Influence of base and structure in the reversible covalent conjugate addition of thiol to polycyclic enone scaffolds

Article abstract of DOI:10.1021/ol400094k

The energetics of thiol addition and elimination reactions to bicyclic enones derived from an indole core structure were explored using ¹H NMR and density functional theory (DFT) calculations. The agreement between experiment and theory is exce

Full text of DOI:10.1021/ol400094k

ORGANIC
LETTERS
XXXX
Vol. XX, No. XX
000–000
Influence of Base and Structure in the
Reversible Covalent Conjugate Addition
of Thiol to Polycyclic Enone Scaffolds
Christopher J. Rosenker,‡ Elizabeth H. Krenske,*,† K. N. Houk,*,§ and Peter Wipf*,‡
School of Chemistry, University of Melbourne, VIC 3010, Australia, and Australian
Research Council Centre of Excellence for Free Radical Chemistry and Biotechnology,
Department of Chemistry and Biochemistry, University of California, Los Angeles,
California 90095, United States, and Department of Chemistry, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
e.krenske@uq.edu.au; houk@chem.ucla.edu; pwipf@pitt.edu
Received January 11, 2013
ABSTRACT
The energetics of thiol addition and elimination reactions to bicyclic enones derived from an indole core structure were explored using 1H NMR
and density functional theory (DFT) calculations. The agreement between experiment and theory is excellent, and the combined results reveal that
even minor changes in the conformation of the enone, substituents on the scaffold, and the use of different bases have a signficant influence on
product distribution. A potential application of these principles is in the rational design of new reversible covalent enzyme inhibitors.
Interest in irreversible inhibitors of enzymatic transfor-
mations or receptor mediated events has surged in recent
years, in part due to a better understanding of the mecha-
nism of action of biologically active natural products,
which often act as covalent modifiers.1 In addition to
R-halo carbonyl groups, oxiranes, acylamides, and vinyl
sulfones, enones are increasingly valuable as tunable cova-
lent inhibitors,2 and the potential use of enones as selective
thiol capture agents in enzyme active sites and allosteric
hot spots has encouraged mechanistic studies.3 Spectro-
scopic and computational methods have been developed
to rapidly classify thiol acceptors,4 and many synthetic
protocols are available to effect Michael reactions of sulfur
donors.5
In previous studies, we have identified thiol capture
pathways in epoxyketones and used reversible thiol addi-
tions to enones in natural products total synthesis.6,7 For
example, the synthesis of (ꢀ)-tuberostemonine 1 required
† University of Melbourne and Australian Research Council Centre of
Excellence for Free Radical Chemistry and Biotechnology. Current address:
School of Chemistry and Molecular Biosciences, University of Queensland,
Brisbane, QLD 4072, Australia.
(3) (a) van Axel Castelli, V.; Bernardi, F.; Dalla Cort, A.; Mandolini,
L.; Rossi, I.; Schiaffino, L. J. Org. Chem. 1999, 64, 8122. (b) Castelli, V.;
Dalla Cort, A.; Mandolini, L.; Reinhoudt, D.; Schiaffino, L. Eur. J. Org.
Chem. 2003, 627. (c) Krenske, E. H.; Petter, R. C.; Zhu, Z.; Houk, K. N.
J. Org. Chem. 2011, 76, 5074.
(4) (a) Suzuki, M.; Mori, M.; Niwa, T.; Hirata, R.; Furuta, K.;
Ishikawa, T.; Noyori, R. J. Am. Chem. Soc. 1997, 119, 2376. (b) Cusack,
K. P.; Arnold, L. D.; Barberis, C. E.; Chen, H.; Ericsson, A. M.; Gaza-
Bulseco, G. S.; Gordon, T. D.; Grinnell, C. M.; Harsch, A.; Pellegrini,
M.; Tarcsa, E. Bioorg. Med. Chem. Lett. 2004, 14, 5503. (c) Gacche, R.;
Khsirsagar, M.; Kamble, S.; Bandgar, B.; Dhole, N.; Shisode, K.;
Chaudhari, A. Chem. Pharm. Bull. 2008, 56, 897. (d) Avonto, C.;
Taglialatela-Scafati, O.; Pollastro, F.; Minassi, A.; Di Marzo, V.; De
Petrocellis, L.; Appendino, G. Angew. Chem., Int. Ed. 2010, 50, 467.
(5) (a) Enders, D.; Luettgen, K.; Narine, A. A. Synthesis 2007, 959.
(b) Breman, A. C.; Smits, J. M. M.; De Gelder, R.; Van Maarseveen,
J. H.; Ingemann, S.; Hiemstra, H. Synlett 2012, 23, 2195.
‡ University of Pittsburgh.
§ University of California.
(1) (a) Newman, D. J.; Cragg, G. M. J. Nat. Prod. 2012, 75, 311. (b)
Wipf, P.; Halter, R. J. Org. Biomol. Chem. 2005, 3, 2053. (c) Drahl, C.;
Cravatt, B. F.; Sorensen, E. J. Angew. Chem., Int. Ed. 2005, 44, 5788.
(2) For reviews and recent examples: (a) Amslinger, S. ChemMed-
Chem 2010, 5, 351. (b) Singh, J.; Petter, R. C.; Baillie, T. A.; Whitty, A.
Nat. Rev. Drug Discovery 2011, 10, 307. (c) Zheng, S.; Santosh Laxmi,
Y. R.; David, E.; Dinkova-Kostova, A. T.; Shiavoni, K. H.; Ren, Y.;
Zheng, Y.; Trevino, I.; Bumeister, R.; Ojima, I.; Wigley, W. C.; Bliska,
J. B.; Mierke, D. F.; Honda, T. J. Med. Chem. 2012, 55, 4837. (d)
Serafimova, I. M.; Pufall, M. A.; Krishnan, S.; Duda, K.; Cohen, M. S.;
€
Maglathlin, R. L.; McFarland, J. M.; Miller, R. M.; Frodin, M.;
Taunton, J. Nat. Chem. Biol. 2012, 8, 471.
(6) Wipf, P.; Jeger, P.; Kim, Y. Bioorg. Med. Chem. Lett. 1998, 8, 351.
r
10.1021/ol400094k
XXXX American Chemical Society

