Structure-property relationship in thioxotriaza-spiro derivative: Crystal structure and molecular docking analysis against SARS-CoV-2 main protease.

Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C-H…O, N-H…O, C-H…N and N-H…S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule-molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of -6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.

I2-Catalyzed transformation of o-aminobenzamide to o-ureidobenzonitrile using isothiocyanates.

The present work describes an unexpected and unique protocol for the iodine catalysed synthesis of o-ureidobenzonitriles using o-aminobenzamides and isothiocyanates via intramolecular rearrangement. The metal-free route achieved here is insensitive to moisture and applicable to the synthesis of a wide variety of o-ureidobenzonitriles with excellent yields even in a scalable fashion.

Design, synthesis and biological evaluation of 2-(4-phenylthiazol-2-yl) isoindoline-1,3-dione derivatives as anti-prostate cancer agents.

The structural modification and molecular docking-based screening approaches on thiazole-based isoindolinediones were imposed to find the novel 2-(4-phenylthiazol-2-yl) isoindoline-1,3-dione derivatives. The best fit compounds (6a-n) were synthesized and evaluated their antiproliferative activities on the prostate cancer cell lines (PC-3 & LNCaP). Among them, the compound, 6m exhibited good activity, particularly on LNCaP (IC50=5.96±1.6µM), moderately active against PC-3 cell lines as compared to bicalutamide. The compound, 6m decreased the androgen-mediated transcription of ARE-mRNA in PSA, TMPRSS2, c-myc and cyclin D1 than R-bicalutamide. The compounds, 6e and 6f were reconfirmed through single crystal XRD analysis. The ADME profiling of the test compounds was evaluated to find the drug-likeness and pharmacokinetic parameters. These findings may provide vital information for the development of anti-prostate cancer agents.

Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus.

The ATP binding cassette (ABC) transporters, represent one of the largest superfamilies of primary transporters, which are very essential for various biological functions. The crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus has been determined at 1.77 Å resolution. The crystal structure revealed that the protomer has two thick arms, (arm I and II), which resemble 'L' shape. The ATP-binding pocket is located close to the end of arm I. ATP molecule is docked into the active site of the protein. The dimeric crystal structure of ATP-binding subunit of ABC transporter from G. kaustophilus has been compared with the previously reported crystal structure of ATP-binding subunit of ABC transporter from Salmonella typhimurium.

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

UDP-N-acetyl-d-mannosamine dehydrogenase (UDP-d-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-d-mannosamine (UDP-d-ManNAc) to Uridine-diphospho-N-acetyl-d-mannosaminuronic acid (UDP-d-ManNAcA) through twofold oxidation of NAD(+). In order to reveal the structural features of the Pyrococcus horikoshii UDP-d-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-d-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.

Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles.

In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77Å and 1.95Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type IIIH and such PGDHs structures having this type are reported for the first time.

Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain.

NADP(+) dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP(+) was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH's. And, small domain and clasp domain showing significant differences when compared to other IDH's of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH's. Also, helices/beta sheets are absent in the small domain, when compared to other IDH's of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit-subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV.

Crystal structure of N-(3-hy-droxy-phenyl)succinimide.

In the title compound, C10H9NO3, the dihedral angle between the benzene and pyrrolidine rings is 53.9 (1)°. In the crystal, mol-ecules are linked through strong O-H⋯O hydrogen bonds into zigzag C(8) chains running along [010]. The chains are linked by C-H⋯π inter-actions forming sheets lying parallel to (100).

Crystal structure of 1-[(2S*,4R*)-6-fluoro-2-methyl-1,2,3,4-tetra-hydro-quinolin-4-yl]pyrrolidin-2-one.

In the title compound, C14H17FN2O, the 1,2,3,4-tetra-hydro-pyridine ring of the quinoline moiety adopts a half-chair conformation, while the pyrrolidine ring has an envelope conformation with the central methyl-ene C atom as the flap. The pyrrolidine ring lies in the equatorial plane and its mean plane is normal to the mean plane of the quinoline ring system, with a dihedral angle value of 88.37 (9)°. The bridging N-C bond distance [1.349 (3) Å] is substanti-ally shorter than the sum of the covalent radii (d cov: C-N = 1.47 Šand C=N = 1.27 Å), which indicates partial double-bond character for this bond, resulting in a certain degree of charge delocalization. In the crystal, mol-ecules are linked by N-H⋯O and C-H⋯O hydrogen bonds, forming sheets lying parallel to (10-1). These two-dimensional networks are linked via C-H⋯F hydrogen bonds and C-H⋯π inter-actions, forming a three-dimensional structure.

Crystal structure of (E)-N-phenyl-N'-[1-(thio-phen-2-yl)ethyl-idene]formo-hydrazide.

