Solid-phase synthesis and chemical space analysis
of a 190-membered alkaloid/terpenoid-like library
Gustavo Moura-Lettsa, Christine M. DiBlasia, Renato A. Bauerb, and Derek S. Tana,b,1
aMolecular Pharmacology and Chemistry Program,
Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, NY 10065
bTri-Institutional Training Program in Chemical Biology, and Tri-Institutional Research Program,
Edited by Stuart L. Schreiber, Broad Institute, Cambridge, MA, and approved February 7, 2011 (received for review November 29, 2010)
Alkaloid and terpenoid natural products display an extensive array
of chemical frameworks and biological activities. However such
scaffolds remain underrepresented in current screening collections
and are, thus, attractive targets for the synthesis of natural pro-
duct-based libraries that access underexploited regions of chemical
space. Recently, we reported a systematic approach to the stereo-
selective synthesis of multiple alkaloid/terpenoid-like scaffolds
using transition metal-mediated cycloaddition and cyclization
reactions of enyne and diyne substrates assembled on a tert-butyl-
sulfinamide lynchpin. We report herein the synthesis of a 190-
membered library of alkaloid/terpenoid-like molecules using this
synthetic approach. Translation to solid-phase synthesis was facili-
tated by the use of a tert-butyldiarylsilyl (TBDAS) linker that closely
mimics the tert-butyldiphenysilyl protecting group used in the
original solution-phase route development work. Unexpected
differences in stereoselectivity and regioselectivity were observed
in some reactions when carried out on solid support. Further, the
sulfinamide moiety could be hydrolyzed or oxidized efficiently
without compromising the TBDAS linker to provide additional
amine and sulfonamide functionalities. Principal component analy-
sis of the structural and physicochemical properties of these mole-
cules confirmed that they access regions of chemical space that
overlap with bona fide natural products and are distinct from areas
addressed by conventional synthetic drugs and drug-like mole-
cules. The influences of scaffolds and substituents were also
evaluated, with both found to have significant impacts on location
in chemical space and three-dimensional shape. Broad biological
evaluation of this library will provide valuable insights into the
abilities of natural product-based libraries to accesssimilarly under-
exploited regions of biological space.
diversity-oriented synthesis ∣ multiscaffold library ∣ asymmetric synthesis ∣
underexploited regions of biologically relevant chemical space to
enable the discovery of new biological probes and potential ther-
apeutic lead compounds (1). A key approach to addressing this
challenge is toemulate natural products andother biogenetic mo-
lecules, which have coevolved with macromolecular biological
targets (2). Toward this end, a variety of natural product-based
libraries have been synthesized, with promising early results
(3). These libraries can be validated initially by evaluation of their
structural and physicochemical properties using principal compo-
nent analysis (PCA) to determine the regions of chemical space
that are accessed. Subsequently, screening across a wide range of
biological assays provides direct biological validation of the func-
tional capabilities of these libraries.
Alkaloids and terpenoids have long served as important
small-molecule drugs and leads for drug discovery (4, 5). Indeed,
alkaloid and terpenoid cores are prevalent among privileged
scaffolds able to bind multiple biological targets (6), and a variety
of alkaloid- and terpenoid-based libraries have been reported
major goal in the field of diversity-oriented synthesis is the
efficient production of small-molecule libraries that address
We recently reported a systematic approach to the synthesis
of multiple polycyclic scaffolds related to structures found in
diverse alkaloid and terpenoid natural products (12). Our syn-
thetic approach was designed to emulate divergent biosynthetic
strategies used in nature by converting a small number of rela-
tively simple, acyclic starting materials into a diverse array of
polycyclic scaffolds (13). A series of enyne and diyne substrates
is assembled using a tert-butylsulfinamide lynchpin that affords
asymmetric induction, a uniquely suited reactivity pattern, and
an unusual structural motif for biological evaluation (14). Transi-
tion metal-mediated cycloaddition and cyclization reactions are
then used to convert these substrates to 10 distinct classes of
polycyclic scaffolds that are primed for further functionalization.
PCA of structural and physicochemical properties indicates that
these scaffolds sample a distinct region of chemical space com-
pared to drugs and drug-like libraries, overlapping with polycyclic
alkaloid and terpenoid natural products.
Building upon this work, we envisioned the construction of
a larger library of alkaloid/terpenoid-like small molecules for
further chemical and biological evaluation. Importantly, our ori-
ginal solution-phase synthesis was designed to facilitate future
translation to solid-phase parallel synthesis through the incor-
poration of a tert-butyldiphenysilyl (TBDPS)-protected primary
alcohol. This moiety serves as a faithful surrogate for a tert-
butyldiarylsilyl (TBDAS) linker that we have previously devel-
oped (15). This robust linker is known to be stable to a variety of
acidic and basic reaction conditions, and was expected to be
similarly compatible with the desired transition metal-mediated
cycloaddition and cyclization reactions, many of which had not
previously been carried out on solid support. Moreover, we
envisioned that the versatile tert-butylsulfinamide moiety could
be used to introduce additional diversity through its inherent
stereochemical diversity, hydrolysis to afford the corresponding
secondary amines, and oxidation to provide related tert-butylsul-
Results and Discussion
Solid-Phase Synthesis of Enyne and Diyne Precursors. Primary alco-
hols can be loaded onto solid support via the TBDAS linker at
any of several stages in the synthesis. To minimize the number
of solution-phase transformations, we elected to synthesize the
R- and S-tert-butylsulfinimine precursors in solution, then load
them onto TBDAS-polystyrene resin to afford 1 (Scheme 1,
R-series shown). The yield of each solid-phase reaction was
determined by cleavage of an aliquot of resin in the presence
of an internal standard, followed by HPLC [evaporative light-
Author contributions: G.M.-L., C.M.D., R.A.B., and D.S.T. designed research; G.M.-L. and
R.A.B. performed research; G.M.-L., R.A.B., and D.S.T. analyzed data; and G.M.-L.,
C.M.D., R.A.B., and D.S.T. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
1To whom correspondence should be addressed. E-mail: email@example.com.