the differentiation of the alkene moieties in the six- and
seven-membered rings of intermediate 2, which was
accomplished by masking the enone as thioether 3
(Scheme 1).7,8a The azepine was then hydrogenated using
Wilkinson’s catalyst, and the enone was regenerated by a
DBU-mediated thiophenol elimination to give 4.8b
found to result in a ΔG of þ1.8 kcal/mol, while the thiol
elimination of 6 using DBU yielded a 5:6 ratio of g50:1 by
1H NMR with a ΔG e ꢀ3.8 kcal/mol. The thiol addition
reaction to provide thioether 8 provided a 2.0ꢀ2.3:1
ratio of stereoisomers and was favored by ΔG = ꢀ4.1
to ꢀ4.0 kcal/mol in the presence of catalytic Et3N or DBU.
Additionally, thiol elimination of 8 to afford 7 was un-
favorable by þ1.0 kcal/mol using Et3N, but favorable by
e ꢀ3.8 kcal/mol in the presence of DBU.
Scheme 1. Thiol Addition/Elimination in the Synthesis of
Tuberostemonine (1)
We were intrigued by the ability to move the equilibrium
between enone 2 and β-thiophenylketone 3 back to en-
one 4, but we could only speculate about the influence
of conformational changes in the tricycle (azepine vs
azepane) or the effect of base (Et3N vs DBU) in this con-
version. Accordingly, we explored, experimentally and
computationally, the energetics of several related indole
derived enones. While the equilibrium constant was of
major interest to us in the current study, we have studied
transition states for related simpler systems elsewhere.3c
The barriers of addition of thiolate to enones are quite
low in aprotic solvents. The amine bases serve to form
thiolates, and the ammonium cations then protonate the
enolate generated by thiolate addition to enone.9
Thiophenol addition reactions were performed in the
presence of a slight excess of thiol (1.15 equiv) and catalytic
base (0.09 equiv of Et3N or DBU), while the thiol elimina-
tions used stoichiometric base (1.06 equiv of Et3N or DBU).
The ratio of starting material to product was analyzed by
1H NMR and used to determine the ΔG of the thiol
addition/elimination processes.
Figure 1. Thiol addition/elimination reactions with enones 5 and
7 using Et3N and DBU.
Addition of thiophenol to tricyclic enone 2 was highly
favorable and exceeded the limits of detection by 1H NMR
(eꢀ4.6 kcal/mol) using either catalytic Et3N or DBU
(Figure 2). Thiol elimination in thioether 3 was unfavor-
able by þ3.4 kcal/mol in the presence of Et3N; however,
the thiol elimination proved favorable by e ꢀ2.6 kcal/mol
in the presence of DBU.
The determination of the equilibrium in the addition
of thiophenol to bicyclic enone 510 in the presence of
either Et3N or DBU gave a ΔG e ꢀ4.6 kcal/mol for this
conversion (Figure 1). Thiol elimination from the major
stereoisomer of thioether 6 in the presence of Et3N was
(7) (a) Wipf, P.; Rector, S. R.; Takahashi, H. J. Am. Chem. Soc. 2002,
124, 14848. (b) Wipf, P.; Spencer, S. R. J. Am. Chem. Soc. 2005, 127, 225.
(8) (a) De Groot, A.; Peperzak, R. M.; Vader, J. Synth. Commun.
1987, 17, 1607. (b) Asaoka, M.; Shima, K.; Fujii, N.; Takei, H. Tetra-
hedron 1988, 44, 4757.
(9) For other studies of the mechanism of reversible sulfa-Michael
reactions, see: (a) Dmuchovsky, B.; Vineyard, B. D.; Zienty, F. B. J. Am.
Chem. Soc. 1964, 86, 2874. (b) Friedman, M.; Cavins, J. F.; Wall, J. S.
J. Am. Chem. Soc. 1965, 87, 3672. (c) De Maria, P.; Fini, A. J. Chem. Soc.
(B) 1971, 2335.
Figure 2. Thiol addition/elimination reactions with enone 2
using Et3N and DBU.
(10) For additional examples of conjugate addition reactions with
enone 5, see: (a) Wipf, P.; Li, W. J. Org. Chem. 1999, 64, 4576. (b) Wipf,
P.; Mareska, D. A. Tetrahedron Lett. 2000, 41, 4723.
Et3N and DBU catalyzed thiophenol additions to tri-
cyclic enone 4 were favorable with a ΔG e ꢀ4.6 kcal/mol
Org. Lett., Vol. XX, No. XX, XXXX
B

