Anti-tubercular activity and molecular docking studies of indolizine derivatives targeting mycobacterial InhA enzyme.

A series of 1,2,3-trisubstituted indolizines (2a-2f, 3a-3d, and 4a-4c) were screened for in vitro whole-cell anti-tubercular activity against the susceptible H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 2b-2d, 3a-3d, and 4a-4c were active against the H37Rv-MTB strain with minimum inhibitory concentration (MIC) ranging from 4 to 32 µg/mL, whereas the indolizines 4a-4c, with ethyl ester group at the 4-position of the benzoyl ring also exhibited anti-MDR-MTB activity (MIC = 16-64 µg/mL). In silico docking study revealed the enoyl-acyl carrier protein reductase (InhA) and anthranilate phosphoribosyltransferase as potential molecular targets for the indolizines. The X-ray diffraction analysis of the compound 4b was also carried out. Further, a safety study (in silico and in vitro) demonstrated no toxicity for these compounds. Thus, the indolizines warrant further development and may represent a novel promising class of InhA inhibitors and multi-targeting agents to combat drug-sensitive and drug-resistant MTB strains.

Crystallography, Molecular Modeling, and COX-2 Inhibition Studies on Indolizine Derivatives.

The cyclooxygenase-2 (COX-2) enzyme is an important target for drug discovery and development of novel anti-inflammatory agents. Selective COX-2 inhibitors have the advantage of reduced side-effects, which result from COX-1 inhibition that is usually observed with nonselective COX inhibitors. In this study, the design and synthesis of a new series of 7-methoxy indolizines as bioisostere indomethacin analogues (5a-e) were carried out and evaluated for COX-2 enzyme inhibition. All the compounds showed activity in micromolar ranges, and the compound diethyl 3-(4-cyanobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5a) emerged as a promising COX-2 inhibitor with an IC50 of 5.84 µM, as compared to indomethacin (IC50 = 6.84 µM). The molecular modeling study of indolizines indicated that hydrophobic interactions were the major contribution to COX-2 inhibition. The title compound diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5c) was subjected for single-crystal X-ray studies, Hirshfeld surface analysis, and energy framework calculations. The X-ray diffraction analysis showed that the molecule (5c) crystallizes in the monoclinic crystal system with space group P 21/n with a = 12.0497(6)Å, b = 17.8324(10)Å, c = 19.6052(11)Å, α = 90.000°, ß = 100.372(1)°, γ = 90.000°, and V = 4143.8(4)Å3. In addition, with the help of Crystal Explorer software program using the B3LYP/6-31G(d, p) basis set, the theoretical calculation of the interaction and graphical representation of energy value was measured in the form of the energy framework in terms of coulombic, dispersion, and total energy.

Molecular Bases for Anesthetic Agents: Halothane as a Halogen- and Hydrogen-Bond Donor.

Although instrumental for optimizing their pharmacological activity, a molecular understanding of the preferential interactions given by volatile anesthetics is quite poor. This paper confirms the ability of halothane to work as a hydrogen-bond (HB) donor and gives the first experimental proof that halothane also works as a halogen-bond (HaB) donor in the solid state and in solution. A halothane/hexamethylphosphortriamide co-crystal is described and its single-crystal X-ray structure shows short HaBs between bromine, or chlorine, and the phosphoryl oxygen. New UV/Vis absorption bands appear upon addition of diazabicyclooctane and tetra(n-butyl)ammonium iodide to halothane solutions, indicating that nitrogen atoms and anions may mediate the HaB-driven binding processes involving halothane as well. The ability of halothane to work as a bidentate/tridentate tecton by acting as a HaB and HB donor gives an atomic rationale for the eudismic ratio shown by this agent.

Orthogonal halogen and hydrogen bonds involving a peptide bond model†Electronic supplementary information (ESI) available: Experimental part, DSC, IR spectroscopic and crystallographic data. CCDC 899779-899785. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4ce01514bClick here for additional data file.Click here for additional data file.