This article contains supporting information online at www.pnas.org/lookup/suppl/
www.pnas.org/cgi/doi/10.1073/pnas.1015268108PNAS ∣ April 26, 2011 ∣ vol. 108 ∣ no. 17 ∣ 6745–6750
scattering detector (ELSD)] and/or1H-NMR analysis (Materials
Diastereoselective solid-phase alkyne additions were then
carried out to introduce a diversity position (R2) in propargyl
sulfinimines 2a–c (16, 17). We were gratified to find that these
reactions proceeded with complete diastereoselectivity [≥95∶5
diastereomeric ratio (DR),1H-NMR] and in yields comparable
to those observed in the corresponding solution-phase reactions
(2a, 91% vs. 85%; 2b, 69% vs. 80%; 2c, 85% vs. 77%) (12). Sub-
sequent desilylation of 2c with K2CO3in MeOH also provided
the terminal alkyne 2d in 78% yield.
Next, the reaction pathway was branched to form the enyne
substrates 3 by N-allylation and the diyne substrates 4 by N-pro-
pargylation (18, 19). Notably, the TBDAS linker withstood these
strongly basic reaction conditions, and the reactions proceeded in
good yields, comparable to those previously obtained in solution
phase (3a, 87% vs. 98%; 3b, 72% vs. 76%; 3c, 88% vs. 80%; 3d,
81%; 4a, 86% vs. 82%; 4b, 82% vs. 90%; 4c, 85% vs. 82%; 4d,
79%) (12). Because the terminal alkynes (3d, 4d) were more
broadly effective substrates compared to the trimethylsilyl
(TMS)-alkynes (3c, 4c) in the original solution-phase studies
(12), and afford identical products after desilylation, the former
were used in most of the subsequent transition metal-mediated
cycloaddition and cyclization reactions.
Transition Metal-Mediated Cycloaddition and Cyclization Reactions.
With the enyne and diyne substrates 3 and 4 in hand, we
were poised to investigate the key transition metal-mediated
solid-phase cycloaddition and cyclization reactions (Scheme 2).
Although there are several examples of such reactions being car-
ried out successfully on solid phase (20), many of these specific
reactions had not been carried out on solid support previously,
and none had been explored in the context of the TBDAS linker.
However, we hoped that this linker would continue to mirror
faithfully the previously established reactivity profile of the
TBDPS protecting group used in the original solution-phase
Indeed, we were delighted to find that translation to solid
phase proved largely uneventful for the majority of these
reactions. Consistent with our solution-phase results, Krische and
(BINAP) catalyzed reductive cyclization (21) proceeded with
reagent-controlled diastereoselectivity for 3a,b, but not for 3d,
affording access to both exo-pyrroline relative diastereomers
6a,b and 6′a,b and the major diastereomer 6d (Scheme 2).
The yields and diastereoselectivities were comparable to those
observed in the original solution-phase studies in this first appli-
cation to solid-phase synthesis.
Enynes 3a,b,d also underwent Evans et al.’s diastereoselective
Rh(I)-catalyzed [4 þ 2 þ 2] reaction with 1,3-butadiene success-
fully (22). This reaction has not previously been used in solid-
phase synthesis and, based on our previous solution-phase
studies, the sulfinamides were oxidized to the corresponding
sulfonamides prior to cycloaddition, leading to cyclooctapyrroli-
Ring-closing metathesis (23) of enynes 3a,b,d proceeded
uneventfully to vinylpyrrolines 8a,b,d. We had previously found
in our solution-phase studies that, although these products were
unreactive to most dienophiles, oxidation to the corresponding
sulfonamides afforded more reactive dienes. Thus, these Diels–
Alder reactions (24, 25) provided tricyclic benzodipyrrolidines
9a,b,d and isoindoline dicarboxylates 10a,b,d.
In the diyne substrate series, Yamamoto et al.’s Ru(II)-
catalyzed [2 þ 2 þ 2] cyclotrimerization reaction with benzyl
isocyanate (26) was also translated effectively to solid-phase
synthesis (27), using diyne substrates 4a,b,d. Some optimization
of reaction conditions was required, because extended reaction
times (12 h vs. 6 h) resulted in formation of an inseparable side
product, apparently due to coupling of a second equivalent of
benzyl isocyanate (M þ 133). Under the optimized conditions,
consistent with our solution-phase results, pyrrolopyridone pro-
ducts 27a,b were formed efficiently with complete regioselectivity
and 27d/27′d were formed as a 1∶1 mixture of regioisomers that
were separable after cleavage from the solid support.
Tanaka et al.’s Ru(I)-catalyzed [2 þ 2 þ 2] cyclotrimerization
of ethyl cyanoformate (28, 29) also proceeded effectively for
diynes 4a,b,d, to afford pyrrolopyridine carboxylates 28a,b,d
regioselectively. Deiters and coworkers have carried out similar
reactions previously on solid support (27, 30).
