Taxifolin prevents postprandial hyperglycemia by regulating the activity of α-amylase: Evidence from an in vivo and in silico studies

There has been a dramatic increase in the prevalence of diabetes mellitus (DM) and its associated complications globally. The postprandial stage of DM involves prompt elevation in the levels of blood glucose and α-amylase, a carbohydrate-metabolizing enzyme is mainly involved in the regulation of postprandial hyperglycemia. This study was designed to assess the ability of a well-known flavonoid, taxifolin (TFN), against postprandial hyperglycemia and its inhibitory effects on α-amylase activity through the assessment of therapeutic potentials of TFN in an alloxan-induced diabetic animal model. The binding potential TFN with an α-amylase receptor was also investigated through molecular dynamics (MD) simulation and docking of to compare the binding affinities and energies of TFN and standard drug acarbose (ACB) with target enzyme. TFN significantly improved the postprandial hyperglycemia, lipid profile, and serum levels of α-amylase, lipase, and C-reactive protein in a dose-dependent manner when compared with that of either DM-induced and ACB-treated alloxan-induced diabetic rats. Moreover, TFN also enhanced the anti-oxidant status and normal functioning of the liver in alloxan-induced diabetic rats more efficiently as compared to that of ACB-treated alloxan-induced diabetic rats. Therapeutic potentials of TFN were also verified by MD simulation and docking results, which exhibited that the binding energy and affinity of TFN to bind with receptor was significantly higher as compared to that of ACB. Hence, the results of this study signify that TFN might be a potent inhibitor of α-amylase that has the potential to regulate the postprandial hyperglycemia along with its anti-inflammatory and anti-oxidant properties during the treatment of DM.     

人工操纵病毒的原子力显微镜研究

人工操纵生物大分子是目前科学研究的一个前沿领域, 我们利用改进的“分子梳”方法,首次实现了复杂的体系——一种线性噬菌体病毒的人工拉直与定向. 这种操纵是在大面积平整的固体表面实现的, 并利用原子力显微镜对拉直前后的病毒进行了观察与测量.     

The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective

The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein–protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.     

Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches,molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development

The essential biological function of phosphodiesterase (PDE) type enzymes is to regulate the cytoplasmic levels of intracellular second messengers, 3′,5′-cyclic guanosine monophosphate (cGMP) and/or 3′,5′-cyclic adenosine monophosphate (cAMP). PDE targets have 11 isoenzymes. Of these enzymes, PDE5 has attracted a special attention over the years after its recognition as being the target enzyme in treating erectile dysfunction. Due to the amino acid sequence and the secondary structural similarity of PDE6 and PDE11 with the catalytic domain of PDE5, first-generation PDE5 inhibitors (i.e. sildenafil and vardenafil) are also competitive inhibitors of PDE6 and PDE11. Since the major challenge of designing novel PDE5 inhibitors is to decrease their cross-reactivity with PDE6 and PDE11, in this study, we attempt to identify potent tadalafil-like PDE5 inhibitors that have PDE5/PDE6 and PDE5/PDE11 selectivity. For this aim, the similarity-based virtual screening protocol is applied for the “clean drug-like subset of ZINC database” that contains more than 20 million small compounds. Moreover, molecular dynamics (MD) simulations of selected hits complexed with PDE5 and off-targets were performed in order to get insights for structural and dynamical behaviors of the selected molecules as selective PDE5 inhibitors. Since tadalafil blocks hERG1 K channels in concentration dependent manner, the cardiotoxicity prediction of the hit molecules was also tested. Results of this study can be useful for designing of novel, safe and selective PDE5 inhibitors.     

