Synthesis of a tetrahydronaphthyridine spiropyrimidinetrione dna gyrase inhibiting antibacterial agent - Differential substitution at all five carbon atoms of pyridine.

Article abstract of DOI:10.1021/ol503256h

The synthesis of (-)-1, a potent antibacterial agent, was achieved stereoselectively in nine steps from readily available starting materials. Directed metalations were developed to assemble a pentasubstituted pyridine with appropriately positioned aldehyde and dimethylmorpholine substituents for a key tertiary amino effect reaction (T-reaction) that led to the spirocylic architecture. Ultimately, (-)-1 was isolated as the thermodynamically most favored stereoisomer.

Full text of DOI:10.1021/ol503256h

Letter
pubs.acs.org/OrgLett
Synthesis of a Tetrahydronaphthyridine Spiropyrimidinetrione DNA
Gyrase Inhibiting Antibacterial Agent - Differential Substitution at all
Five Carbon Atoms of Pyridine.
Gregory S. Basarab,* Vincent Galullo, Nancy DeGrace, Sheila Hauck, Camil Joubran,
and Steven S. Wesolowski
Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
S
* Supporting Information
ABSTRACT: The synthesis of (−)-1, a potent antibacterial agent, was
achieved stereoselectively in nine steps from readily available starting
materials. Directed metalations were developed to assemble a pentasub-
stituted pyridine with appropriately positioned aldehyde and dimethylmor-
pholine substituents for a key tertiary amino effect reaction (T-reaction)
that led to the spirocylic architecture. Ultimately, (−)-1 was isolated as the thermodynamically most favored stereoisomer.
ompound 1 (Figure 1) is a potent antibacterial developed
with an ortho-morpholinyl benzaldehyde.4,7 Compound 1 with
the tetrahydronaphthyridine scaffold, isosteric to the tetra-
hydroquinoline core of 2, presented synthetic challenges for the
specific substitutions called for by the medicinal chemistry SAR.
Toward this end, a series of pyridines were required with a
variety of substituents at the 4-, 5-, and 6-positions, an aldehyde
at the 2-position, and an amine at the 3-position to set up the
T-reaction. Herein we report the assembly of pyridine
intermediates with five different substituents through selective
pyridine metalation reactions and their conversions to both
( )-1 and (−)-1.
C
in a medicinal chemistry optimization program1 to
Figure 1. SPT antibacterials 1, 2, and 3.
3,5-Difluoropyridine-2-carboxylic acid 4 was envisioned as
the starting point toward the synthesis of a 3-amino-2-pyridine
aldehyde to set up the final T-reaction. Treating 4 with cis-
dimethylmorpholine in dioxane at reflux afforded 6 in high
yield (Scheme 1). SNAr displacement of fluoride from the 2-
improve upon the properties of PNU-286607 (2), a DNA
gyrase inhibitor from Pharmacia-Upjohn showing Gram-
positive and fastidious Gram-negative antibacterial activity.2,3
These and benzisoxazole 34 represent an emerging spiropyr-
imidinetrione (SPT) class of agents that share the DNA gyrase
mode-of-action with fluoroquinolone antibacterials, but differ in
their mode of inhibition. Among the bacteria susceptible to the
SPT class are Staphylococcus aureus (including MRSA,
methicillin resistant S. aureus), Streptococcus pneumoniae,
Streptococcus pyogenes, and Haemophilus influenzae. The
spirocyclic architecture of 1, 2, and 3 is constructed via the
tertiary amino effect reaction (T-reaction) in which a
substituent ortho to an N,N-dialkylaniline induces an oxidation
of one of the aniline alkyl groups.5 Reinhoudt first reported a T-
Scheme 1. Traceless SNAr Reaction
reaction wherein Knovenagel adducts of ortho-dialkylaniline
̈
carboxaldehydes undergo the internal redox reaction ([1,5]-
hydride shift) followed by Mannich cyclization to the
tetrahydroquinoline ring (Figure 2).6 The syntheses of 2 and
and 4-positions of pyridines occurs straightforwardly due to the
inherent electronic activation.8 However, SNAr displacement of
3-pyridyl halides is electronically disfavored requiring an
activating group ortho or para to the leaving halide. In the
conversion of 4 to 6, the carboxylate served as a traceless
activating group for such displacement. Alternatively, one might
3 used barbituric acid as the Knovenagel condensation partner
̈
Received: November 13, 2014
Figure 2. Tertiary amino effect reaction.