Similarly, Saito and coworkers’ Ni(0)-catalyzed [3 þ 2 þ 2]
cycloaddition with ethyl cyclopropylidene acetate (31) was trans-
lated effectively to solid support-bound diynes 4a–c. The initial
cycloheptapyrrolidine ester products were then converted to
the corresponding Weinreb amides 29a–c/29′a–c (32) to facilitate
downstream separation of E and Z isomers after cleavage from
the solid support.
Although translation to solid-phase synthesis was gratifyingly
straightforward for most of these reactions, interesting differ-
ences from the original solution-phase results were noted in
certain cases. For example, application of the Pauson–Khand
reaction (19, 33, 34) to solid support-bound enynes 3 showed a
slight trend toward higher yields and diastereoselectivities for the
cyclopentapyrrolidinone products 5 in most cases (Scheme 3).
This trend was particularly evident in the case of the phenyl-sub-
stituted product 5b (74% vs. 64% yield, 70∶30 vs. 50∶50 DR).
Recognizing that the choice of solvent is known to affect this
reaction in solution (35), we hypothesized that the polystyrene
matrix might provide a more hydrophobic reaction milieu than
suggested by the CH3CN solvent used to induce the cycloaddition
reaction. Consistent with this idea, when the corresponding
solution-phase reaction was carried out in benzene or toluene,
similarly improved diastereoselectivities were observed. The dia-
stereoselectivity of the solid-phase reaction could also be further
improved by changing the solvent to benzene or toluene. This
finding highlights the influence of the solid support in “solvent
effects” on some reactions.
In the [2 þ 2 þ 2] cyclotrimerization (36–38) of diynes 4a,b,d
using Grubbs’ first-generation catalyst and propargyl alcohol
(39), one significant difference in regioselectivity was noted in
comparison to our original solution-phase results. While isoindo-
lines 26a,d were formed in the expected regioselectivities (26a,
100∶0; 26d/26′d, 50∶50), the corresponding phenyl-substituted
product 26b/26′b was formed in significantly lower regioselectiv-
ity on solid support (67∶33 vs. 91∶9). We again postulate that this
difference may result from interactions of this aromatic substrate
with the polystyrene matrix in the solid-phase reaction. Notably,
however, this decreased selectivity was advantageous in this
particular context, because it afforded access to the minor regioi-
shown). Yields determined by cleavage of an aliquot of resin in the presence
of p-methoxybenzylalcohol internal standard, followed by HPLC (ELSD)
analysis. (HMPA = hexamethylphosphoramide, LiHMDS = lithium hexa-
methyldisilazide, TBS = tert-butyldimethylsilyl, TMS = trimethylsilyl)
Solid-phase synthesis of enyne and diyne substrates (R-series
www.pnas.org/cgi/doi/10.1073/pnas.1015268108 Moura-Letts et al.
somer 26′b that was not accessible in useful quantities via the
Diversification of Sulfinamide Moiety and Library Cleavage. With
these 10 classes of scaffolds in hand, we next investigated diver-
sification of the tert-butylsulfinamide moieties. We had originally
selected this lynchpin in part because of its known acid-lability
(40), and were pleased to find that the support-bound sulfina-
mides could be cleaved with HCl [1 M in dioxane/THF, room
temperature (RT)] to afford the corresponding secondary amines
without compromising the TBDAS linker (Scheme 2). This result
opens the door for additional diversification of this position in the
(*) Diversification of the sulfinamide in each scaffold series as indicated by the arrows. (†) The sulfonamide 35b was not recovered. (‡) Cleavage of library
members derived from 29c and 29′c concurrently removes the TMS group to provide 45d–50d. [BINAP = 2,2′-bis(diphenylphosphino)-1,1′-binaphthyl;
COD = 1,4-cyclooctadiene; Cp* = pentamethylcyclopentadienyl; m-CPBA = meta-chloroperbenzoic acid; DDQ = 2,3-dichloro-5,6-dicyano-1,4-benzoquinone;
DMAD = dimethylacetylene dicarboxylate; Grubbs I = benzylidene-bis(tricyclohexylphosphine)dichlororuthenium; Grubbs II = benzylidene[1,3-bis(2,4,6-tri-
methylphenyl)-2-imidazolidinylidene]dichloro(tricyclohexylphosphine)ruthenium; IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazoly-2-ylidene; Tf = trifluoro-
Solid-phase synthesis of a 190-membered library of alkaloid/terpenoid-like small molecules from enynes 3 and diynes 4 (R-series shown).
Moura-Letts et al.PNAS
April 26, 2011
future (N-acylation, N-alkylation, etc.). Alternatively, treatment
of the sulfinamides with meta-chloroperbenzoic acid (m-CPBA)
(CH2Cl2, 0 °C) also provided the corresponding tert-butylsulfona-
Accordingly, seven scaffolds (5, 6, 8, 26–29) were produced
with three variations at this position (amine, sulfinamide, sulfo-
namide). Three scaffolds required prior oxidation to the tert-
butylsulfonamide to enable the cycloaddition reactions (7, 9, 10)
and were limited to this functionality because it could not be
cleaved effectively under a variety of conditions (e.g., PhSH,
K2CO3; TFA, anisole; TfOH, anisole).
Finally, all library members were cleaved from the solid
support using HF·pyridine (pyridine, THF, 50 °C) and purified
by preparative reverse-phase HPLC to afford the final library
of 190 alkaloid/terpenoid-like compounds (both enantiomeric
series), comprised of 18 cyclopentapyrrolidinones (11–13), 30
exo-pyrrolines (14–19), 6 cyclooctapyrrolidines (20), 18 vinylpyr-
rolines (21–23), 6 benzodipyrrolidines (24), and 6 isoindoline
dicarboxylates (25) derived from the enyne substrates and 28
isoindoline alcohols (30–38), 24 pyrrolopyridones (36–41), 18
pyrrolopyridine carboxylates (42–44), and 36 cycloheptapyrroli-
dine amides (45–50) derived from the diyne substrates. The pro-
ducts were isolated in 20.2% average yield over 5–8 solid-phase
steps, at 74.0% average yield per step (SI Appendix, Table S1).
