In silico platform for predicting and initiating β‐turns in a protein at desired locations

Numerous studies have been performed for analysis and prediction of β‐turns in a protein. This study focuses on analyzing, predicting, and designing of β‐turns to understand the preference of amino acids in β‐turn formation. We analyzed around 20,000 PDB chains to understand the preference of residues or pair of residues at different positions in β‐turns. Based on the results, a propensity‐based method has been developed for predicting β‐turns with an accuracy of 82%. We introduced a new approach entitled “Turn level prediction method,” which predicts the complete β‐turn rather than focusing on the residues in a β‐turn. Finally, we developed BetaTPred3, a Random forest based method for predicting β‐turns by utilizing various features of four residues present in β‐turns. The BetaTPred3 achieved an accuracy of 79% with 0.51 MCC that is comparable or better than existing methods on BT426 dataset. Additionally, models were developed to predict β‐turn types with better performance than other methods available in the literature. In order to improve the quality of prediction of turns, we developed prediction models on a large and latest dataset of 6376 nonredundant protein chains. Based on this study, a web server has been developed for prediction of β‐turns and their types in proteins. This web server also predicts minimum number of mutations required to initiate or break a β‐turn in a protein at specified location of a protein. Proteins 2015; 83:910–921. © 2015 Wiley Periodicals, Inc.     

含preS2免疫表位的HBsAg基因质粒的构建及表达

目的：应用表位设计构建高效表达乙型肝炎表面抗原含preS2免疫原位基因的真核表达质粒。方法：PCR法从慢性乙型肝炎患者血清中扩增和分离preS2 120-146表位和S基因片段,将两者融合并置于载体pcDNA3.1的巨细胞病（CMV）启动子作用之下,构建真核表达质粒pcDNA-S2S。序列分析和脂质体转染COS-7细胞瞬时表达鉴定。结果：序列测定结果表明插入序列与乙型肝炎病毒中国株全基因参照序列（adr亚型）一致,COS-7细胞瞬时表达鉴定实验中,ELISA检测到preS2-Ag和HBsAg的OD450分别为0.469和0.426。结论：应用表位设计成功地构建了含preS2免疫表位基因的重组质粒pcDNA-S2S所构建质粒能高效表达和分泌目的的蛋白。     

Iodine catalyzed three component synthesis of 1-((2-hydroxy naphthalen-1-yl)(phenyl)(methyl))pyrrolidin-2-one derivatives: Rationale as potent PI3K inhibitors and anticancer agents

A series of 1-((2-hydroxynaphthalen-1-yl)(phenyl)(methyl))pyrrolidin-2-one derivatives by an efficient iodine catalyzed domino reaction involving various aromatic aldehydes, 2-pyrrolidinone and β-naphthol was achieved and the structures were elucidated by FTIR ¹H NMR, ¹³C NMR, and HRMS. Subsequently they were evaluated for cytotoxicity against breast cancer (MCF-7), colon cancer (HCT116) cell lines. In the cytotoxicity, the relative inhibition activity was remarkably found to be high in MCF-7 cell lines as 79% (4c), 83% (4f) and the IC₅₀values were 1.03 µM (4c), 0.98 µM (4f). Compounds 4a, 4e, 4k–m, and 4q were found to be inactive and rest showed a moderate activity. In order to get more insight into the binding mode and inhibitor binding affinity, compounds (4a–q) were docked into the active site phosphoinositide 3-kinase (PI3K) (PDB ID: 4JPS) which is a crucial regulator of apoptosis or programmed cell death. Results suggested that the hydrophobic interactions in the binding pockets of PI3K exploited affinity of the most favourable binding ligands (4c and 4f: inhibitory constant (ki) = 66.22 nM and 107.39 nM). The SAR studies demonstrated that the most potent compounds are 4c and 4f and can be developed into precise PI3K inhibitors with the capability to treat various cancers.     

A facile method for the construction of synthetic genes

A simple protocol for rapid assembly of chemically synthesized deoxyoligonucleotides into double stranded DNA is described. Several parameters of a ligation-free method were investigated to allow efficient assembly of a large number of oligonucleotides into double stranded DNA by polymerase chain reaction. Synthesis of a 701 bp DNA was carried out in a single reaction by assembling 28 oligonucleotides designed with partial overlaps at complementary ends. An estimate of error rate was made by sequencing several independent clones of the synthesized DNA     

MAPS Database: Medicinal plant Activities,Phytochemical and Structural Database

Drug development from natural sources is an important and fast developing area. Natural sources (plants) have been used to cure a range of diseases for Thousands of years. Different online medicinal plant databases provide information about classifications, activities, phytochemicals and structure of phytochemicals in different formats. These databases do not cover all aspects of medicinal plants. MAPS (Medicinal plant Activities, Phytochemicals & structural database) has been constructed with uniqueness that it combines all information in one web resource and additionally provides test targets on which particular plant found to be effective with reference to the original paper as well. MAPS database is user friendly information resource, including the data of > 500 medicinal plants. This database includes phytochemical constituents, their structure in mol format, different activities possessed by the medicinal plant with the targets reported in literature.