Differential recognition of resveratrol isomers by the human estrogen receptor-alpha: molecular dynamics evidence for stereoselective ligand binding

Resveratrol (RSVL) is a phytoestrogen that occurs naturally in two forms (trans- (E) and cis- (Z)). We have conducted molecular dynamics (MD) studies to differentially characterize the estrogen receptor-alpha (ER-alpha) binding profiles of RSVL stereoisomers. Favorable orientations for RSVL isomers at the ER-alpha pocket were first inferred from (1) alignment with pharmacophoric elements of the pure ER-alpha agonists estradiol (E2) and (2) assessment of ligand recognition by the ER-alpha binding domain. Subsequently, these orientations for RSVL isomers were subjected to MD analyses versus E2. A 100-picosecond MD simulation revealed that E2 contributed four stable hydrogen bonds with the key ER-alpha pocket residue: Arg394, Glu353, His524, and Leu525. Further, E2 displayed favorable binding energy, conformational energy change (DeltaE), and movement of the binding pocket residues (RMSd). Compared to E2, (E)-RSVL lacked a hydrogen bond (HB) with His524 but formed three additional bonds with Gly521, Phe404, and Met343 of the ER-alpha pocket. Further, (E)-RSVL conferred more favorable energy of interaction, less favorable DeltaE, but comparable RMSd values. In contrast, (Z)-RSVL orientations missed hydrogen bonding (HB) with His524 and Leu525, two essential ligand binding residues, and/or produced considerably less favorable-binding energy, -DeltaE, and -RMSd values than did (E)-RSVL. In conclusion, the present study demonstrates the utility of this MD model in distinguishing between RSVL stereoisomers. The weak binding of (Z)-RSVL by the human ER-alpha binding is congruent with its inferior ligand profiles in ER-endowed biological systems. Further, evidence is provided for a considerable variation in the mode of recognition of the mixed agonist/antagonist (E)-RSVL, and the pure agonist E2.     

Exploration of the chlorpyrifos escape pathway from acylpeptide hydrolases using steered molecular dynamics simulations

Acylpeptide hydrolases (APH) catalyze the removal of an N-acylated amino acid from blocked peptides. APH is significantly more sensitive than acetylcholinesterase, a target of Alzheimer’s disease, to inhibition by organophosphorus (OP) compounds. Thus, OP compounds can be used as a tool to probe the physiological functions of APH. Here, we report the results of a computational study of molecular dynamics simulations of APH bound to the OP compounds and an exploration of the chlorpyrifos escape pathway using steered molecular dynamics (SMD) simulations. In addition, we apply SMD simulations to identify potential escape routes of chlorpyrifos from hydrolase hydrophobic cavities in the APH-inhibitor complex. Two previously proposed APH pathways were reliably identified by CAVER 3.0, with the estimated relative importance of P1 > P2 for its size. We identify the major pathway, P2, using SMD simulations, and Arg526, Glu88, Gly86, and Asn65 are identified as important residues for the ligand leaving via P2. These results may help in the design of APH-targeting drugs with improved efficacy, as well as in understanding APH selectivity of the inhibitor binding in the prolyl oligopeptidase family.     

Convergent adaptation to dangerous prey proceeds through the same first‐step mutation in the garter snake Thamnophis sirtalis

Convergent phenotypes often result from similar underlying genetics, but recent work suggests convergence may also occur in the historical order of substitutions en route to an adaptive outcome. We characterized convergence in the mutational steps to two independent outcomes of tetrodotoxin (TTX) resistance in separate geographic lineages of the common garter snake (Thamnophis sirtalis) that coevolved with toxic newts. Resistance is largely conferred by amino acid changes in the skeletal muscle sodium channel (Na_V1.4) that interfere with TTX‐binding. We sampled variation in Na_V1.4 throughout western North America and found clear evidence that TTX‐resistant changes in both lineages began with the same isoleucine‐valine mutation (I1561V) within the outer pore of Na_V1.4. Other point mutations in the pore, shown to confer much greater resistance, accumulate later in the evolutionary progression and always occur together with the initial I1561V change. A gene tree of Na_V1.4 suggests the I1561V mutations in each lineage are not identical‐by‐decent, but rather they arose independently. Convergence in the evolution of channel resistance is likely the result of shared biases in the two lineages of T. sirtalis—only a few mutational routes can confer TTX resistance while maintaining the conserved function of voltage‐gated sodium channels.     