Chemical Space Analysis of Small-Molecule Library. We have pre-
viously analyzed a subset of 32 sulfinamides from this alkaloid/
terpenoid-like library for 20 structural and physicochemical para-
meters to define their positions in chemical space in comparison
to natural products, drugs, and drug-like libraries using our estab-
lished PCA protocol (3, 12). Importantly, the alkaloid/terpenoid-
like scaffolds were found to overlap with related polycyclic
alkaloid and terpenoid natural products (SI Appendix, Fig. S1),
sampling regions of chemical space distinct from those accessed
by drugs and drug-like libraries. To delve more deeply into the
impacts of various structural features upon positioning in chemi-
cal space, we expanded our PCA-based analysis to the complete
190-membered alkaloid/terpenoid library synthesized herein
(Fig. 1A and Dataset S1). In this analysis, the first two principal
components represented 81% of the variance in the total data set.
Analysis of component loadings (SI Appendix, Fig. S2) indicated
hydrophobicity (positive) and multiple factors correlating with
size (negative) influenced positioning on the x axis (PC1), while
aromatic ring count (positive) and stereochemical density (nega-
tive) impacted positioning on the y axis (PC2).
Overall, the complete alkaloid/terpenoid library again over-
lapped with bona fide alkaloid and terpenoid natural products,
while also covering a larger area of the plot than the original
32 sulfinamides (Fig. 1A). Notably, the individual scaffolds had
a significant influence on positioning, with many of the enyne-
derived products appearing more natural product-like, because
of their higher stereochemical content and lower aromatic ring
content compared to the diyne-derived products (Fig. 1B). The
nature of the alkyne substituent (R2¼ CH2CH2OH, Ph, or H)
also had a strong influence on position, with the phenyl-substi-
tuted library members overlapping partially with drugs and drug-
like libraries whereas the other two nonaryl substituents led to
more natural product-like structures (Fig. 1C). In contrast, the
nature of the N-capping group (R3¼ sulfinamide, free amine,
or sulfonamide) had relatively less influence, although a slight
bias toward drug-like chemical space could be observed in the
sulfonamide series (Fig. 1D).
We also carried out a shape-based analysis of the library based
on normalized principal moment of inertia (PMI) ratios (SI
Appendix, Figs. S7–S9) (41–45). In this analysis, the library mem-
bers exhibited a diverse range of rod-like and disc-like shapes,
with more limited sphere-like character. Individual scaffolds were
biased toward slightly different regions of the plot, whereas
the nature of the alkyne substituent (R2) and N-capping group
(R3) did not result in obvious trends. Thus, the shapes of the
library members were dependent upon the combination of
both scaffold and substituents.
We have synthesized a library of 190 polycyclic, alkaloid/terpe-
noid-like small molecules using solid-phase transition metal-
mediated cycloaddition and cyclization reactions of relatively
simple enyne and diyne substrates. The key sulfinamide lynchpin
top-selling drugs (red circles), 60 diverse natural products (open blue triangles), 20 polycyclic alkaloids and terpenoids (filled blue triangles), 20 ChemBridge and
ChemDiv library members (crosses), and 190 multiscaffold library members (green diamonds). (B) Influence of the scaffold: enyne-derived scaffolds (filled
diamonds), diyne-derived scaffolds (filled squares). (C) Influence of the R2substituent: CH2CH2OH (green fill), Ph (yellow fill), H (pink fill). (D) Influence of
the R3N capping group: sulfinamides (green fill), free amines (pink fill), sulfonamides (yellow fill). See SI Appendix for full details and high-resolution images.
Chemical space analysis of alkaloid/terpenoid-like library. (A) Principal component analysis of 20 structural and physicochemical descriptors of the 40
tion. Yields and DR shown for reactions carried out on solid phase (R1=
TBDAS) andin solution phase (parentheses, R1= TBDPS, ref. 12 and data here-
in). Solid-phase reactions analyzed by cleavage of an aliquot of resin in the
presence of p-methoxybenzylalcohol internal standard, followed by HPLC
(ELSD) and1H-NMR analysis.
Resin and solvent effects in the solid-phase Pauson–Khand reac-
www.pnas.org/cgi/doi/10.1073/pnas.1015268108Moura-Letts et al.
was also diversified to the corresponding free amines and sulfo-
namides. Translation to solid-phase synthesis using a TBDAS
linker was greatly facilitated by the use of a TBDPS surrogate
during earlier solution-phase studies. Principal component ana-
lysis of structural and physicochemical parameters indicates that
this library samples regions of chemical space that overlap with
bona fide natural products and are distinct from those areas
accessed by conventional drugs and drug-like libraries. Aromatic
ring content and stereochemical complexity were identified as
two major factors that distinguish natural products from synthetic
drugs. The complete set of 190 compounds is now being screened
in a variety of assays at The Rockefeller University High-
Throughput Screening Resource Center. In addition, 94 com-
pounds have been submitted for broad screening in the National
Institutes of Health (NIH) Molecular Libraries Program (Pub-
Chem Substance search term: DST_AT1_*, http://pubchem.
ncbi.nlm.nih.gov). These efforts will provide critical data to
evaluate the biological properties of this library and to assess
the abilities of natural product-based libraries to address challen-
ging biological targets that remain intractable to conventional
Materials and Methods
See SI Appendix for detailed methods and complete analytical data.