The peptide bond model N-methylacetamide self-assembles with a range of dihalotetrafluorobenzenes forming co-crystals that all show the occurrence of orthogonal hydrogen and halogen bonds.

Methyl 4-(4-chloro-phen-yl)-8-iodo-2-methyl-6-oxo-1,6-dihydro-4H-pyrimido[2,1-b]quinazoline-3-carboxyl-ate.

In the title compound, C20H15ClIN3O3, the dihedral angle between the quinazolinone ring system [r.m.s. deviation = 0.047 (2) Å] and the pendant benzene ring is 82.63 (11)°. The mol-ecular conformation is stabilized by intra-molecular C-H⋯O inter-actions. In the crystal, the mol-ecules are linked by N-H⋯O hydrogen bonds into chains along the a-axis direction. Another set of chains propagating along [101] is formed due to inter-molecular I⋯Cl short contacts of 3.427 (1) Å, thus giving layers parallel to (010). The layers are connected by C-H⋯π and π-π inter-actions, the shortest distance between the centroids of aromatic rings being 3.8143 (16) Å.

2-(4-Bromo-anilino)-6-(4-chloro-phen-yl)-5-meth-oxy-carbonyl-4-methyl-3,6-dihydro-pyrimidin-1-ium chloride.

In the title molecular salt, C19H18BrClN3O2 (+)·Cl(-), the dihedral angles between the pyrimidine ring and the chlorobenzene and bromobenzene rings are 72.4 (2) and 45.5 (2)°, respectively. The dihedral angle between the chlorobenzene and bromobenzene rings is 27.5 (2)°. The conformation of the mol-ecule is stabilized by an intra-molecular C-H⋯O inter-action. In the crystal, the anion and cation are linked by an N-H⋯Cl hydrogen bond. Pairs of weak C-H⋯O and C-H⋯Cl hydrogen bonds form inversion dimers. Further N-H⋯Cl hydrogen bonds form R 2 (1)(6) motifs and link the dimers into chains along [101]. Br⋯Cl short contacts [3.482 (2) Å] inter-link the hydrogen-bonded chains along the b-axis direction.

{2-[(1,3-Benzo-thia-zol-2-yl)meth-oxy]-5-bromo-phen-yl}(phen-yl)methanone.

In the title compound, C21H14BrNO2S, the dihedral angle between the planes of the benzo-thia-zole and phenyl-methanone groups is 63.4 (2)°. In the crystal, pairs of C-H⋯N hydrogen bonds link the mol-ecules to form inversion dimers, which are further linked by C-H⋯O inter-actions into chains along the c axis. C-H⋯π and π-π inter-actions [centroid-centroid distance = 3.863 (1) Å] further stabilize the mol-ecular assembly.

{2-[(1,3-Benzo-thia-zol-2-yl)meth-oxy]-5-chloro-phen-yl}(4-chloro-phen-yl)methan-one.

In the title compound, C21H13Cl2NO2S, the benzo-thia-zole ring makes dihedral angles of 0.94 (1) and 70.65 (5)° with the 4-chloro-phenyl-methanone unit and the 5-chloro-phenyl ring, respectively. The dihedral angle between the 4-chloro-phenyl-methanone unit and the 5-chloro-phenyl ring is 66.20 (5)°. The crystal structure consists of dimeric units generated by C-H⋯N hydrogen bonds, further linked by C-H⋯O and C-H⋯π inter-actions, leading to a three-dimensional network.

[2-(1,3-Benzothia-zol-2-ylmeth-oxy)-5-bromo-phen-yl](4-chloro-phen-yl)methanone.

