Hu Teng

Comparative molecular dynamics simulations of histone deacetylase‐like protein: Binding modes and free energy analysis to hydroxamic acid inhibitors

Histone deacetylases (HDACs) play an important role in gene transcription, and inhibitors of HDACs can induce cell differentiation and suppress cell proliferation in tumor cells. Histone deacetylase1 (HDAC1) binds suberanilohydroxamic acid (SAHA) and 7‐phenyl‐2, 4, 6‐hepta‐trienoyl hydroxamic acid (CG‐1521) with moderately low affinity (ΔG = −8.6 and −7.8 kcal mol−1). The structurally related (E)‐2‐(3‐(3‐(hydroxyamino)‐3‐oxoprop‐1‐enyl)phenyl)‐N1,N3‐diphenylmalonamide (SK‐683), a Trichostatin A (TSA)‐like HDAC1 inhibitor, and TSA are bound to the HDAC1 with −12.3 and −10.3 kcal mol−1 of ΔG, higher binding free energies than SAHA and CG‐1521. Histone deacetylase‐like protein (HDLP), an HDAC homologue, shows a 35.2% sequence identity of HDLP and human HDAC1. Molecular dynamics simulation and the molecular mechanics/generalized‐Born surface area (MM‐GBSA) free energy calculations were applied to investigate the factors responsible for the relatively activity of these four inhibitors to HDLP. In addition, computational alanine scanning of the binding site residues was carried out to determine the contribution components from van der Waals, electrostatic interaction, nonpolar and polar energy of solvation as well as the effects of backbones and side‐chains with the MM‐GBSA method. MM‐GBSA methods reproduced the experimental relative affinities of the four inhibitors in good agreement (R2 = 0.996) between experimental and computed binding energies. The MM‐GBSA calculations showed that, the number of hydrogen bonds formed between the HDLP and inhibitors, which varied in the system studied, and electrostatic interactions determined the magnitude of the free energies for HDLP‐inhibitor interactions. The MM‐GBSA calculations revealed that the binding of HDLP to these four hydroxamic acid inhibitors is mainly driven by van der Waals/nonpolar interactions. This study can be a guide for the optimization of HDAC inhibitors and future design of new therapeutic agents for the treatment of cancer. Proteins 2008.

Nonlinear Mathematical Simulation and Analysis of Dha Regulon for Glycerol Metabolism in Klebsiella pneumoniae

Abstract Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.

Metabolic Flux Analysis of Bioconversion of Glycerol into 1,3-Propandiol by Klebsiella Pneumoniae

This study presents an analysis of metabolic fluxes of the anaerobic glycerol metabolism by Klebsiella pneumoniae for the production of 1,3-propanediol (1,3-PD). A metabolic network was reconstructed from the partly annotated genome sequence as well as from biochemical and physiological literatures. Extracellular fluxes measured in continuous culture under steady condition were used to estimate intracellular fluxes. A comparison of changes in the branch point of 3- hydroxypropionaldehyde (3-HPA) flux distribution reveals that glycerol dehydratase (GDHt) is the rate-limiting enzyme at high glycerol concentration and 1,3-propanediol oxidoreductase (PDOR) is the rate-limiting enzyme at low initial glycerol concentration for the production of 1,3-PD due to an insufficient supply of reducing equivalents.

Robustness and Nonlinear Dynamic Analysis for Trp Operon and Optimization of Tryptophan Production: An Integrated Model Considering Gene Regulation, Genes Interaction and Product Excretion

The tryptophan operon (trp operon), paradigm for repressible operons, is regulated by three different negative-feedback mechanisms of repression, transcription attenuation and enzyme inhibition. Initiation of transcription is controlled by the interaction of the tryptophan repressor with its target site on the operator. Moreover, the interaction among the regulator genes, the operator genes and the structure genes and excretion of tryptophan play an important factor according to previous works. In this study, an expended mathematical model for the tryptophan operon regulation on the effects of repression, feedback enzyme inhibition, attenuation, interaction among genes and excretion of tryptophan is presented. The new model is first translated into the corresponding S-system version. The robustness of this model is then discussed by using the S-system model and the sensitivity analysis shows that the model is robust enough. The influences of cell growth rate on the biosynthesis of tryptophan, stability and dynamic behavior of the trp operon are also well investigated. The transportation of tryptophan through cytoplasmic membranes, especially the inhibition of tryptophan transport can influence the level of intracellular tryptophan significantly. The theoretical analysis indicates that an increase of inhibition constant of tryptophan transport is favorable for the biosynthesis of tryptophan. Furthermore, a steady-state optimization model is established based on trp operon models. The optimization results indicate that it is possible to attain a stable and robust steady state with a rate of tryptophan production increased more than 4.8 times in which the growth rate is kept as 0.00624h-1 and some key parameters is modulated.

QSAR and Molecular Stereoelectronic Properties of Phloroglucinol Derivatives as Potential Anti-Tumor Agents

The quantitative structure-activity relationship (QSAR) was performed on the phloroglucinol derivatives, a kind of anti-tumor agents, to predict their biological activities through their molecular features and properties. Using genetic algorithm (GA) as the statistical method, a robust model with R2 = 0.9504, q2 = 0.9096, was achieved, which could explain more than 90% of the variance of data. Molecular orbital (MO) theoretical calculations under quantum chemical semi-empirical approach AMI were carried out to investigate the stereoelectronic properties of the phloroglucinol derivatives. The results show that the carbonyl is an essential structure for the phloroglucinol derivatives to show their activities. Carbonylic oxygens could be considered as potential binding sites for the target molecules. The charge transfer is not likely to happen during the interaction between the phloroglucinol derivatives and the target molecules.

Molecular Modeling of a Hexacyclopeptide Dichotomin B Based on B3LYP, HF and ONIOM Methods: Comparison with Dichotomin A

Dichotomin B shows cell growth inhibitory activities against p-388 lymphocytic leukemia cells. However, its spatial conformation and the primary factors affecting its activity are not very clear. Here we optimize the primary structure of dichotomin B at the DFT (density functional theory) with B3LYP parameterization, HF (Hartree-Fock) and ONIOM (our own N- layered integrated molecular orbital and molecular mechanics) levels of theory. As a result, all the optimized geometries contain one beta-turn and two intramolecular hydrogen bonds which presumably maintain the steady spatial arrangements of dichotomin B in solid state and contribute to its activity, while there are two beta-turns and two intramolecular hydrogen bonds in the crystal structure of dichotomin A, which may be the reason that the activity of dichotomin A is higher than that of dichotomin B. In addition, the 13C chemical shifts of the three optimized geometries are calculated. We find that the structure obtained with HF/6-31G(d) method is the most similar to the experimental structure of dichotomin B. Furthermore, the RMS (root mean square) errors for 13C chemical shifts relative to TMS determined using the B3LYP hybrid functional with the 6- 311G(d,p) basis set are smaller than those determined using HF at this same basis set.