General Procedure for Monitoring Solid-Phase Reactions. An aliquot of
vacuum-dried resin (4 mg) was swollen with THF (5 mL) for 10 min. A solution
of 4-methoxybenzylalcohol (internal standard) (25 mM in THF, 1 eq) was
added, followed by tetra-n-butylammonium fluoride (0.1 M in THF, 3 eq).
After stirring for 2 h, the THF solution was recovered from the resin, and
the solution concentrated by rotary evaporation. The residue was taken
up in CH3CN (300 μL) and filtered through a Pasteur pipette with a 0.5-inch
plug of normal phase silica gel over a 0.5-inch plug of reverse-phase silica
gel. The plug was rinsed carefully with 3 mL CH3CN, and the crude cleavage
products were recovered by rotary evaporation. HPLC analysis (ELSD) was
used to determine the ratio of cleaved scaffold to internal standard, and
the yield was calculated based on a calibration curve. Analysis by1H-NMR
was used to determine product ratios where appropriate.
Sulfinimine Alcohol Loading (1). The (R,E)- and (S,E)-N-(3-hydroxypropylidene)-
2-methylpropane-2-sulfinamide (SI Appendix) were loaded onto TBDAS
resin (800 mg, 1.53 meq∕g, where meq is milliequivalent) by the previously
described general procedure (12) to afford sulfinimine resins R-1 and S-1.
General Procedure for Diastereoselective Alkyne Addition (2). Lithium hexa-
methyldisilazide (LiHMDS) (1 M in THF, 4.4 mmol, 4.0 eq) was dissolved in an-
hydrous hexanes (20 mL) at −78°C, the appropriate alkyne (4.4 mmol, 4.0 eq)
was added, and the reaction was removed from the cold bath and stirred for
10 min, then recooled to −78°C. Vacuum-dried resin 1 (800 mg, 1.11 meq,
1.0 eq) was swollen with THF (20 mL) for 10 min, then cooled to −78°C
and the lithium acetylide solution was added via cannula. The reaction
was allowed to warm to RT with stirring over 24 h. The reaction was
quenched with water (100 mL), then the resin was washed and dried to
afford propargyl sulfinamides 2.
General Procedure for Sulfinamide N-Alkylation (3, 4). Propargyl sulfinamide
resin 2 (800 mg, 0.92 meq, 1.0 eq) was swollen with THF (20 mL) for
10 min, then the mixture was cooled to −78°C and a solution of n-BuLi
(2.4 M in hexanes, 2.02 mmol, 2.2 eq) was added by syringe. The reaction
was stirred for 45 min, then hexamethylphosphoramide (640 μL, 3.68 mmol,
4.0 eq) was added. After stirring for an additional 30 min, allyl or pro-
pargyl bromide (9.2 mmol, 10 eq) was added. The mixture was stirred at
−78°C for 6 h, then allowed to warm to RT overnight. The reaction was
quenched with water (100 mL), then the resin was washed and dried to
afford enynes 3 or diynes 4.
General Procedure for Pauson–Khand Reaction (5). Vacuum-dried enyne resin 3
(800 mg, 0.86 meq, 1.0 eq) was swollen with CH2Cl2(20 mL) for 10 min, then
Co2ðCOÞ8(1.18 g, 3.44 mmol, 4.0 eq) was added and the slurry was stirred at
RT for 3 h. The solution was decanted from the flask under positive Ar pres-
sure and the resin was washed with anhydrous CH3CN (2 × 25 mL). The resin
was swollen with anhydrous CH3CN (20 mL) and heated to 75 °C for 12 h,then
allowed to cool to RT. The resin was washed and dried to afford cyclopenta-
General Procedure for Krische Reductive Cyclization (6). Vacuum-dried resin 3
(800 mg, 0.86 meq, 1.0 eq) was swollen with 1,2-dichloroethane (DCE) (20 mL)
for 10 min, then a stock solution of RhðCODÞ2OTf, where COD is 1,4-cyclooc-
tadiene, and (R)- or (S)-BINAP (1∶1 molar ratio, 0.1 M in DCE, 3.4 mL,
0.34 mmol, 0.4 eq) was added via cannula. The reaction atmosphere was
flushed with H2, and the mixture was stirred under a balloon of H2at RT
for 12 h. The resin was washed and dried to afford exo-pyrrolines 6 or 6′.
General Procedure for Evans Butadiene [4 þ 2 þ 2] Cycloaddition (7). Vacuum-
dried resin 3 (800 mg, 0.86 meq, 1.0 eq) was swollen with CH2Cl2(20 mL) for
10 min, then cooled to 0°C. Solid m-CPBA (580 mg, 2.58 mmol, 3.0 eq) was
added and the reaction was stirred at 0°C for 1 h, then allowed to warm to
RT and stirred for 6 h. The resin was washed and dried, then swollen with
toluene (20mL) for 10min.A stock solution of RhðIMesÞðCODÞCl4, where IMes
is 1,3-bis(2,4,6-trimethylphenyl)imidazoly-2-ylidene, and AgOTf (1∶2 molar
ratio, 0.1 M Rh in degassed toluene, 3.44 mL, 0.34 mmol Rh, 0.4 eq) was
added to the resin, and the reaction atmosphere was flushed with 1,3-buta-
diene gas, then the mixture was stirred under a balloon of 1,3-butadiene at
RT for 2 h, refilling the balloon when empty. The balloon was removed and
the mixture was heated to 108°C for 24 h. The resin was cooled, washed, and
dried to afford cyclooctapyrrolidines 7.
