Structure guided lead generation for M. tuberculosis thymidylate kinase (Mtb TMK): discovery of 3-cyanopyridone and 1,6-naphthyridin-2-one as potent inhibitors.

M. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through which we discovered two novel classes of inhibitors, 3-cyanopyridones and 1,6-naphthyridin-2-ones, respectively. We describe three cyanopyridone subseries that arose during our hit to lead campaign, along with cocrystal structures of representatives with Mtb TMK. Structure aided optimization of the cyanopyridones led to single digit nanomolar inhibitors of Mtb TMK. Fragment based lead generation, augmented by crystal structures and the SAR from the cyanopyridones, enabled us to drive the potency of our 1,6-naphthyridin-2-one fragment hit from 500 µM to 200 nM while simultaneously improving the ligand efficiency. Cyanopyridone derivatives containing sulfoxides and sulfones showed cellular activity against M. tuberculosis. To the best of our knowledge, these compounds are the first reports of non-thymidine-like inhibitors of Mtb TMK.

(Z)-Ethyl 2-cyano-3-(1H-imidazol-2-yl)acrylate.

The crystal structure of the title compound, C9H9N3O2, features N-H⋯N and C-H⋯O inter-actions. The N-H⋯N inter-action generates a chain running along the a axis and the C-H⋯O inter-action generates a chain along the c axis. An intra-molecular C-H⋯O inter-action is also observed.

(E)-Ethyl 2-cyano-3-(furan-2-yl)acrylate.

There are two independent mol-ecules in the asymmetric unit of the title compound, C(10)H(9)NO(3), in both of which, all non-H atoms except for the methyl C atom lie nearly in the same plane [maximum deviations = 0.094 (3) and 0.043 (2) Å]. In the crystal, each independent mol-ecules is linked by pairs of C-H⋯O inter-actions, generating inversion dimers with R(2) (2)(10) ring motifs.

1-(3,5-Dichloro-phen-yl)-1H-1,2,3,4-tetra-zole.

In the title compound, C(7)H(4)Cl(2)N(4), the dihedral angle between the tetra-zole and benzene rings is 17.2 (2)°. In the crystal, C-H⋯N inter-actions link the mol-ecules into a flattened helical chain along the b axis.

(E)-Ethyl 2-cyano-3-(1H-pyrrol-2-yl)acrylate.

All the non-H atoms of the title compound, C(10)H(10)N(2)O(2), are nearly in the same plane with a maximum deviation of 0.093 (1) Å. In the crystal, adjacent mol-ecules are linked by pairs of inter-molecular N-H⋯O hydrogen bonds, generating inversion dimers with R(2) (2)(14) ring motifs.

8-Formyl-4-methyl-2-oxo-2H-chromen-7-yl 4-methyl-benzenesulfonate.

In the title compound, C(18)H(14)O(6)S, the coumarin ring system is nearly planar, with a maximum out-of-plane deviation of 0.032 (2) Å. The dihedral angle between the benzene ring and the coumarin ring system is 32.41 (8)°. The crystal packing is stabilized by inter-molecular C-H⋯O inter-actions, generating C(8), C(10) and C(11) chains and an R(2) (2)(10) ring. The formyl group is disordered over two sets of sites, with occupancies of 0.548 (5) and 0.452 (5).

8-[(Hydrazinyl-idene)meth-yl]-4-methyl-2-oxo-2H-chromen-7-yl 4-methyl-benzene-sulfonate.

In the title compound, C(18)H(16)N(2)O(5)S, the coumarin ring system is nearly planar, with a maximum out-of-plane deviation of 0.078 (1) Š(r.m.s. deviation = 0.046 Å). The dihedral angle between the coumarin ring system and the toluene ring (r.m.s. deviation = 0.004 Å) is 2.77 (1)°. The crystal packing is stabilized by C-H⋯O and N-H⋯O inter-molecular hydrogen bonds generating C(8), C(9) and C(11) chains and R(2) (2)(14), R(2) (2)(23) and R(4) (3)(13) ring graph sets.

(Z)-2-[2-(4-Methyl-benzyl-idene)hydrazin-yl]pyridine.

Mol-ecules of the title compound, C(13)H(13)N(3), are essentially planar (r.m.s. deviation for all non-H atoms = 0.054 Å). The dihedral angle between the two aromatic rings is 6.33 (5)°. In the crystal, pairs of centrosymmetrically related mol-ecules are linked through N-H⋯N hydrogen bonds, forming N-H⋯N dimers with graph-set motif R(2) (2)(8).

1-(2-Azido-acet-yl)-3-methyl-2,6-diphenyl-piperidin-4-one.

In the title compound, C(20)H(20)N(4)O(2), the piperidine ring adopts a distorted boat conformation. The two phenyl rings form dihedral angles of 82.87 (1) and 84.40 (1)° with respect to the piperidine ring. The crystal packing is stabilized by inter-molecular C-H⋯O and C-H⋯N inter-actions.

Ethyl 4-(3-bromo-phen-yl)-6-methyl-2-oxo-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

In the title compound, C(14)H(15)BrN(2)O(3), the dihydro-pyrimidin-one ring adopts a boat conformation. In the crystal, adjacent mol-ecules are linked through N-H⋯O hydrogen bonds forming an R(2) (2)(8) ring motif and generating a zigzag chain extending in [010].

Synthesis and biological activities of some new fluorinated coumarins and 1-aza coumarins.

A series of new fluorinated coumarins and 1-aza coumarins have been synthesized and the presence of fluorine in these molecules and its effect on their anti-microbial, anti-inflammatory and analgesic activities are discussed. The results of bioassay showed that these newly synthesized compounds containing fluorine exhibit moderate analgesic and excellent anti-inflammatory and potential anti-bacterial and anti-fungal activities, compared to the other halogenated compounds. All the newly synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR, 19F NMR, EI-MS, and FAB-MS. The ORTEP diagram of one of the compounds is reported herein.

N-(2-Chloro-quinolin-3-ylmethyl-ene)aniline.

The title compound, C(16)H(11)ClN(2), displays a trans configuration across the C=N bond and a transoid arrangement across the quinoline ring and the azomethine C atom. This arrangement facilitates C-H⋯Cl interactions. The packing in the crystal structure is due to inter-molecular C-H⋯π and Cl⋯π (3.52 and 3.84 Å) inter-actions. The dihedral angle between the least-squares planes of 2-chloro-quinoline and phenyl-amine is 16.61 (2)°.