© XXXX American Chemical Society
A
dx.doi.org/10.1021/ol503256h | Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
have considered palladium catalyzed amination of 3-bromo-5-
fluoropyridine to 6,9 but the traceless activation reaction is
simple to run and does not incur the expense and purification
issues associated with transition metal catalysis. Displacement
of the 3-position fluorine with the morpholine at rt afforded
carboxylic acid 5, which upon heating underwent decarbox-
ylation to afford 6. Thermal decarboxylation of 2-picolinic acids
is known, but proceeds at a considerably higher temperature
without the amine substituent.10 It is noteworthy and useful
(see below) that the selectivity of room temperature displace-
ment with morpholine is 30:1 for the 3- over the 5-position
fluorine atom due to the carboxylate directing the morpholine
nucleophile similar to reported amine displacements of 2,4-
difluorobenzoic acids.11
Scheme 3. Synthesis of T-Reaction Precursor
Continuing the synthetic sequence from 6 (Scheme 2), a
series of directed lithiations were carried out. Though lithiation
Scheme 2. Sequential Lithiations of the Pyridine Ring
avenues to incorporate other functionality through either SNAr
chemistry or cross-coupling methodology. Clearly, a variety of
electrophiles could be envisioned for reaction with lithium
intermediates in the sequences, expanding again the range of
substituents that can be introduced onto the pyridine ring.
With 13 in hand, the T-reaction was carried out at 80 °C for
20 h leading to ( )-1 as the predominate product (>95%) with
trace 14 (<1%) suggested by 19F NMR. The two optical
antipodes of ( )-1 were separated by chiral SFC purification,
and biological activity (inhibition of DNA gyrase and bacterial
growth, Scheme 3) resided with (−)-1 in line with the absolute
configurations previously reported for (−)-2 and (−)-3.
Notably, the MRSA S. aureus strain was also resistant to
fluoroquinolone antibacterials including ciprofloxacin (MIC >
50 μM versus MIC = 0.78 for MSSA, methicillin susceptible S.
aureus). Beyond correlation of activity and rotation with (−)-2
and (−)-3, the absolute configuration of (−)-1 was also
established by an enantiospecific synthesis (see below).
Running the T-reaction with 13 for 30 min afforded a 3.4:1
ratio of ( )-14 and ( )-1 (see Table 1). Compound 14 was
stable as a solid at rt as a mixture with 1; however, its isolation
by chromatography (normal or reversed phase HPLC or SFC)
could not be achieved due to facile epimerization to 1. The
configuration of 14 correlated with the minor kinetic material
observed during the preparation of ( )-2,7 also not isolated
due to configurational instability. Running the T-reaction at
120 °C for 4 h afforded a 28:5.5:1 mixture of ( )-1, ( )-15,
and ( )-16 as determined by 19F and 1H NMR, the
thermodynamic mixture of diastereomers. A trace (∼1%) of
the fourth possible diastereomer ( )-14 was suggested by 19F
NMR (Table 1).
of 6 can occur at the 2-, 4-, or 6-positions, the fluorine atom
was presumed to dominate the morpholine as an ortho-
directing group. Lithiations of 3-fluoropyridine can occur
selectively at either the 2- or 4-position depending on reaction
conditions with thermodynamic control (LDA in THF)
favoring the 4-position.12 Less certain was whether the
morpholine ring of 6 would enhance the lithiation at the
pyridine 4-position or, through steric hindrance, drive lithiation
to the 2-position. In any event, treatment of 6 with LDA
followed by chlorination showed predominant lithiation at the
4-position to give 7. Subsequent lithiation of 7 occurred
selectively next to the fluorine atom as determined by reaction
with a brominating reagent to afford 8, in line with the fluorine
operating as a better ortho-directing group than the morpholine
substituent. Next, treatment of 8 with LDA followed by DMF
to install the aldehyde did not lead to the expected 9, but rather
to 10, the product of bromine migration.13 Presumably,
lithiation proceeded adjacent to the morpholine ring, and
bromine migration led to the thermodynamically favored
position of lithium next to the fluorine atom.