General Procedure for Enyne Metathesis (8). Vacuum-dried resin 3 (800 mg,
0.86 meq, 1.0 eq) was swollen with degassed toluene (200 mL) for 10 min,
then a stock solution of Grubbs’ second-generation catalyst (0.1 M in
degassed toluene, 5.1 mL, 0.51 mmol, 0.6 eq) was added via syringe and
the mixture was stirred at 60 °C overnight. The resin was cooled, washed,
and dried to afford vinylpyrrolines 8.
General Procedure for Diels–Alder Reactions (9, 10). Vacuum-dried resin 3
(800 mg, 0.86 meq, 1.0 eq) was swollen with CH2Cl2(20 mL) for 10 min, then
cooled to 0°C. Solid m-CPBA (580 mg, 2.58 mmol, 3.0 eq) was added and the
reaction was stirred at 0 °C for 1 h, then allowed to warm to RTand stirred for
6 h. The resin was washed and dried, then swollen with CH2Cl2(200 mL)
for 10 min. A stock solution of Grubbs’ second-generation catalyst (0.1 M
in degassed toluene, 5.1 mL, 0.51 mmol, 0.6 eq) was added and the mixture
stirred at 80 °C overnight. The resin was cooled, washed, and dried, then
swollen in toluene (20 mL). For 9, N-phenylmaleimide (1.14 g, 6.6 mmol,
7.7 eq) was added and the mixture was stirred at 80°C for 36 h. The resin
was cooled, washed, and dried to afford benzodipyrrolidines 9. For 10,
dimethyl acetylenedicarboxylate (650 μL, 5.16 mmol, 6.0 eq) was added
and the mixture was stirred at 100°C for 48 h. The resin was cooled, washed
quickly with benzene, and swollen in benzene (20 mL) for 10 min. A stock
solution of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (1.0 M in benzene,
3.44 mL, 3.44 mmol, 4.0 eq) was added and the mixture was stirred at
80°C for 48 h. The resin was cooled, washed, and dried to afford isoindoline
General Procedure for Propargyl Alcohol [2 þ 2 þ 2] Cyclotrimerization (26).
Vacuum-dried resin 4 (800 mg, 0.86 meq, 1.0 eq) was swollen with
degassed toluene (20 mL) for 10 min. A stock solution of Grubbs’ first-gen-
eration catalyst (0.1 M in degassed toluene, 3.4 mL, 0.34 mmol, 0.4 eq) and
propargyl alcohol (500 μL, 8.6 mmol, 10.0 eq) were added via syringe and the
mixture was stirred at 90 °C overnight. The resin was cooled, washed, and
dried to afford isoindolines 26/26′.
General Procedure for Yamamoto Benzyl Isocyanate [2 þ 2 þ 2] Cyclotrimeriza-
tion (27). Vacuum-dried resin 4 (800 mg, 0.86 meq, 1.0 eq) was swollen with
degassed DCE (20 mL) for 10 min. A stock solution of benzyl isocyanate and
RuCp*(COD)Cl (40∶1 molar ratio, 0.5 M isocyanate in DCE, 7 mL, 3.5 mmol
isocyanate, 4.0 eq) was added and the slurry was stirred at 90 °C for 6 h.
The resin was cooled, washed, and dried to afford pyrrolopyridones 27/27′.
General Procedure for Tanaka Ethyl Cyanoformate [2 þ 2 þ 2] Cyclotrimeriza-
tion (28). Vacuum-dried resin 4 (800 mg, 0.86 meq, 1.0 eq) was swollen with
degassed DCE (20 mL) for 10 min. A stock solution of ethyl cyanoformate,
RhðCODÞ2BF4, and rac-BINAP (50∶1.5∶2 molar ratio, 0.5 M nitrile in DCE,
8 mL, 4.0 mmol, 4.65 eq) was added and the mixture was stirred at 80 °C
for 12 h. The resin was cooled, washed, and dried to afford pyrrolopyridine
Moura-Letts et al.PNAS
April 26, 2011
General Procedure for Saito [3 þ 2 þ 2] Cyclotrimerization (29). Vacuum-dried
resin 4 (800 mg, 0.86 meq) was swollen with degassed DCE (20 mL) for 10 min.
A stock solution of ethyl cyclopropylidineacetate, NiðCODÞ2and PPh3
(30∶3.5∶7 molar ratio, 0.5 M cyclopropylidine in degassed toluene, 8 mL,
4.0 mmol cyclopropylidine, 4.65 eq) was added and the mixture was stirred
at 70°C for 36 h. The resin was cooled, washed, and swollen in THF, then
cooled to −10°C. Solid HN(Me)OMe·HCl (850 mg, 8.6 mmol, 10.0 eq) and
cyclopentyl-MgCl (2.0 M in Et2O, 13 mL, 26 mmol, 30 eq) were
added, and the resulting mixture was stirred at −10°C for 4 h. The reaction
was quenched with water and the resin was washed and dried to afford
General Procedure for Hydrolysis of Sulfinimides to Amines. The vacuum-dried
resin (400 mg, 0.42 meq, 1.0 eq) was swollen with THF (16 mL) for 10 min. HCl
(4 M in dioxane, 0.42 mL, 1.68 mmol, 4.0 eq) was added and the
mixture was stirred at RT for 4 h. The resin was washed and dried to afford
the corresponding free secondary amines.