(Figure 3). The thiol elimination reaction of 9 was un-
favorable by 2.3 kcal/mol using Et3N and favorable
by ꢀ2.9 kcal/mol using DBU.
toward the addition of PhSH than the OH- and OBz-
substituted enones 5 and 7. The gas-phase ΔG values
predict the same trend, although the reactivities of the
more conformationally flexible enones 5 and 7 appear to
diminish somewhat owing to the larger predicted values
of ꢀTΔS. We explored the use of several solvation models
to estimate the free energies in dichloromethane and found
that SMD15 solvation energies computed at the B3LYP/
6-31G(d) level gave the best agreement with experiment.
The solution-phase ΔG values are 2ꢀ3 kcal/mol higher
than those in the gas phase and underestimate the experi-
mental reactivities. This is likely due to the tendency of
continuum solvation to overestimate solute entropies.
Among the base-catalyzed thiol additions to enones
investigated, our experiments show that additionsof PhSH
to enones 5, 2, and 4 are highly favorable. The thiol
addition to enone 7 is slightly less favorable, possibly due
to the increased steric bulk placed on the tertiary alcohol
bythebenzoylgroup, althoughthecomputed energeticsdo
not fully capture this decreased reactivity.
Figure 3. Thiol addition/elimination reactions with enone 4
using Et3N and DBU.11
Computed energetics for the deprotection of the
thioethers by stoichiometric Et3N or DBU are presented
in Table 2. The structure of the byproduct ion pair
Et3NHþPhSꢀ could not be located in the gas phase, and
therefore the structures of both ion pairs (Et3NHþPhSꢀ
and DBUHþPhSꢀ) were optimized in solvent.
We used density functional theory calculations12 to
analyze the effect of base on the thiol addition/elimination
equilibria. Geometries of the enones and their PhSH
adducts were optimized at the B3LYP/6-31G(d) level,13
and single-point energies were then computed at the M06-
2X/6-311G(2d,p) level.14,3c The theoretical values of ΔH
and ΔG for the addition of thiophenol to the four enones
are shown in Table 1.
Table 2. Computed Thermodynamics for Elimination of PhSH
from Enone Adducts by Stoichiometric Et3N or DBU [kcal/mol]a
Table 1. Computed Thermodynamics for Additions of PhSH to
Enones [kcal/mol]a
ΔH
ΔG
ΔG
ΔG
adduct
enone
base
(gas)
(gas)
(soln)
(expt)
6
5
Et3N
DBU
Et3N
DBU
Et3N
DBU
Et3N
DBU
21.0
19.0
21.1
19.1
23.1
21.1
23.1
21.1
17.1
15.8
17.1
15.7
20.4
19.1
20.3
19.0
1.1
ꢀ2.7
1.1
1.8
eꢀ3.8
1.0
ΔH
ΔG
ΔG
ΔG
enone
adduct
(gas)
(gas)
(soln)
(expt)
8
3
9
7
2
4
ꢀ2.7
5.1
eꢀ3.8
3.4
5
7
2
4
6
8
3
9
ꢀ18.1
ꢀ18.1
ꢀ20.1
ꢀ20.2
ꢀ2.9
ꢀ2.9
ꢀ6.3
ꢀ6.2
ꢀ0.1
0.0
eꢀ4.6
ꢀ4.1, ꢀ4.0
eꢀ4.6
1.4
eꢀ2.6
2.3
ꢀ4.1
5.0
ꢀ3.9
eꢀ4.6
1.2
ꢀ2.9
a M06-2X/6-311G(2d,p)//B3LYP/6-31G(d), 1 mol/L, 298.15 K,
kcal/mol; solution-phase data include SMD solvation energies in
CH2Cl2 computed at the B3LYP/6-31G(d) level.
a M06-2X/6-311G(2d,p)//B3LYP/6-31G(d), 1 mol/L, 298.15 K,
kcal/mol; solution-phase data include SMD solvation energies in
CH2Cl2 computed at the B3LYP/6-31G(d) level.
The computed values of ΔH predict that the tricyclic
enones 2 and 4 should be considerably more reactive
The calculated ΔG values for the deprotection reactions
in solution lie within ∼1 kcal/mol of experiment for
bicyclic thioethers 6 and 8 but are 2ꢀ4 kcal/mol too
positive for tricyclic 3 and 9. Theory predicts that the
elimination of PhSH from any thioether by stoichiometric
DBU should be 3.8 kcal/mol more favorable than
(11) During the thiol elimination of 9 in the presence of DBU, enone 4
epimerizes to a 2.5:1 mixture of epimers R to the carbonyl group.
(12) Calculations were performed with Gaussian 09 (Frisch, M. J.,
et al.); see Supporting Information.
(13) (a) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785. (b)
Becke, A. D. J. Chem. Phys. 1993, 98, 1372. (c) Becke, A. D. J. Chem.
Phys. 1993, 98, 5648.
(14) (a) Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215.
(b) Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157.
(15) Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B
2009, 113, 6378.
Org. Lett., Vol. XX, No. XX, XXXX
C