Cladogram of Panamanian Clusia Based on Nuclear DNA: Implications for the Origins of Crassulacean Acid Metabolism

Abstract: The internal transcribed spacer (ITS) region of 18-26S nuclear ribosomal DNA repeat was sequenced for 31 of the approximately 40 species of Clusia known to occur in Panama. Several species from other genera of the Clusiaceae were used as outgroups in the phylogenetic calculation. High sequence alignment and minimal length variation among ITS-1, 5.8S and ITS-2 sequences facilitated determination of positional homology of nucleotide sizes. Sequence alignment was evaluated with character state (Maximum Parsimony) and distance methods (Neighbour Joining). Phylogenetic trees obtained with the two methods were largely concordant and revealed three main groups that roughly correspond to previous arrangements of species into three large morphological groups, the C. flava group, the C. minor group and the C. multiflora group. Because species of Clusia are either regular C₃ plants or exhibit crassulacean acid metabolism (CAM) involving varying proportions of CO₂ fixation in the dark versus the light, we mapped photosynthetic pathways onto the cladograms. Photosynthetic pathway classification was based on measurements of ¹³C/¹²C ratios of plant carbon and also on information available from the literature. Both the C. flava and C. minor group contained species exhibiting CAM, distributed on distinct branches of the cladograms, whereas the third group ( C. multiflora group) was composed of species which are not known to use CAM.     

Molecular docking, 3D-QSAR,molecular dynamics,synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors

Abstract

A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3?D quantitative structure–activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.     

Insights into the interaction of ulipristal acetate and human serum albumin using multi-spectroscopic methods,molecular docking,and dynamic simulation

Interaction between ulipristal acetate (UPA) and human serum albumin (HSA) was investigated in simulated physiological environment using multi-spectroscopic and computational methods. Fluorescence experiments showed that the quenching mechanism was static quenching, which was confirmed by the time-resolved fluorescence. Binding constants (K_a) were found to be 1?×?10⁵ L mol^?1, and fluorescence data showed one binding site. Thermodynamic constants suggested the binding process was mainly controlled by electrostatic interactions. Results from the competition experiments indicated that UPA bound to site I of HSA. Fourier transform infrared spectra, circular dichroism spectra, synchronous fluorescence spectra, and 3D fluorescence indicated that UPA can induce conformation change in the HSA. The content of α-helix and β-sheet increased, while β-turn decreased. Hydrophobicity around the tryptophan residues declined, whereas its polarity increased. Molecular docking results were consistent with the experimental results. Results suggested that UPA located at the hydrophobic cavity site I of HSA, and hydrophobic force played the key role in the binding process. Moreover, molecular dynamics simulation was performed to determine the stability of free HSA and HSA-UPA system. Results indicated that UPA can stabilize HSA to a certain degree and enhance the flexibility of residues around site I.

Communicated by Ramaswamy H. Sarma     

分子标记技术在玉米品种分析中的初步应用

以玉米沈丹16、沈丹2100的可见叶片为材料,采用CTAB-Ⅱ方法提取玉米基因组DNA,然后应用RAPD分子标记技术对基因组DNA进行多态性扩增。结果是：从RAPD反应所用的40个随机引物中筛选出11个适宜引物,共扩增出63条谱带,其中14条为差异性谱带,其余引物没有扩增出谱带,被淘汰;此次实验的RAPD反应系统虽然较成功,但不是最佳的,今后要进一步优化。     

Dynamic control of allosteric antagonism of leukocyte function antigen-1 and intercellular adhesion molecule-1 interaction

Leukocyte function associated antigen-1 (LFA-1) plays a critical role in T cell migration and has been recognized as a therapeutic target for immune disorders. Several classes of small molecule antagonists have been developed to block LFA-1 interaction with intercellular adhesion molecule-1 (ICAM-1). Recent structural studies show that the antagonists bind to an allosteric site in the I-domain of LFA-1. However, it is not yet clear how these small molecules work as antagonists since no significant conformational change is observed in the I-domain-antagonist complex structures. Here we present a computational study suggesting how these allosteric antagonists affect the dynamics of the I-domain. The lowest frequency vibrational mode calculated from an LFA-1 I-domain structure shows large scale "coil-down" motion of the C-terminal alpha7 helix, which may lead to the open form of the I-domain. The presence of an allosteric antagonist greatly reduces this motion of the alpha7 helix as well as other parts of the I-domain. Thus, our study suggests that allosteric antagonists work by eliminating breathing motion that leads to the open conformation of the I-domain.     