General Procedure for Oxidation of Sulfinamides to Sulfonamides. The vacuum-
dried resin (400 mg, 0.42 meq, 1.0 eq) was swollen with CH2Cl2(10 mL)
for 10 min, then cooled to 0°C. Solid m-CPBA (150 mg, 0.63 mmol, 1.5 eq)
was added and the mixture was stirred at 0 °C for 1 h, then allowed to
warm to RT and stirred for 6 h. The resin was washed and dried to afford
the corresponding tert-butylsulfonamides.
General Procedure for Product Cleavage from the TBDAS Resin. Vacuum-dried
resin (400 mg, 0.42 meq, 1.0 eq) was swollen with THF (10 mL) for 10 min.
A stock solution of HF·pyridine and pyridine (1∶2 molar ratio, 0.5 M HF·pyr-
idine in THF, 5.1 mL, 2.5 mmol, 6 eq) was added and the resulting mixture was
stirred at 50°C for 3 h. The reaction was quenched with methoxytrimethyl-
silane (0.35 mL, 2.52 mmol, 6.0 eq), and the supernatant was recovered. The
resin was extracted with additional THF (2 × 50 mL), and the combined super-
natants were concentrated by rotary evaporation. Initial purification was
carried out on an ISCO Optix 10 CombiFlash system, and the products were
further purified by preparative reverse-phase HPLC. The purified library
members were analyzed by HPLC (ELSD/MS) and1H-NMR and submitted
for biological screening at The Rockefeller University High-Throughput
Screening Resource Center and NIH Molecular Libraries Program.
ACKNOWLEDGMENTS. We thank Dr. Lakshmi B. Akella (Broad Institute) for
carrying out the PMI analysis and Dr. George Sukenick, Dr. Hui Liu, Hui Fang,
and Dr. Sylvi Rusli for mass spectral analyses. D.S.T. is an Alfred P. Sloan
Research Fellow. JChem for Excel was generously provided by ChemAxon.
Financial support from the National Institutes of Health (R21 GM104685,
P41 GM076267, T32 CA062948-Gudas) is gratefully acknowledged.
1. Tan DS (2005) Diversity-oriented synthesis: Exploring the intersections between
chemistry and biology. Nat Chem Biol 1:74–84.
2. Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK (2009) Quantifying biogenic bias in
screening libraries. Nat Chem Biol 5:479–483.
3. Bauer RA, Wurst JM, Tan DS (2010) Expanding the range of “druggable” targets
with natural product-based libraries: An academic perspective. Curr Opin Chem Biol
4. Ganesan A (2008) The impact of natural products upon modern drug discovery. Curr
Opin Chem Biol 12:306–317.
5. Newman DJ, Cragg GM, Snader KM (2003) Natural products as sources of new drugs
over the period 1981–2002. J Nat Prod 66:1022–1037.
6. Welsch ME, Snyder SA, Stockwell BR (2010) Privileged scaffolds for library design and
drug discovery. Curr Opin Chem Biol 14:347–361.
7. Boldi AM (2004) Libraries from natural product-like scaffolds. Curr Opin Chem Biol
8. Taylor SJ, Taylor AM, Schreiber SL (2004) Synthetic strategy toward skeletal diversity
via solid-supported, otherwise unstable reactive intermediates. Angew Chem Int Ed
9. Lo MMC, Neumann CS, Nagayama S, Perlstein EO, Schreiber SL (2004) A library of
spirooxindoles based on a stereoselective three-component coupling reaction. J Am
Chem Soc 126:16077–16086.
10. Oguri H, Schreiber SL (2005) Skeletal diversity via a folding pathway: Synthesis of
indole alkaloid-like skeletons. Org Lett 7:47–50.
11. Díaz-Gavilán M, Galloway WRJD, O’Connell KMG, Hodkingson JT, Spring DR (2010)
Diversity-oriented synthesis of bicyclic and tricyclic alkaloids. Chem Commun
12. Bauer RA, DiBlasi CM, Tan DS (2010) The tert-butylsulfinamide lynchpin in transition
metal-mediated multiscaffold library synthesis. Org Lett 12:2084–2087.
13. Ortholand JY, Ganesan A (2004) Natural products and combinatorial chemistry: Back
to the future. Curr Opin Chem Biol 8:271–280.
14. Ferreira F, Botuha C, Chemla F, Pérez-Luna A (2009) tert-Butanesulfinimines: Structure,
synthesis, and synthetic applications. Chem Soc Rev 38:1162–1186.
15. DiBlasi CM, Macks DE, Tan DS (2005) An acid-stable tert-butyldiarylsilyl (TBDAS) linker
for solid-phase organic synthesis. Org Lett 7:1777–1780.
16. Ding CH, Chen DD, Luo ZB, Dai LX, Hou XL (2006) Highly diastereoselective synthesis
of N-tert-butylsulfinylpropargylamines through direct addition of alkynes to N-tert-
butanesulfinimines. Synlett 1272–1274.
17. Chen BL, Wang B, Lin GQ (2010) Highly diastereoselective addition of alkynylmagne-
sium chlorides to N-tert-butanesulfinyl aldimines: A practical and general access to
chiral α-branched amines. J Org Chem 75:941–944.
18. Kuduk SD, Marco CND, Pitzenberger SM, Tsou N (2006) Asymmetric addition reactions
of Grignard reagents to chiral 2-trifluoromethyl tert-butyl (Ellman) sulfinimine-
ethanol adducts. Tetrahedron Lett 47:2377–2381.
19. Hiroi K, Watanabe T (2001) Asymmetric Pauson–Khand reactions of chiral sulfina-
mides: Asymmetric synthesis of 3-azabicyclo[3.3.0]oct-5-en-7-one derivatives. Hetero-
20. Nandy JP, et al. (2009) Advances in solution- and solid-phase synthesis toward the
generation of natural product-like libraries. Chem Rev 109:1999–2060.