To circumvent the bromine migration, a modified sequence
was developed to 9 for subsequent conversion to ( )-1
(Scheme 3). Carboxylic acid 5, the product of room
temperature fluorine displacement (Scheme 1), was reduced
to the alcohol and protected as the DPS ether 11. As in Scheme
2, chlorine was introduced onto the pyridine 4-position and
bromine onto the 6-position to afford 12. Deprotection of the
alcohol and oxidation led to 9 utilized in a Stille cross-coupling
with 3-pyridylstannane to give 13. Overall the sequences for 6
to 10 and 5 to 9 demonstrated that efficient and selective
functionalization of the pyridine ring can be achieved at all five
carbon positions. Compounds 9 and 10 are notable in that five
different heavy atom types are incorporated at the five
positions, perhaps unprecedented. The fluorine, chlorine, and
bromine atoms along the synthetic sequences to 9 and 10 offer
An enantioselective synthesis of (−)-1 was achieved starting
with the treatment of 4 with chiral (R,R)-dimethylmorpholine
rather than meso-cis-dimethylmorpholine (Scheme 4) and
continuing in a sequence analogous to that for ( )-1.
Reduction of acid 17 and protection of the alcohol to 18 was
followed by chlorination and bromination to 19. Deprotection
to the alcohol, oxidation to the aldehyde, and Stille cross-
B
dx.doi.org/10.1021/ol503256h | Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
Table 1. Distribution of T-Reaction Stereoisomers
a
ND = not detected.
The relative stereochemistry for (−)-1 using the (R,R)-
dimethylmorpholine of Table 1 was the same as that using the
meso-dimethylmorpholine for ( )-1, which had been rational-
ized from the mechanism of the T-reaction in the reported
synthesis of 2.7 Under thermodynamic equilibrating conditions
Scheme 4. Chiral Synthesis of (−)-1 and Stereoisomers
after the Knovenagel condensation and [1,5]-hydride transfer,
̈
the methyl group adjacent to the transient iminium species can
epimerize as diagrammed in Figure 3. In line with the previous
coupling afforded 20. Heating 20 with barbituric acid at 120 °C
for 4 h led to the 28:5.5:1 ratio of (−)-1 to (−)-15 to (−)-16,
the thermodynamic distribution of isomers. Again, a 1% trace of
14 (rotation unknown) could be inferred from the 19F NMR.
Running the T-reaction for only 30 min at 80 °C (non-
thermodynamic conditions) led to a separable 1.4:1 mixture of
(−)-16 to (−)-15 (Table 1). Treating purified (−)-1, (−)-15,
or (−)-16 at 120 °C for 4 h returned the same 28:5.5:1 ratio
with perhaps a trace of 14. This ratio differed from that seen
during the preparations of (−)-2 and (−)-3 where closer to 9:1
ratios were observed for only the two predominate diaster-
eomers.4,7 The configurations of (−)-1, ( )-14, (−)-15, and
(−)-16 were determined by detailed NOESY/ROESY analysis.
Notably, the conformation for (−)-15 from the NMR analysis
differed significantly from that reported for the analogous
minor diastereomer seen under thermodynamic equilibrating
conditions during the synthesis of (−)-3. The morpholine ring
of (−)-15 adopts a twisted boat conformation with equatorial
orientations for the two methyl groups leading to a (1,3)-diaxial
NOE for C1 and C4-morpholine H-atoms. The analogous
diastereomer of (−)-3 was shown to exist in a chair
conformation with one methyl group being axial and the
other being equatorial.4 The steric influences of chlorine versus
fluorine and of the pyridine nitrogen lone pair versus C−H
account for the different conformations as well as the difference
in diastereomer distribution at thermodynamic equilibrium.
