Modeling subtype-selective agonists binding with alpha4beta2 and alpha7 nicotinic acetylcholine receptors: effects of local binding and long-range electrostatic interactions.

The subtype-selective binding of 14 representative agonists with alpha4beta2 and alpha7 nicotinic acetylcholine receptors (nAChRs) has been studied by performing homology modeling, molecular docking, geometry optimizations, and microscopic and phenomenological binding free energy calculations. All of the computational results demonstrate that the subtype selectivity of the agonists binding with alpha4beta2 and alpha7 7 nAChRs is affected by both local binding and long-range electrostatic interactions between the receptors and the protonated structures of the agonists. The effects of the long-range electrostatic interactions are mainly due to the distinct difference in the net charge of the ligand-binding domain between the two nAChR subtypes.

Hydrophilic anilinogeranyl diphosphate prenyl analogues are Ras function inhibitors.

Sequential processing of H-Ras by protein farnesyl transferase (FTase), Ras converting enzyme (Rce1), and protein-S-isoprenylcysteine O-methyltransferase (Icmt) to give H-Ras C-terminal farnesyl-S-cysteine methyl ester is required for appropriate H-Ras membrane localization and function, including activation of the mitogen-activated protein kinase (MAPK) cascade. We employed a Xenopus laevis oocyte whole-cell model system to examine whether anilinogeranyl diphosphate analogues of similar shape and size, but with a hydrophobicity different from that of the FTase substrate farnesyl diphosphate (FPP), could ablate biological function of H-Ras. Analysis of oocyte maturation kinetics following microinjection of in vitro analogue-modified H-Ras into isoprenoid-depleted oocytes revealed that analogues with a hydrophobicity near that of FPP supported H-Ras biological function, while the analogues p-nitroanilinogeranyl diphosphate (p-NO2-AGPP), p-cyanoanilinogeranyl diphosphate (p-CN-AGPP), and isoxazolaminogeranyl diphosphate (Isox-GPP) with hydrophobicities 2-5 orders of magnitude lower than that of FPP did not.

Development of quantitative structure-activity relationships and its application in rational drug design.

Over forty years have elapsed since Hansch and Fujita published their pioneering work of quantitative structure-activity relationships (QSAR). Following the introduction of Comparative Molecular Field Analysis (CoMFA) by Cramer in 1998, other three-dimensional QSAR methods have been developed. Currently, combination of classical QSAR and other computational techniques at three-dimensional level is of greatest interest and generally used in the process of modern drug discovery and design.

Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations.

Molecular dynamics simulations were performed to unfold a homologous pair of thermophilic and mesophilic cold shock proteins at high temperatures. The two proteins differ in just 11 of 66 residues and have very similar structures with a closed five-stranded antiparallel beta-barrel. A long flexible loop connects the N-terminal side of the barrel, formed by three strands (beta1-beta3), with the C-terminal side, formed by two strands (beta4-beta5).

[Polymorphism of DYS287 on Y chromosome in 28 ethnic populations of China].

Objective: To investigate the polymorphism of DYS287 among 28 ethnic populations in 9 provinces of China.

Method: YAP element was detected by Touchdown PCR amplification and 2% agarose gel electrophoresis.

Results: YAP+ frequencies in these ethnic populations were as follows: Zang 36.

Structural and functional characterization of human microsomal prostaglandin E synthase-1 by computational modeling and site-directed mutagenesis.

Microsomal prostaglandin (PG) E synthase-1 (mPGES-1) has recently been recognized as a novel, promising drug target for inflammation-related diseases. Functional and pathological studies on this enzyme further stimulate to understand its structure and the structure-function relationships. Using an approach of the combined structure prediction, molecular docking, site-directed mutagenesis, and enzymatic activity assay, we have developed the first three-dimensional (3D) model of the substrate-binding domain (SBD) of mPGES-1 and its binding with substrates prostaglandin H2 (PGH2) and glutathione (GSH).

Modeling multiple species of nicotine and deschloroepibatidine interacting with alpha4beta2 nicotinic acetylcholine receptor: from microscopic binding to phenomenological binding affinity.