Availability

http://www.mapsdatabase.com     

DNA polymerase III α subunit from Mycobacterium tuberculosis H37Rv: Homology modeling and molecular docking of its inhibitor

The alpha subunit of Mycobacterial DNA polymerase III holo enzyme catalyzes the polymerization of both DNA strands. The present investigation reports three dimensional (3-D) structure model of DNA polymerase III α subunit of Mycobacterium tuberculosis H37Rv (MtbDnaE1) generated using homology modeling with the backbone structure of DNA polymerase III α of Thermus aquaticus as a template. The model was evaluated at various structure verification servers, which assess the stereo chemical parameters of the residues in the model, as well as structural and functional domains. Comparative analysis of MtbDnaE1 structure reveals the structure of its catalytic domain to be unrelated to that of the human. Successful docking of known inhibitor of bacterial DNA polymerases, 251D onto the modeled MtbDnaE1 was also performed. Therefore, the structure model of MtbDnaE1, a potential anti-mycobacterial target, opens a new avenue for structure-based drug designing against the pathogen. ABBREVIATIONS: aa - amino acid(s), PolIIIα - DNA polymerase III alpha subunit, Taq Pol IIIα - Pol IIIα of Thermus aquaticus, MtbDnaE1 - PolIIIα of Mycobacterium tuberculosis.     

Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria

CTX-M-15 are the most prevalent types of β-lactamases that hydrolyze almost all antibiotics of β-lactam group lead to multiple-antibiotic resistance in bacteria. Three β-lactam inhibitors are available for use in combination with different antibiotics of cephalosporine group against the CTX-M-15-producing strains. Therefore, strategies to identify novel anti β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we screened three novel non-β-lactam inhibitors against CTX-M-15 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Hence, we proposed a study to understand the binding mode of CTX-M-15 with inhibitors using bioinformatics and experimental approach. We calculated the dissociation constants (K_d), association constant (K_a), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets. Molecular dynamic simulation carried out for 25 ns, revealed that these complexes were found stable throughout the simulation with relative RMSD in acceptable range. Moreover, microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as a lead molecule for future drug candidates against β-lactamases-producing bacteria.     

t—PA S165W突变体的分子设计及其生物活性的初步分析

为得到对纤维蛋白的亲和力提高的ｔ－ＰＡ突变体,采用计算机分子技术提出对纤维蛋白亲和力提高的ｔ－ＰＡ结构改造方案（ｔ－ＰＡＳ１６５Ｗ）,并将共在ＣＨＯ细胞中进行表达,对表达产物进行生物活性及与纤维蛋白亲和力的分析表明;ｔ－ＰＡ Ｓ１６５Ｗ突变体与野生型ｔ－ＰＡ对蛋白的亲和力没有明显的变化,说明单一的Ｓ１６５Ｗ的点 变并不能导致ｔ－ＰＡ对蛋白亲和力的提高。     

生态旅游区的景观生态问题及其调控

目前,在生态旅游开发过程中存在着许多生态破坏现象,严重影响生态旅游的可持续发展,是生态旅游区建设中亟待重视的问题。本文总结了当前我国生态旅游区在发展生态旅游过程中存在的生态破坏问题,并运用景观生态学、旅游生态学的原理和方法提出了解决生态旅游区生态问题的景观生态调控对策和措施,包括进行旅游景观生态规划、设计合理的旅游生态管理容量、对旅游景观结构进行生态化设计、构建景观生态安全格局、加强旅游生态教育和旅游环境监测等方面。     

Stenotrophomonas maltophilia Gd2: A potential and novel isolate for fibrinolytic enzyme production

The bacterium with an ability to produce extracellular fibrinolytic protease was isolated and identified as Stenotrophomonas maltophilia Gd2 based on ribotyping. The in-vitro fibrinolytic profile of this enzyme depicted 73% of fibrin clot dissolution within 4 h. Fibrinolytic enzyme yield influenced by different physiological (incubation time, temperature, agitation and pH), nutritional (macronutrients such as carbon and nitrogen sources) and biological (inoculums age and inoculums concentration) parameters of fermentation which were optimized based on one-factor-at-a-time (OFAT) approach. The enzyme yield improved from 886 to 1795 FU ml⁻¹ upon OFAT; optimized conditions include temperature – 33 °C, pH – 8.0, incubation time – 36 h, agitation – 150 RPM, 3% v/v inoculums and age of inoculum – 18 h. Further optimization of enzyme production was achieved with implementation of Plackett-Burman media designing where the production levels increased to 3411 FU ml⁻¹ and noticed that peptone, pH, dextrose and K₂HPO₄ was found to be significant factor. This ms reports the highest fibrinolytic enzyme yield with S. maltophilia to that of literature reports.