deprotection by Et3N, in good agreement with the experi-
mental measurements. The experiment shows the DBU
deprotections to be 4.8ꢀ6.0 kcal/mol more favorable than
the corresponding Et3N deprotections.
substitution pattern is an important consideration in the
design of enones as tunable covalent modifiers of enzyme
thiol groups.
The investigations described herein demonstrate that
the conversion of a substituted cyclohexenone to its
PhSH adduct is a weakly exergonic reaction, and the
elimination of the thiol from the adduct depends on the
strength of the base. In an ion-pairing solvent such as
CH2Cl2, the equilibrium Base þ RSH / BaseHþRSꢀ
determines whether elimination of the thiol is favored or
not, and the use of DBU rather than Et3N in CH2Cl2
provides approximately 4 kcal/mol of driving force. In a
Acknowledgment. This work was supported by the
National Science Foundation (CHE 1059084 to K.N.H.),
Australian Research Council (DP0985623 to E.H.K.),
ARC Centre of Excellence for Free Radical Chemistry
and Biotechnology (funding to E.H.K.), and the National
Institutes of Health (GM067082 to P.W.). Computing
resources were provided by the National Computational
Infrastructure National Facility (Australia) and the
University of Melbourne.
polar solvent, the relevant equilibrium is Base þ Hþ
/
BaseHþ. The pKa values of DBU and Et3N in DMSO,16
for example, indicate a 4.1 kcal/mol greater driving force
for deprotection when using DBU. Accordingly, the fine
control exerted over the enone/thioether equilibrium by
base strength and, in particular, the effect of the enone
Supporting Information Available. Experimental pro-
cedures and spectral data for all new compounds,
including copies of 1H and 13C NMR spectra, and com-
putational data. This material is available free of charge
via the Internet at http://pubs.acs.org.
(16) pKa values in DMSO: DBUHþ 12, TEAHþ 9.
The authors declare no competing financial interest.
D
Org. Lett., Vol. XX, No. XX, XXXX