Figure 3. Mechanism of diastereomer equilibration; relative energies
of formation.
report for the synthesis of 2, an equilibrium is established with
retro-Mannich opening and closing of the tetrahydronaphthy-
ridine ring. Using a higher 120 °C temperature for the T-
reaction versus 80 °C enabled epimerization toward establish-
ing thermodynamic equilibration sampling for all possible
diastereomers. The iminium species can collapse by cyclization
above and below the morpholine ring with the two methyl
groups either cis or trans to one another. Of the four possible
diastereomers, (−)-1 and (−)-15 prevail being lowest in energy
(see below). The T-reaction with 20 and barbituric acid at 80
°C approached the thermodynamic equilibrium over 4 days
indicating that 15 isomerizes more easily than 1. By contrast,
running the T-reaction with meso-13 at 80 °C did not
equilibrate to a mixture of ( )-1 and ( )-15 even after
heating for multiple days, but rather mainly ( )-1 was isolated.
C
dx.doi.org/10.1021/ol503256h | Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
Hurd, A. R.; Barbachyn, M. R. Antimicrob. Agents Chemother. 2008, 52,
2806−2812.
Nor does heating purified (−)-1 at 80 °C for longer periods of
time lead to isomerization to (−)-15. Higher temperatures are
necessary to epimerize the methyl of 1 relative to 15, consistent
with the former being more stable than the latter. Shorter,
nonthermodynamic 80 °C conditions afforded materials
without epimerization of the methyl substituent. Thus, meso-
13 led to 1 and 14 maintaining the cis-dimethylmorpholine
configurations at 80 °C, while chiral 20 formed the two trans-
dimethylmorpholine diastereomers.
To corroborate the experimental results, the ground state
energies of the four possible diastereomers were determined by
DFT (def2-TZVPP/M06-2X) calculation, and the relative
values in a water solvent model are shown in Figure 3. See
Supporting Information (Table S1) for full set of computations
in the gas phase and in solvent models using various basis sets
and density functionals. The thermodynamically favored
diastereomer 1 was used as a reference with the three other
diastereomers calculated to have higher energies. Compound
15 was the next most prevalent diastereomer from thermody-
namic equilibration corresponding to the next lowest ground
state energy from the calculations. The conformations for the
four diastereomers calculated by DFT correlated with those
determined by NMR analysis (see Supporting Information, S1
p 29−41).
In conclusion, we are aware of only one other report (other
than a patent application related to this work)1 wherein
pyridines were utilized in the T-reaction to afford a tetra-
hydronaphthyridine scaffold.14 Examples of the T-reaction with
other heterocycles have included quinolines, pyrazoles,
pyridazines, indoles, and uracils.15 The sequences developed
herein for the syntheses of ( )-1 and (−)-1 offer new strategies
to fully substitute the pyridine ring. Diastereomer distribution
of the T-reaction was shown to depend on substrate
stereochemistry and reaction temperature in the context of
whether thermodynamic equilibration is reached.
(3) (a) Barbachyn, M. R.; Dobrowolski, P. J.; Hagen, S. E.;
Heimbach, T. H.; Hurd, A. R.; Johnson, T. A.; McNamara, D. J.;
Ruble, J. C.; Sherry, D. A.; Thomasco, L. M.; Toogood, P. L. PCT
Patent WO 2006120563 A2, 2006. (b) Barbachyn, M. R.;
Dobrowolski, P. J.; Hurd, A. R.; McNamara, D. J.; Palmer, J. R.;
Romero, A. G.; Ruble, J. C.; Sherry, D. A.; Thomasco, L. M.; Toogood,
P. L. PCT Patent WO 2004031195 A1, 2004. (c) Johnson, T. A.;
Sherry, D. A.; McNamara, D. J.; Toogood, P. L. PCT Patent WO
2007072151, 2007.
(4) Basarab, G. S.; Brassil, P.; Doig, P.; Galullo, V.; Haimes, H. B.;
Kern, G.; Kutschke, A.; McNulty, J.; Schuck, V. J. A.; Stone, G.;
Gowravaram, M. J. Med. Chem. 2014, 57, 9078−9095.
(5) Meth-Cohn, O.; Suschitzky, H. In Heterocycles by Ring Closure of
Ortho-Substituted t-Anilines (The t-Amino Effect); Advances in
Heterocyclic Chemistry; Katritzky, A.R., Boulton, A. J., Eds.; Academic
Press: 1972; Vol. 14, pp 211−278.
(6) (a) Visser, G. W.; Verboom, W.; Benders, P. H.; Reinhoudt, D.
