B.M.) and the National Defense Medical Center of Taiwan (fellowship to Y.-T.K.).

Author information

Author notes

  1. Nathan Gesmundo

    Present address: AbbVie, North Chicago, IL, USA

  2. Bérengère Sauvagnat

    Present address: Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA, USA

  3. Josep Saurí

    Present address: Institut Químic de Sarrià, Barcelona, Spain

  4. Tim Cernak

    Present address: Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA

Authors and Affiliations

  1. Merck & Co., Inc., Boston, MA, USA

    Nathan Gesmundo, Bérengère Sauvagnat, Josep Saurí & Tim Cernak

  2. Merck & Co., Inc., Kenilworth, NJ, USA

    Kevin Dykstra, Ron Ferguson & Spencer Dreher

  3. Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA

    James L. Douthwaite, Yu-Ting Kao, Ruheng Zhao, Babak Mahjour & Tim Cernak

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Contributions

N.G., K.D., Y.-T.K., R.Z. and T.C. performed experiments. R.F. and S.D. assisted in preliminary experiments. B.S. and J.S. performed analysis of products. J.L.D. and B.M. and performed data analysis. N.G., J.L.D., B.M. and T.C. wrote the paper. All authors reviewed the data. T.C. supervised the work.

Corresponding author

Correspondence to Tim Cernak.

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Competing interests

The majority of experimental work was performed at Merck & Co., Inc., Rahway, NJ, USA. The Cernak Lab at University of Michigan has received research funding or in-kind donations from MilliporeSigma, Relay Therapeutics, Janssen Therapeutics, Entos, Inc., SPT Labtech and Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA. T.C. is a former employee of Merck Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA, holds equity in Scorpion Therapeutics, and is a cofounder and equity holder of Entos, Inc. The other authors declare no competing interests.

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Peer review information

Nature Synthesis thanks Magnus Johansson, Steven Mennen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Peter Seavill, in collaboration with the Nature Synthesis team.

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Supplementary information

Supplementary Information

Experimental details, Sections 1–8 and Supplementary Figs. 1–7.

Supplementary Data 1

Excel file containing all raw high-throughput experimentation data.

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Gesmundo, N., Dykstra, K., Douthwaite, J.L. et al. Miniaturization of popular reactions from the medicinal chemists’ toolbox for ultrahigh-throughput experimentation. Nat. Synth 2, 1082–1091 (2023). https://doi.org/10.1038/s44160-023-00351-1

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