In the title compound, C13H12N2OS, the planes of the thio-phene and phenyl rings are nearly perpendicular to each other, making a dihedral angle of 86.42 (12)°. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming a helical chain along the b-axis direction.

Crystal structure of 1-ethyl-spiro-[imid-az-olidine-4,1'-indane]-2,5-dione.

In the title compound, C13H14N2O2, the C5 ring has an envelope conformation with the C atom adjacent to the quaternary C being the flap. The five atoms comprising the imidazolidine-2,4-dione ring are almost planar (r.m.s. deviation = 0.004 Å). The dihedral angle between the five-membered rings is 89.66 (10)°. In the crystal, inversion-related mol-ecules are connected via {⋯HNCO}2 synthons. These are linked into a helical supra-molecular chain along [010] by C-H⋯O inter-actions.

Crystal structure of cis-1-(2-methyl-1,2,3,4-tetra-hydro-quinolin-4-yl)azepan-2-one.

In the title compound, C16H22N2O, the azepan-2-one ring adopts a chair conformation, while the 1,2,3,4-tetra-hydro-pyridine ring adopts a half-chair conformation. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds, forming supra-molecular chains propagated along [10-1], with weak C-H⋯O inter-actions occurring between the chains.

N'-Benzyl-idene-2-chloro-N-(4-chloro-phen-yl)acetohydrazide.

In the title compound, C15H12Cl2N2O, the atoms not making up the chloro-benzene ring are approximately coplanar (r.m.s. deviation = 0.073 Å). The dihedral angle between these 13 atoms and the chloro-benzene ring is 67.37 (10)°. The C=O and Csp (2)-Cl groups are almost eclipsed [Cl-C-C=O = -6.5 (3)°]. In the crystal, C(6) chains linked by C-H⋯O hydrogen bonds result in [100] chains.

(1Z)-1-(1-Benzo-furan-2-yl)ethanone oxime.

The title compound, C10H9NO2, is almost planar (r.m.s. deviation for the non-H atoms = 0.027 Å) and the conformation across the C=N bond is syn. Further, the O atom of the benzo-furan ring is syn to the CH3 group in the side chain. In the crystal, mol-ecules are linked into C(3) chains propagating in [010] by O-H⋯N hydrogen bonds.

(4-Fluoro-phen-yl)(4-hy-droxy-3-methyl-phen-yl)methanone.

In the title compound, C14H11FO2, the two benzene rings are not coplanar, with a dihedral angle of 57.45 (12)° between their planes. In the crystal, mol-ecules are linked by an O-H⋯O hydrogen bond, forming a 21 helical chain along the b axis.

2-(6-Hy-droxy-1-benzo-furan-3-yl)acetamide.

In the title compound, C10H9NO3, the dihedral angle between the benzo-furan ring system (r.m.s. deviation for the non-H atoms = 0.009 Å) and the -C-C(O)-N- segment is 83.76 (1)°. In the crystal, mol-ecules are linked by N-H⋯O and O-H⋯O hydrogen bonds, generating (001) sheets, which feature C(4) and C(10) chains.

Bis(2-bromo-benz-yl) ether.

In the title compound, C14H12Br2O, the dihedral angle between the aromatic rings is 2.7 (3)° and the Br atoms lie on the same side of the mol-ecule. No inter-molecular inter-actions occur in the crystal beyond van der Waals contacts.

5-(4-Chloro-phen-oxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde.

In the title compound, C17H13ClN2O2, the phenyl and chloro-benzene rings are inclined to the central pyrazole ring at 40.84 (9) and 65.30 (9)°, respectively. In the crystal, pairs of C-H⋯π inter-actions link the mol-ecules into inversion dimers and C-H⋯O hydrogen bonds link these dimers into columns extended in [010]. The crystal packing exhibits short inter-molecular O⋯Cl contacts of 3.0913 (16) Å.

2-Nitro-benzyl methane-sulfonate.

In the title compound, C8H9NO5S, the dihedral angle between the benzene ring and the nitro group is 5.86 (15)° and the C-C-O-S group adopts an anti conformation [torsion angle = -168.44 (15)°]. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, generating a three-dimensional network.

Crystal structure of ethyl (6-hy-droxy-1-benzo-furan-3-yl)acetate sesquihydrate.

In the title hydrate, C12H12O4·1.5H2O, one of the water mol-ecules in the asymmetric unit is located on a twofold rotation axis. The mol-ecule of the benzo-furan derivative is essentially planar (r.m.s. deviation for the non-H atoms = 0.021 Å), with the ester group adopting a fully extended conformation. In the crystal, O-H⋯O hydrogen bonds between the water mol-ecules and the hy-droxy groups generate a centrosymmetric R 6 (6)(12) ring motif. These R 6 (6)(12) rings are fused, forming a one-dimensional motif extending along the c-axis direction.