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Supported by the German Research Foundation (CRC 746 to
C.H.; ZI 552/3-1 to V.Z.) and the Excellence Initiative of the
German Federal and State Governments (EXC 115 to H.S.,
U.B., and V.Z.; EXC 294 BIOSS to C.H.). We thank the Swiss
Light Source and European Synchrotron Radiation Facility
for beamline access and staff support during visits, and
A. Duchene and G. Beyer for excellent technical assistance.
Coordinates and structure factors are deposited in the
Protein Data Bank with accession code 4wz7.
Materials and Methods
Figs. S1 to S11
Tables S1 to S3
References ( 40–58)
11 August 2014; accepted 1 December 2014
chemistry for the synthesis of
Alexander Buitrago Santanilla,1 Erik L. Regalado,1 Tony Pereira,2 Michael Shevlin,1
Kevin Bateman,2 Louis-Charles Campeau,1 Jonathan Schneeweis, 3 Simon Berritt,1
Zhi-Cai Shi, 4 Philippe Nantermet, 5 Yong Liu,1 Roy Helmy,1 Christopher J. Welch,1
Petr Vachal, 6 Ian W. Davies,1 Tim Cernak, 7 Spencer D. Dreher1*
At the forefront of new synthetic endeavors, such as drug discovery or natural product
synthesis, large quantities of material are rarely available and timelines are tight. A miniaturized
automation platform enabling high-throughput experimentation for synthetic route scouting
to identify conditions for preparative reaction scale-up would be a transformative advance.
Because automated, miniaturized chemistry is difficult to carry out in the presence of solids
or volatile organic solvents, most of the synthetic “toolkit” cannot be readily miniaturized. Using
palladium-catalyzed cross-coupling reactions as a test case, we developed automation-friendly
reactions to run in dimethyl sulfoxide at room temperature. This advance enabled us to
couple the robotics used in biotechnology with emerging mass spectrometry–based
high-throughput analysis techniques. More than 1500 chemistry experiments were carried
out in less than a day, using as little as 0.02 milligrams of material per reaction.
High-throughput experimentation (HTE) chemistry tools have been used to aid in the discoveryof new reactions (1– 6)andin the scale-up optimization of known reac- tions ( 7–9), both areas where substrates
for experimentation are plentiful. However, HTE
is rarely used in the area where it might have
the greatest impact: the synthesis of complex
natural products or highly functionalized drug
leads. What is needed is a tool that would allow
chemists to locate successful reaction conditions
( 10) on a microgram (nanomole) scale in a high-throughput fashion without depleting precious
In the search for breakthrough medicines in
biomedical research, the rapid preparation of new,
complex molecules for biological evaluation is of
paramount importance, but substrates for the
synthesis of such compounds are invariably in
short supply. In later stages of chemistry de-
velopment, substrates are abundant, and state-
of-the-art microvial ( 8, 9) or microfluidic ( 11) HTE
tools can be effective in “turning on” reactions
that were otherwise unsuccessful by exploring
combinations of catalysts, reagents, and other
key reaction variables ( 12, 13). Such studies re-
quire at least milligram (micromole) quantities
of substrate per reaction—a prohibitively large
amount in early drug discovery, where new mol-
ecules are prepared for the first time. Consequent-
ly, the set of desirable compounds designed to test
a biological hypothesis is often winnowed to the
much smaller subset of compounds that can be
successfully synthesized using a single set of re-
action conditions, with little opportunity to study
and improve unsuccessful syntheses ( 14, 15). Min-
iaturizing chemistry to the nanomole scale is a
potential solution to this problem that has here-
tofore met with substantial engineering problems,
such as accurately bringing together extremely
small charges of materials that are often hetero-
geneous, effectively agitating reaction mixtures,
preventing loss of volatile solvents, and incorpo-
rating general analytical approaches to assay re-
action outcomes. We present the first results of a
study aimed at developing general nanomole
reaction screening capabilities to support the
rapid synthesis of complex, highly functional-
ized drug leads.
Figure 1A shows highly functionalized molecules from Merck’s compound collection representative of the cores of drug molecules (1 to 8),
which in the search for new molecules with optimal biological properties would be coupled to a
diversity of polar building blocks ( 9 to 20) such
as those in Fig. 1B. Modern organic synthesis
(and especially transition metal catalysis) is redefining the rules with which new bonds can be
forged; however, it is important to recognize that
many “solved” synthetic transformations are far
from universal, performing well on simple model
substrates yet often failing when applied to complex substrates in real-world synthesis ( 16). A
recent analysis of 2149 metal-catalyzed C-N
1Department of Process and Analytical Chemistry, Merck
Research Laboratories, Merck and Co. Inc., Rahway, NJ 07065,
USA. 2Department of Pharmacokinetics, Pharmacodynamics
and Drug Metabolism, Merck Research Laboratories, Merck and
Co. Inc., West Point, PA 19486, USA. 3Department of
Pharmacology, Merck Research Laboratories, Merck and Co.
Inc., Kenilworth, NJ 07033, USA. 4Department of Discovery
Chemistry, Merck Research Laboratories, Merck and Co. Inc.,
Kenilworth, NJ 07033, USA. 5Department of Discovery Chemistry,
Merck Research Laboratories, Merck and Co. Inc., West Point,
PA 19486, USA. 6Department of Discovery Chemistry, Merck
Research Laboratories, Merck and Co. Inc., Rahway, NJ 07065,
USA. 7Department of Discovery Chemistry, Merck Research
Laboratories, Merck and Co. Inc., Boston, MA 02115, USA.
*Corresponding author. E-mail: email@example.com (T.C.);