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


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


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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

Authors and Affiliations



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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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

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).

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