Towards optimal packing and diffusion of fullerene molecules in the Pc-PBBA covalent organic framework

We studied the adsorption and diffusion of the prototypical n-type semiconducting fullerene molecule, C₆₀, inside the pores of the p-type semiconductor, phthalocyanine phenylene-bis(boronic acid) (Pc-PBBA), a member of the class of two-dimensional covalent organic framework (COF) materials. This C₆₀/Pc-PBBA system is an example of an ordered p–n heterojunction suitable for photovoltaic solar cell applications. We found that the small 1.7 Å lateral offset present between COF layers leads to discrete adsorption sites inside the pore, forming essentially a periodic ‘lattice’ on which the fullerene diffuses. By categorising the location of such lattice sites, we found the maximum theoretical packing density of fullerene in representative helical, zigzag and staircase Pc-PBBA stacks, as well as an average packing density in randomly stacked Pc-PBBA layers. All these simulated packing densities (51% of bulk) closely matched related experimental results by Dogru et al. [M. Dogru, M. Handloser, F. Auras, T. Kunz, D. Medina, A. Hartschuh, P. Knochel, T. Bein. A photoconductive thienothiophene-based covalent organic framework showing charge transfer towards included fullerene. Angew Chem Int Ed. 2013;52:2920–2924]. (49% of bulk) for a similar fullerene–COF system, [6,6]-phenyl-C₆₁-butyric acid methyl ester/thienothiophene–COF, which produced a low power conversion efficiency. This shows that there is little improvement to be made to the electron transport in terms of fullerene packing density. We present values of the barriers for all diffusion pathways between neighbouring lattice sites categorised uniquely by a set of symmetry rules. Knowledge of these barriers allows us to generalise fullerene transport mechanisms within the Pc-PBBA pore. We observe that diffusion along the (vertical) pore axis is faster than (lateral) diffusion perpendicular to the pore axis; this will facilitate pore filling.     

单核苷酸多态性在作物遗传及改良中的应用

单核苷酸多态性（single nucleotide polymorphism,SNP）是等位基因间序列差异最为普遍的类型,可作为一种高通量的遗传标记。已建立了PCR扩增目标序列及其产物测序和电子SNP（eSNP）等多种发现和检测SNP的方法。玉米和大豆等作物也已开展了SNP分析。一些栽培作物种质的多样性不断减少,其结果使连锁不平衡（linkage disequilibrium,LD）增加,这有利于目的基因座上SNP单元型（haplotype）与表型的相关性分析。SNP已在作物基因作图及其整合、分子标记辅助育种和功能基因组学等领域展示了广泛的应用价值。 Abstract:Single nucleotide polymorphism(SNP) is the most common type of sequence difference between alleles,which can be used as a kind of high-throughput genetic marker.Several different routes have been developed to discover and identify SNP.These include the direct sequencing of PCR amplicons,electronic SNP(eSNP) and so on.SNP assays have been made in many crop species such as maize and soybean.The elite germplasm of some crops have been narrowed in genetic diversity,increasing the amount of linkage disequilibrium(LD) present and facilitating the association of SNP haplotypes at candidate gene loci with phenotypes.SNP analysis has been broadly used in the field of plant gene mapping,integration of genetic and physical maps,DNA marker-assisted breeding and functional genomics.     

Insight into the key active sites of afChiA1 based on molecular dynamics simulations and free energy calculations

In this study, the binding of the enzyme chitinase A1 (afChiA1) from the plant-type Aspergillus fumigatus with four potent inhibitors, allosamidin (ASM), acetazolamide (AZM), 8-chloro-theophylline (CTP) and kinetin (KIT) is investigated by molecular docking, molecular dynamics simulation and binding free energy calculation. The results reveal that the electrostatic interactions play an important role in the stabilisation of the binding of afChiA1 with inhibitors. Based on the binding energy of afChiA1-ligands, the key residues (Gln37 and Trp312) in the active binding pocket of the complex systems are confirmed by molecular mechanics/Poisson–Boltzmann surface area method, and the active inhibitors, ASM and AZM, both could form strong interaction with Gln37 and Trp312, and the non-active ligands, CTP and KIT, could not interact with these two residues, which is consistent with the result of experimental report. Then, it is identified that Gln37 and Trp312 should be one of the important active site residues of afChiA1.     

Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize

Vgt1 (Vegetative to generative transition 1) is a quantitative trait locus (QTL) for flowering time in maize (Zea mays L.). Vgt1 was initially mapped in a ca. 5-cM interval on chromosome bin 8.05, using a set of near-isogenic lines (NILs) in the genetic background of the late dent line N28, with the earliness allele introgressed from the early variety Gaspé Flint. A new large mapping population was produced by crossing N28 and one early NIL with a ca. 6-cM long Gaspé Flint introgression at the Vgt1 region. Using PCR-based assays at markers flanking Vgt1, 69 segmental NILs homozygous for independent crossovers near the QTL were developed. When the NILs were tested in replicated field trials for days to pollen shed (DPS) and plant node number (ND), the QTL followed a Mendelian segregation. Using bulk segregant analysis and AFLP profiling, 17 AFLP markers linked to the QTL region were identified. Statistical analysis indicated a substantial coincidence of the effects of Vgt1 on both DPS and ND. Vgt1 was mapped at ca. 0.3 cM from an AFLP marker. As compared to DPS, the higher heritability of ND allowed for a more accurate assessment of the effects of Vgt1. The feasibility of the positional cloning of Vgt1 is discussed.     

Molecular docking and CoMFA studies of thiazoloquin(az)olin(on)es as CD38 inhibitors: determination of inhibitory mechanism,pharmacophore interactions,and design of new inhibitors

In this research, molecular docking and 3D-QSAR studies were carried out on a series of 79 thiazoloquin(az)olin(on)es as CD38 inhibitors. Based on docking results, four interactions including hydrogen bonding with main chain of GLU-226 (H-M-GLU-226), Van der Waals interactions with side chain of TRP-125 (V-S-TRP-125), TRP-189 (V-S-TRP-189), and THR-221 (V-S-THR-221) were considered as pharmacological interactions. Active conformation of each ligand was extracted from docking studies and was used for carrying out 3D-QSAR modeling. Comparative molecular field analysis (CoMFA) was performed on CD38 inhibitory activities of these compounds on human and mouse. We developed CoMFA models with five components as optimum models for both data-sets. For human data-set, a model with high predictive power was developed. R², RMSE, and F-test values for training set of this model were .94, .24, and 179.58, respectively, and R² and RMSE for its test set were .92 and .32, respectively. The q² and RMSE values for leave-one-out cross validation test on training set were .78 and .46, respectively, that demonstrate created model is robust. Based on extracted steric and electrostatic contour maps for this model, three inhibitors with pIC₅₀ larger than 8.85 were designed.     

A randomized clinical trial on the antitumoral effects of low molecular weight heparin in the treatment of esophageal cancer

The current treatment approaches for esophageal cancer are associated with poor survival, and there are ongoing efforts to find new and more effective therapeutic strategies. There are several reports on the antitumoral effects of low-molecular-weight heparins (LMWHs). We have assessed the possible survival benefit of LMWHs in esophageal malignancies. This was a randomized, single-blind, multicenter, Phase II clinical trial on nonmetastatic esophageal cancer candidate for neoadjuvant chemoradiotherapy. Patients were randomly assigned to the chemoradiotherapy-only arm or chemoradiotherapy plus enoxaparin arm using 1:1 allocation. Radiotherapy was delivered in 1.8-Gy daily fractions to a dose of 50.4 Gy in both groups. Paclitaxel 50 mg/m² and carboplatin (AUC 2) were administered weekly, concurrent with radiotherapy. In the intervention group, patients received enoxaparin (40 mg) and chemoradiation daily. 4–6 weeks after treatment, all patients underwent esophagectomy. After a median follow up of 7 months, estimated 1 year disease-free survival (DFS) in the intervention group was 78.9% and was 70% in the control groups ( p = 0.5). Toxicity from the experimental treatment was minimal, and there were no treatment-related deaths. A pathologically complete response in intervention and control group was 64.8% and 62.5%, respectively ( p = 0.9). There was a nonsignificant trend toward improved survival by the addition of enoxaparin to the concurrent chemoradiotherapy regimen. However, 1 y DFS of both groups were high as expected. A longer follow-up and a larger sample size are required.