In the title compound, C21H13BrClNO2S, the dihedral angle between the planes of the benzothia-zole and chloro-phenyl-methanone groups is 71.34 (6)°. In the crystal, weak C-H⋯N hydrogen bonds lead to dimer formation, whereas Br⋯Cl short contacts [3.4966 (11) Å] form infinite chains along the a-axis direction. Further, the C-H⋯O, C-H⋯π and π-π [centroid-centroid distance = 3.865 (2) Å] inter-actions stabilize the three-dimensional network.

{2-[(1,3-Benzo-thia-zol-2-yl)meth-oxy]-5-fluoro-phen-yl}(4-chloro-phen-yl)methanone.

The asymmetric unit of the title compound, C21H13ClFNO2S, contains two independent mol-ecules with similar conformations. In the mol-ecules, the thia-zole ring is essentially planar [maximum atomic deviations = 0.014 (4) and 0.023 (5) Å] and is oriented with respect to the fluoro-phenyl ring and chloro-phenyl rings at 9.96 (18) and 70.39 (18)° in one mol-ecule and at 7.50 (18) and 68.43 (18)° in the other; the dihedral angles between the fluoro-phenyl and chloro-phenyl rings are 64.9 (2) and 64.6 (2)°, respectively. Inter-molecular C-H⋯O and C-H⋯F hydrogen bonds stabilize the three-dimensional supra-molecular architecture. Weak C-H⋯π and π-π inter-actions [centroid-centroid distance = 3.877 (3) Å] lead to a criss-cross mol-ecular packing along the c axis.

Fluoride Anions: Unexploited but Effective Halogen Bond Acceptors.

Due to their high electron density, fluoride anions can be considered the most effective halogen bond (HaB) acceptors among the halides. However, under common experimental conditions, F- uncommonly acts as HaB acceptor, expectedly as it is present in hydrated form. Herein we report that under specific crystallization conditions a hydrogen bond-free F- functioning as donor of electron density can be obtained, with the formed HaBs constituting the driving force of the observed crystal packings. Computations confirm the strength of these HaBs compared to analogous interactions involving other halides.

Methyl (E)-2-[(3-chloro-4-cyano-phenyl)-imino]-4-(4-chloro-phen-yl)-6-methyl-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

In the title compound, C(20)H(16)Cl(2)N(4)O(2), the dihedral angles between the planes of the chloro-phenyl, chloro-cyano-phenyl-imine and ester groups and the plane of the six-membered tetra-hydro-pyrimidine ring are 86.9 (2), 72.6 (2) and 7.9 (2)°, respectively. The Cl atom substituent on the cyano-phenyl ring is disordered over two rotationally related sites [occupancy factors 0.887 (2):0.113 (2)], while the mol-ecular conformation is stabilized by the presence of an intra-molecular aromatic C-H⋯π inter-action. Both N-H groups participate in separate inter-molecular hydrogen-bonding associations with centrosymmetric cyclic motifs [graph sets R(2) (2)(8) and R(2) (2)(12)], resulting in ribbons parallel to [010]. Further weak C-H⋯O hydrogen bonds link these ribbons into a two-dimensional mol-ecular assembly.

Methyl 2,6-diphenyl-1-p-tolyl-4-(p-tolyl-amino)-1,2,5,6-tetra-hydro-pyridine-3-carboxyl-ate.

In the title compound, C(33)H(32)N(2)O(2), the tetra-hydro-pyridine ring adopts a boat conformation with the carbonyl group in an s-cis conformation with respect to the C=C bond of the six-membered tetra-hydro-pyridine ring. The mol-ecular conformation is stabilized by intra-molecular N-H⋯O, C-H⋯O and C-H⋯π inter-actions. Formation of centrosymmetric head-to-head dimers is observed through pairwise inter-molecular N-H⋯O hydrogen bonds. Additional weak C-H⋯O and C-H⋯π inter-actions stabilize the three-dimensional mol-ecular assembly.

(2-(Benzo[d]thia-zol-2yl-meth-oxy)-5-chloro-phen-yl)(phen-yl)methanone.