21. Jang HY, et al. (2005) Enantioselective reductive cyclization of 1,6-enynes via rhodium-
catalyzed asymmetric hydrogenation: C-C bond formation precedes hydrogen
activation. J Am Chem Soc 127:6174–6175.
22. Evans PA, Robinson JE, Baum EW, Fazal AN (2002) Intermolecular transition metal-
catalyzed [4 þ 2 þ 2] cycloaddition reactions: A new approach to the construction
of eight-membered rings. J Am Chem Soc 124:8782–8783.
23. Diver ST, Giessert AJ (2004) Enyne metathesis (enyne bond reorganization). Chem Rev
24. Schurer SC, Blechert S (1999) Sequences of yne-ene cross metathesis and Diels–Alder
cycloaddition reactions—Modular solid-phase synthesis of substituted octahydroben-
zazepinones. Synlett 1879–1882.
25. Schurer SC, Blechert S (1999) Synthesis of pseudo-oligosaccharides by a sequence
of yne-ene cross metathesis and Diels–Alder reaction. Chem Commun 1203–1204.
26. Yamamoto Y, et al. (2005) Cp*RuCl-catalyzed [2 þ 2 þ 2] cycloadditions of α,ω-diynes
with electron-deficient carbon-heteroatom multiple bonds leading to heterocycles.
J Am Chem Soc 127:605–613.
27. Young DD, Deiters A (2007) A general approach to chemo- and regioselective
cyclotrimerization reactions. Angew Chem Int Ed 46:5187–5190.
28. Tanaka K, Suzuki N, Nishida G (2006) Cationic rhodium(I)/modified-BINAP catalyzed
[2 þ 2 þ 2] cycloaddition of alkynes with nitriles. Eur J Org Chem 3917–3922.
29. Otake Y, Tanaka R, Tanaka K (2009) Cationic rhodium I ð Þ∕H8-BINAP complex catalyzed
[2 þ 2 þ 2] cycloadditions of 1,6- and 1,7-diynes with carbonyl compounds. Eur J Org
30. Senaiar RS, Young DD, Deiters A (2006) Pyridines via solid-supported [2 þ 2 þ 2] cyclo-
trimerization. Chem Commun 1313–1315.
31. Maeda K, Saito S (2007) Nickel-catalyzed [3 þ 2 þ 2] cycloaddition of ethyl
cyclopropylideneacetate and diynes. Synthesis of 7,6- and 7,5-fused bicyclic
compounds. Tetrahedron Lett 48:3173–3176.
32. Williams JM, et al. (1995) A new general method for preparation of N-methoxy-
N-methylamides. Application in direct conversion of an ester to a ketone. Tetrahedron
33. Schore NE (1991) The Pauson–Khand cycloaddition reaction for synthesis of cyclopen-
tenones. Org React 40:1–90.
34. Kubota H, Lim J, Depew KM, Schreiber SL (2002) Pathway development and pilot
library realization in diversity-oriented synthesis. Exploring Ferrier and Pauson–
Khand reactions on a glycal template. Chem Biol 9:265–276.
35. Suh WH, Choi M, Lee SI, Chung YK (2003) Rh(I)-Catalyzed asymmetric intramolecular
Pauson–Khand reaction in aqueous media. Synthesis 2003:2169–2172.
36. Sun Q, Zhou XM, Islam K, Kyle DJ (2001) Solid-phase synthesis of isoindolines via a
rhodium-catalyzed [2 þ 2 þ 2] cycloaddition. Tetrahedron Lett 42:6495–6497.
37. Young DD, SenaiarRS, Deiters A (2006) Solid-supported [2 þ 2 þ 2] cyclotrimerizations.
Chem—Eur J 12:5563–5568.
38. Senaiar RS, Teske JA, Young DD, Deiters A (2007) Synthesis of indanones via solid-
supported [2 þ 2 þ 2] cyclotrimerization. J Org Chem 72:7801–7804.
39. Witulski B, Stengel T, Fernández-Hernández JM (2000) Chemo- and regioselective
crossed alkyne cyclotrimerisation of 1,6-diynes with terminal monoalkynes mediated
by Grubbs’ catalyst or Wilkinson’s catalyst. Chem Commun 1965–1966.
40. Robak MT, Herbage MA, Ellman JA (2010) Synthesis and applications of tert-butane-
sulfinamide. Chem Rev 110:3600–3740.
41. Sauer WHB, Schwarz MK (2003) Molecular shape diversity of combinatorial libraries: A
prerequisite for broad bioactivity. J Chem Inf Comput Sci 43:987–1003.
42. Akella LB, DeCaprio D (2010) Cheminformatics approaches to analyze diversity in
compound screening libraries. Curr Opin Chem Biol 14:325–330.
43. Marcaurelle LA, et al. (2010) An aldol-based build/couple/pair strategy for the synth-
esis of medium- and large-sized rings: Discovery of macrocyclic histone deacetylase
inhibitors. J Am Chem Soc 132:16962–16976.
44. Pizzirani D, Kaya T, Clemons PA, Schreiber SL (2010) Stereochemical and skeletal
diversity arising from amino propargylic alcohols. Org Lett 12:2822–2825.
45. Rolfe A, Lushington GH, Hanson PR (2010) Reagent based DOS: A “Click, Click, Cyclize”
strategy to probe chemical space. Org Biomol Chem 8:2198–2203.
www.pnas.org/cgi/doi/10.1073/pnas.1015268108 Moura-Letts et al.