A variety of molecular modeling, molecular docking, and first-principles electronic structure calculations were performed to study how the alpha4beta2 nicotinic acetylcholine receptor (nAChR) binds with different species of two typical agonists, (S)-(-)-nicotine and (R)-(-)-deschloroepibatidine, each of which is distinguished by different free bases and protonation states. On the basis of these results, predictions were made regarding the corresponding microscopic binding free energies. Hydrogen-bonding and cation-pi interactions between the receptor and the respective ligands were found to be the dominant factors differentiating the binding strengths of different microscopic binding species.

hTERT extends proliferative lifespan and prevents oxidative stress-induced apoptosis in human lens epithelial cells.

Purpose: Telomerase is a specialized polymerase that catalyzes synthesis of telomeres in most eukaryotes. When introduced into somatic cells, it extends the proliferative lifespan and prevents replicative senescence. Whether it has similar functions in lens epithelial cells, especially in human lens epithelial cells (HLECs) remains to be determined.

[Gene frequencies and haplotypes of nine Y-short tandem repeat loci in four minority populations of China].

Objective: To investigate the polymorphism of nine Y-short tandem repeat loci in 117 male individuals from four minority populations of China, and to obtain the polymorphism information in these populations.

Methods: Nine loci in all samples were amplified by PCR. Products were electrophoresed on ABI PRISM 377 DNA sequencer.

Electrostatic recognition and induced fit in the kappa-PVIIA toxin binding to Shaker potassium channel.

Brownian dynamics (BD) and molecular dynamics (MD) simulations and electrostatic calculations were performed to study the binding process of kappa-PVIIA to the Shaker potassium channel and the structure of the resulting complex. BD simulations, guided by electrostatic interactions, led to an initial alignment between the toxin and the channel protein. MD simulations were then carried out to allow for rearrangements from this initial structure.

Human telomerase reverse transcriptase immortalizes bovine lens epithelial cells and suppresses differentiation through regulation of the ERK signaling pathway.

Telomerase is a specialized reverse transcriptase that extends telomeres of eukaryotic chromosomes. The functional telomerase complex contains a telomerase reverse transcriptase catalytic subunit and a telomerase template RNA. We have previously demonstrated that human telomerase reverse transcriptase (hTERT) catalytic subunit is functionally compatible with a telomerase template RNA from rabbit.

[Polymorphism of HLA-DRB1 in Han population in Yunnan and comparison with 9 Han populations].

129 samples of Han population in Yunnan province were detected by polymerase chain reaction and microtitre plate hybridization (PCR-MPH). The samples of DR*15 subgroup being detected by PCR-MPH were further analyzed by Single-Strand Conformation Polymorphism (SSCP). By first polymerase chain reaction and microtitre plate hybridization (PCR-MPH), all of the 129 samples were divided into the following subgroups, viz.

[Genetic analysis of 17 biallelic markers on Y chromosome in 3 Chinese ethnic group populations].

Objective: To study the genetic polymorphism of Y chromosome in different Chinese ethnic group populations.

Methods: Genotypes of 17 biallelic markers located in the nonrecombining portion of the Y chromosome in 76 men from 3 Chinese ethnic group populations (Han in Shandong, Bai in Yunnan, and Tu in Qinghai) were examined with polymerase chain reaction (PCR) and allelic-specific PCR (ASPCR). Their haplotypes made of these 17 binary markers were constructed.

[Regulation of pre-mRNA alternative spicing in U251 cells by TPA].

By using the mini-gene construct containing partial sequence of Bcl-X gene as model, we examined the function of TPA on Bcl-X pre-mRNA alternative splicing in vivo and vitro with RT-PCR and site-directed mutagesis assay. The results show that PKA signaling system can regulate Bcl-X pre-mRNA alternative splicing, the possible mechanism is that the responsible sequence affect the choice of the 5'-downstream or upstream splice site of Bcl-X pre-mRNA.

Human Bcl-2 activates ERK signaling pathway to regulate activating protein-1, lens epithelium-derived growth factor and downstream genes.

The proto-oncogene, bcl-2, has various functions besides its role in protecting cells from apoptosis. One of the functions is to regulate expression of other genes. Previous studies have demonstrated that Bcl-2 regulates activities of several important transcription factors including NF-kappaB and p53, and also their downstream genes.