In the title compound, C(21)H(14)ClNO(2)S, the dihedral angle between the benzothia-zole and diphenyl methanone groups is 68.6 (2)°. The crystal structure consists of dimeric units generated by C-H⋯N bonds, further linked by C-H⋯O bonds and C-H⋯π and π-π inter-actions [centroid-centroiddistance = 3.856 (2) Å], which lead to a criss-cross assembly parallel to (001).

Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study.

Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase.

Ethyl 6-methyl-2-sulfanyl-idene-4-[4-(trifluoro-meth-yl)phen-yl]-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

The title compound, C(15)H(15)F(3)N(2)O(2)S, adopts a conformation with an intra-molecular C-H⋯π inter-action. The dihedral angles between the planes of the 4-(trifluoro-meth-yl)phenyl and ester groups with the plane of the six-membered tetra-hydro-pyrimidine ring are 81.8 (1) and 16.0 (1)°, respectively. In the crystal structure, inter-molecular N-H⋯S hydrogen bonds link pairs of mol-ecules into dimers and N-H⋯O inter-actions generate hydrogen-bonded mol-ecular chains along the crystallographic a axis.

Ethyl 4-(1,3-benzodioxol-5-yl)-6-methyl-2-sulfanylidene-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

In the title compound, C(15)H(16)N(2)O(4)S, the dihedral angles between the planes of the benzodioxole and ester groups and the plane of the six-membered tetra-hydro-pyrimidine ring are 89.5 (1) and 20.2 (1)°, respectively. Inter-molecular N-H⋯S hydrogen bonds assemble the mol-ecules into dimers, which are further connected via N-H⋯O inter-actions into chains parallel to [010]. Weak C-H⋯S and C-H⋯π inter-actions enhance the stability of the crystal structure.

Interplay of Halogen and Hydrogen Bonding through Co-Crystallization in Pharmacologically Active Dihydropyrimidines: Insights from Crystal Structure and Energy Framework.

A solvent-assisted grinding method has been used to prepare co-crystals in substituted dihydropyrimidines (DHPM) that constitutes pharmacologically active compounds. These were characterized using FT-IR, PXRD, and single-crystal X-ray diffraction. In order to explore the possibility of formation of halogen (XB) and hydrogen bonding (HB) synthons in the solid state, co-crystallization attempts of differently substituted DHPM molecules, containing nitro, hydoxy, and chloro substituents, with different co-formers, such as 1,4-diiodo tetrafluorobenzene (1,4 DITFB) and 3-nitrobenzoic acid (3 NBA) were performed. The XB co-crystals (C2aXB, C2bXB, and C2cXB) prefer the formation of C-I⋅⋅⋅O/C-I⋅⋅⋅S XB synthon, whereas the HB co-crystal (C2dHB) is stabilized by N-H⋅⋅⋅O H-bond formation. Hirshfeld surface analysis revealed that the percentage contribution of intermolecular interactions for XB co-crystals prefer equal contribution of XB synthon along with HB synthon. Furthermore, the interaction energy was analyzed using energy frameworks, which suggests that their stability, a combination of electrostatics and dispersion, is enhanced through XB/HB in comparison to the parent DHPMs.

Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix.

4-Azido-methyl-7-methyl-2-oxo-2H-chromene-6-sulfonyl azide.

In the title compound, C(11)H(8)N(6)O(4)S, the plane of the coumarin aromatic ring is twisted by 17.2 (2)° with respect to the plane of the azide group bound to the methyl-ene substituent, whereas it is twisted by 83.2 (2)° to the plane of the azide attached to the sulfonyl group. The crystal structure is stabilized by weak C-H⋯O inter-actions, leading to the formation of dimers with R(2) (2)(12) graph-set motifs. These dimers are further linked by weak S-O⋯π and π-π contacts [centroid-centroid distance = 3.765 (2) Å], leading to the formation of a layered structure.