Supaporn Dokmaisrijan

Experimental FTIR and theoretical studies of gallic acid–acetonitrile clusters

Gallic acid (3,4,5-trihydroxybenzoic acid, GA) has many possible conformers depending on the orientations of its three OH and COOH groups. The biological activity of polyphenolic compounds has been demonstrated to depend on their conformational characteristics. Therefore, experimental FTIR and theoretical studies of the GA-solvent clusters were performed to investigate the possible most favored conformation of GA. Acetonitrile (ACN) was selected as the solvent since its spectrum did not interfere with the OH stretching bands of GA. Also of importance was that these OH groups, in addition to the carboxyl group, of the GA are the most likely groups to interact with receptors. The solution of GA in the ACN solution was measured and the complex OH bands were deconvoluted to four component bands. These component bands corresponded to the three OH bands on the benzene ring and a broad band which is a combination band of mainly the OH of the COOH group and the inter- and intramolecular H-bonds from the OH groups on the ring. The conformations, relative stabilities and vibrational analysis of the GA monomers and the GA-ACN clusters were investigated using the B3LYP/6-311++G(2d,2p) method. Conformational analysis of the GA monomer yielded four most possible conformers, GA-I, GA-II, GA-III and GA-IV. These conformers were subsequently used for the study of the GA:ACN clusters at the 1:1, 1:2 and 1:4 mole ratios. The IR spectra of the most stable structures of these clusters were simulated and the vibrational wavenumbers of the OH and C=O groups were compared with those from the experiment. The FTIR component bands were comparable to the computed OH bands of the GA-I-(ACN)(2), GA-IV-(ACN)(2) and GA-I-(ACN)(4) clusters. Furthermore, the C=O stretching bands and the bands in the regions of 1800-1000 cm(-1) obtained by computing and the experiment were similar for these clusters. Thus, GA-I and GA-IV are the most preferable conformations of GA in ACN and perhaps in the polar environment around the receptor sites of GA.

Conformations and spectroscopic properties of laccaic acid A in the gas phase and in implicit water

Conformations and spectroscopic properties of laccaic acid A (lacA) were studied by means of the experimental and theoretical approaches. The minimum energy conformers of lacA in the gas phase and in implicit water obtained from the B3LYP/6-311G(d,p) calculations displayed the same orientation of the COOH and OH groups on the anthraquinone-based component. The intramolecular hydrogen bonds (H-bonds) formed between the COOH, C=O and OH groups are very strong. In contrast, the orientations of the Ph(OH)CH(2)CH(2)NHCOCH(3) substituent moiety on the anthraquinone-based component in the gas phase and in implicit water are completely different. The substituent prefers to bind with the anthraquinone-based component in the gas phase while it moves away from the anthraquinone-based component in implicit water. The calculated IR spectra of the two lowest-lying energy conformers of lacA in the gas phase fit to the experimental FTIR spectrum. The full assignments of the vibrational modes with the correlated vibrational wavenumbers of those conformers were proposed here, for the first time. The intramolecular H-bond formations in lacA can cause the shift of the vibrational wavenumber for the COOH, C=O, OH and NH groups as compared to the normal vibrations of these groups. The NMR spectra showed that the stabilities of the two lowest-lying energy conformers of lacA in the gas phase are comparable and this is consistent with their computational energies. The UV-Vis spectra of the lowest-lying energy conformers of lacA in implicit water were compared with the experimental UV-Vis spectrum. The calculations suggested that the electronic transition in the visible region involves with the singlet π→π(*) excitation which the electron density transfers to a COOH group on the anthraquinone ring.

Computational screening of fatty acid synthase inhibitors against thioesterase domain

Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids, and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP). Based on this computational technique, rosmarinic acid and its eight analogs were observed as a new series of potential FAS inhibitors, which showed a stronger binding affinity than MGLFP. Afterward, nine docked complexes were studied by molecular dynamics simulations for investigating protein–ligand interactions and binding free energies using MM-PB(GB)SA, MM-3DRISM-KH, and QM/MM-GBSA methods. The binding free energy calculation indicated that the ZINC85948835 (R34) displayed the strongest binding efficiency against the TE domain of FAS. There are eight residues (S2308, I2250, E2251, Y2347, Y2351, F2370, L2427, and E2431) mainly contributed for the R34 binding. Moreover, R34 could directly form hydrogen bonds with S2308, which is one of the catalytic triad of TE domain. Therefore, our finding suggested that R34 could be a potential candidate as a novel FAS-TE inhibitor for further drug design.

GPU accelerated molecular dynamics simulations for protein-protein interaction of ankyrin complex

The ankyrin repeat (AR) can be used as a versatile scaffold for protein–protein interactions. It consists of a 33-residues sequence motif found in proteins with diverse functions, such as transcription initiation, cell cycle regulation, cytoskeletal integrity, ion transport, and cell–cell signaling. Using AR with high affinity for the Escherichia coli maltose binding protein (MBP) as our model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot-spots at protein–protein interfaces. In this study, the long time scale dynamics simulations with GPU accelerated molecular dynamics (MD) simulations in AMBER12 have been performed to locate the hot-spots of protein-protein interaction by the analysis of the Molecular Mechanics–Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA) of the MD trajectories. The two designed AR systems with different binding affinities from ELISA were simulated. Our calculations gave the absolute binding affinity predictions which are in agreement with the kinetic experiment. The difference in binding affinity of the two selected clones is due to the framework mutations which are mostly conserved at a β-hairpin/loop region. AR domain is most probably not affected by the alteration of this framework from the long time scale MDs.

Theoretical structures and binding energies of RNA-RNA/cyanine dyes and spectroscopic properties of cyanine dyes

Cyanine dyes have been widely used as a fluorescence probe for biomolecules and protein labeling. The mostly used cyanine dyes for nucleic acids labeling are DiSC2(3), DiSC2(5), and DiSC2(7). The possible structures and binding energies of RNA-RNA/Cyanine dyes were predicted theoretically using AutoDock Vina. The results showed that cyanine dyes and bases of RNA-RNA have the van der Waals and pi-pi interactions. The maximum absorption wavelength in the visible region obtained from the TD-DFT calculations of all cyanine dyes in the absence of the RNA-RNA double strand showed the bathochromic shift.