N. J. Chem. Soc., Chem. Commun. 1982, 669−671. (b) Verboom, W.;
Reinhoudt, D. N.; Visser, R.; Harkema, S. J. Org. Chem. 1984, 49,
269−276.
(7) Ruble, J. C.; Hurd, A. R.; Johnson, T. A.; Sherry, D. A.;
Barbachyn, M. R.; Toogood, P. L.; Bundy, G. L.; Graber, D. R.;
Kamilar, G. M. J. Am. Chem. Soc. 2009, 131, 3991−3997.
(8) (a) Schlosser, M.; Bobbio, C.; Rausis, T. J. Org. Chem. 2005, 70,
2494−2502. (b) Stroup, B. W.; Szklennik, P. V.; Forster, C. J.;
Serrano-Wu, M. Org. Lett. 2007, 9, 2039−2042.
(9) (a) Navarro, O.; Marion, N.; Mei, J.; Nolan, S. P. Chem.Eur. J.
2006, 12, 5142−5148. (b) Samblanet, D. C.; Schmidt, J. A. R. J.
Organomet. Chem. 2012, 720, 7−18. (c) Schrimpf, M. R.; Sippy, K. B.;
Daanen, J. F.; Ryther, K. B.; Ji, J. PCT Patent WO 2000071534 A1,
2000.
(10) Dunn, G. E.; Thimm, H. F. Can. J. Chem. 1977, 55, 1342−1347.
(11) Wendt, M. D.; Kunzer, A. R. Tetrahedron Lett. 2010, 51, 641−
644.
(12) (a) Queguiner, G.; Marsais, F.; Snieckus, V.; Epsztajn, J. In
Directed Metalation of Pi-Deficient Azaaromatics: Strategies of
Functionalization of Pyridines, Quinolines, and Diazines; Advances in
Heterocyclic Chemistry; Katrizky, A. R., Ed.; Academic Press: 1991; Vol.
ASSOCIATED CONTENT
52, pp 187−304. (b) Mongin, F.; Queg
́
uiner, G. Tetrahedron 2001, 57,
■
4059−4090.
S
* Supporting Information
(13) (a) Stanetty, P.; Schnuerch, M.; Mereiter, K.; Mihovilovic, M. D.
J. Org. Chem. 2005, 70, 567−574. (b) Schnuerch, M. In Recent Progress
on the Halogen Dance Reaction on Heterocycles; Iskra, J., Ed.; Topics in
Heterocyclic Chemistry, Halogenated Heterocycles; Springer-Verlag:
New York, 2012; Vol. 27, pp 185−218.
Experimental procedures, analytical data, computational
methods, and models of the four possible diastereomers. This
material is available free of charge via the Internet at http://
pubs.acs.org.
(14) Ojea, V.; Muinelo, I.; Figueroa, M. C.; Ruiz, M.; Quintela, J. M.
Synlett 1995, 1995, 622−624.
(15) (a) D’yachenko, E. V.; Glukhareva, T. V.; Dyudya, L. V.; Eltsov,
O. V.; Morzherin, Y. Y. Molecules 2005, 10, 1101−1108. (b) Rabong,
C.; Hametner, C.; Mereiter, K.; Kartsev, V. G.; Jordis, U. Heterocycles
2008, 75, 799−838.
AUTHOR INFORMATION
■
Corresponding Author
*E-mail: greg.basarab@astrazeneca.com.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
The authors are grateful for synthesis of intermediates by
Biocon, LTD and GVKBio.
REFERENCES
■
(1) Basarab, G. S.; Dumas, J.; Hill, P. PCT Patent WO 2009004382
A2, 2009.
(2) Miller, A. A.; Bundy, G. L.; Mott, J. E.; Skepner, J. E.; Boyle, T.
P.; Harris, D. W.; Hromockyj, A. E.; Marotti, K. R.; Zurenko, G. E.;
Munzner, J. B.; Sweeney, M. T.; Bammert, G. F.; Hamel, J. C.; Ford,
C. W.; Zhong, W.; Graber, D. R.; Martin, G. E.; Han, F.; Dolak, L. A.;
Seest, E. P.; Ruble, J. C.; Kamilar, G. M.; Palmer, J. R.; Banitt, L. S.;
D
dx.doi.org/10.1021/ol503256h | Org. Lett. XXXX, XXX, XXX−XXX