Synthesis, characterization and molecular docking studies on some new N-substituted 2-phenylpyrido[2,3-d]pyrimidine derivatives

We report a novel scaffold of N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives with potent antibacterial activity by targeting this biotin carboxylase enzyme. The series of eighteen N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives were synthesized, characterized and further molecular docking studied to determine the mode of binding and energy changes with the crystal structure of biotin carboxylase (PDB ID: 2V58) was employed as the receptor with compounds 6a-r as ligands. The results obtained from the simulation were obtained in the form of dock score; these values represent the minimum energies. Compounds 6d, 6l, 6n, 6o, 6r and 6i showed formation of hydrogen bonds with the active site residues and van Der Walls interactions with the biotin carboxylase enzyme in their molecular docking studies. This compound can be studied further and developed into a potential antibacterial lead molecule.

Computational Study of Novel 2,3-Bis[(1-methyl-1H-imidazole-2-yl)sulfanyl]quinoxaline: Structural Aspects, Spectroscopic Investigation, HOMO-LUMO, MESP, NLO, ADMET Predictions and Molecular Docking Studies as Potential Biotin Carboxylase and Antibiotics Resistant Aminoglycoside Phosphotransferase APH(2")IVA Enzyme Inhibitor

In this paper, a complete quantum chemical calculation has been done to describe the relevant structural aspects of novel 2,3-bis[(1-methyl-1H-imidazole-2-yl)sulfanyl]quinoxaline with combination of DFT/B3LYP method 6-311++G(d,p) basis set in gas phase and in solvent phase. The molecular structure was examined by using IR, 1H & 13C NMR and UV-visible techniques and solvent effect on spectroscopic properties are also discussed. The vibrational assignments are analyzed by PED using Gauss View 5.0 and VEDA 4.0 program. The 1H NMR and 13C NMR chemical shifts are calculated using the gauge-independent atomic orbital method (GIAO method) in gas phase and in solvents (water, DMSO and chloroform). The UV spectrum is calculated by using TD-DFT/6-311++G(d,p) method in gas phase and in solvent (water, DMSO and chloroform) using IEF-PCM model. With the help of theoretical calculations chemical activities, electrophilic/nucleophilic nature and sites in the molecule, molecular and chemical properties that cannot be obtained by experimental way are obtained. Accordingly, molecular electrostatic potential (MESP), hardness (η)/softness (S) parameters, net charges analyses are investigated to gain electrophilic and nucleophilic nature. Also the sites in molecule and Fukui function analysis are discussed. The dipole moment (μ), polarizability (αtot), anisotropic polarizability (Δα) and first-order hyperpolarizability (βtot) of the title compound are reported and results shows that the material is capable to generate non-linear effect (NLO). The in silico study of all th e biological and ADMET properties of title molecule are also discussed and compared with reference drug ciprofloxacin antibiotics. The title molecule and reference drug ciprofloxacin docked with biotin carboxylase enzyme (PDB ID: 2V59) of E. coli and aminoglycoside phosphotransferase APH(2")IVA (PDB ID: 4DFU) of Enterococcus casseliflavus receptor with the help of Molegro molecular viewer 2.5 program and binding affinity (ΔG) were determined by ParDock server.

Discovery and characterization of regulatory mechanisms affecting the heteromeric acetyl-coenzyme a carboxylase in Arabidopsis

Fatty acid biosynthesis (FAS) is an essential metabolic pathway used by all organisms to generate fatty acids. A staple component of this pathway is the enzyme acetyl-CoA carboxylase (ACCase), which catalyzes the committed step by converting acetyl-CoA to malonyl-CoA. The heteromeric form of this enzyme requires four different subunits for activity: biotin carboxylase, biotin carboxyl carrier protein (BCCP), and alpha- and beta-carboxyltransferase (CT). Heteromeric ACCase is present in prokaryotes and the plastids of most plants, and has been a focus of biotechnology research due to its prominent role in FAS. Many different regulatory mechanisms have been identified in both plants and E. coli. However, it is still unknown how most of these regulatory mechanisms are mediated. For example, ACCase is known to be feedback inhibited by 18:1-acyl carrier protein in plants, yet it is unknown how this inhibition is exerted on the enzyme. Therefore it was posited that other unknown factors, such as proteins or post-translational modifications, might play a role in ACCase regulation. To identify suspected regulatory factors associated with ACCase, we performed in vivo co-immunoprecipitation (co-IP) using subunit-specific antibodies to isolate the ACCase complex from Arabidopsis thaliana leaves. Quantitative mass spectrometry of these co-IPs revealed all four known subunits to ACCase and two unknown proteins annotated as 'biotin/lipoyl attachment domain containing' (BADC) proteins. The BADC proteins are a family of three proteins in A. thaliana and resemble the BCCP subunit to ACCase, but lack the conserved biotinylation motif. All three BADC proteins interacted with the two A. thaliana BCCP isoforms and the biotin carboxylase subunit of ACCase based on yeast two-hybrid and heterologous co-expression analyses. None of the BADC proteins were biotinylated in planta or when expressed in Escherichia coli, unlike BCCP controls. Gene orthologs to BADC were found only in plant and green algae species that contain a heteromeric ACCase suggesting BADC genes co-evolved with this form of ACCase. Expression of BADC proteins in a temperature-sensitive E. coli BCCP mutant in minimal media strongly inhibited cell growth through interaction with the homologous, bacterial ACCase. Also, addition of recombinant BADC protein to in vitro ACCase activity assays significantly reduced enzyme activity. Finally, partial silencing of one of the BADC genes in A. thaliana seed led to a slight, yet significant, increase in seed oil content. We conclude the BADC proteins are ancient BCCPs that acquired a new function through mutation of the biotinylation motif. We propose a poisoned complex model whereby BADCs function as negative regulators of ACCase by competing with BCCP for access to the holo-ACCase complex. In addition, a study was performed to identify the role of phosphorylation of the alpha-CT subunit. Multiple studies had identified two phosphorylation sites on the C-terminal domain of alpha-CT in A. thaliana. This C-terminal domain is not found in all plant species and has an unknown function. To determine the potential regulatory effect of phosphorylation on this domain, phosphomimic and phospho-deficient alpha-CT mutants were made and expressed in wild type A. thaliana. Multiple independent transgenic lines containing at least two-fold alpha-CT protein compared to empty vector controls were screened for seed oil content. The resulting data showed no clear phenotype that could be attributed to expression of the mutants. This result could be explained by a number of factors such as the presence of endogenous alpha-CT, the complexity of the seed oil phenotype, or a large margin of technical error in some lines. However, in vitro ACCase activity assays showed that a transgenic line overexpressing native alpha-CT contained increased specific activity of the enzyme compared to controls. Furthermore, analysis of transgenic lines expressing phosphomimic or phospho-deficient alpha-CT mutants also showed increased ACCase specific activity which was indistinguishable from the native alpha-CT overexpression line, regardless of the mutation. Therefore it appears that increased alpha-CT expression can increase ACCase activity by allowing for the formation of more active complexes. This observation suggests that alpha-CT is the limiting subunit of the ACCase complex in the stroma.