[Immunogenecity of combined hepatitis A and B vaccine].

Objective: To observe the immunogenicity of combined hepatitis A and B vaccine (HAB).

Methods: The combined HAB vaccine was prepared and different concentrations of HAB were administered on mice in week 0, 4 and 24, and then we tested the antibodies to both hepatitis A virus and B virus. After the first injection, we tested the hepatitis A antigen-induced and hepatitis B surface antigen-induced stimulation indices in spleen monocyte as well as changes of CD4+ and CD8+ cell numbers.

Conformational flexibility of beta-secretase: molecular dynamics simulation and essential dynamics analysis.

Aim: Based on the structural analysis to reveal the mechanism of ligand binding to beta-secretase and the specificity of each binding sub-site.

Methods: Molecular dynamics was used to simulate on the ligand free beta-secretase and ligand bound beta-secretase. The trajectories were analyzed using the essential dynamics, and the significant conformational change was illustrated employing the DynDom program.

Simulating the interactions of toxins with K+ channels.

Toxins have been important tools to characterize the structures and functions of K+ channels in recent years due to their unique blockage of the K+ current and other physiological functions to the K+ channels, especially the voltage-gated K+ channels. Knowledge of the interacting surfaces between the toxins and the channels has been accumulated both from biological explorations and theoretical simulations. It has been found that the electrostatic potentials act as the driving force for the recognition of the toxins with the channels, and the orientation of the toxins over the channels follows the direction of the dipole moment.

Molecular dynamics simulations on SDF-1alpha: binding with CXCR4 receptor.

Insights into the interacting mode of CXCR4 with SDF-1alpha are crucial in understanding the structural and functional characteristics of CXCR4 receptor. In this paper a computational pipeline, integrating protein structure prediction, molecular dynamics simulations, automated molecular docking, and Brownian dynamics simulations were employed to investigate the dynamic and energetic aspects of CXCR4 associating with SDF-1alpha. The entire simulation revealed the surface distribution feature of electrostatic potentials and conformational "open-close" process of the receptor.

Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A.

The interaction of a series gag peptide analogues with human cyclophilin A (hCypA) have been studied employing molecular docking and 3D-QSAR approaches. The Lamarckian Genetic Algorithm (LGA) and divide-and-conquer methods were applied to locate the binding orientations and conformations of the inhibitors interacting with hCypA. Good correlations between the calculated interaction free energies and experimental inhibitory activities suggest that the binding conformations of these inhibitors are reasonable.

Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels.

The recognition of the scorpion toxin maurotoxin (MTX) by the voltage-gated potassium (Kv1) channels, Kv1.1, Kv1.2, and Kv1.

Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1: molecular docking and 3D QSAR analyses.

The Lamarckian genetic algorithm of AutoDock 3.0 has been employed to dock 40 1,5-diarylpyrazole class compounds into the active sites of cyclooxygenase-2 (COX-2) and cyclooxygenase-1 (COX-1). The binding models were demonstrated in the aspects of inhibitor's conformation, subsite interaction, and hydrogen bonding.

[A study of the relationship between MICA gene and systemic lupus erythematosus].

Objective: To investigate the relationship between major histocompatibility complex class I chain-related A(MICA) gene and systemic lupus erythematosus (SLE).

Methods: The alleles and frequencies of exons 4 and 5 of MICA gene were determined in 70 cases of SLE and 152 controls of Yunnan Hans by STR genotyping, polymerase chain reaction, single strand conformation polymorphism and bidirection DNA sequencing.

Results: Five alleles of exon 5 and 10 alleles of exon 4 were found in this study.

New p-methylsulfonamido phenylethylamine analogues as class III antiarrhythmic agents: design, synthesis, biological assay, and 3D-QSAR analysis.

Class III antiarrhythmic agents selectively delay the effective refractory period (ERP) and increase the transmembrane action potential duration (APD). Using dofetilide (2) as a template of class III antiarrhythmic agents, we designed and synthesized 16 methylsulfonamido phenylethylamine analogues (4a-d and 5a-l). Pharmacological assay indicated that all of these compounds showed activity for increasing the ERP in isolated animal atrium; among them, the effective concentration of compound 4a is 1.