Molecular Design of Novel Ligands for 5-HT1A Receptors

Abstract

Serotonin (5-HT) is a potent bioactive substance known to function through a number of different receptor types and subtypes. In our attempt to develop new agents that would interact selectively at certain 5-HT receptors, especially the 5-HT_1A subtype, 8-hydroxy-2-di-n-propylamino tetralin (8-OH-DPAT) served as a template for the design of novel agents sharing aspects of the pharmacophore of 8-OH-DPAT and 5-HT. 5-HT contains no center of asymmetry, and 8-OH-DPAT shows only very modest stereospecificity for 5-HT_1A receptors. To develop agents having enhanced potency and selectivity for the 5-HT_1A site, several ring systems offering enhanced conformational rigidity which approximate the oxygen to nitrogen interatomic distances of 8-OH-DPAT and (to a lesser extent) 5-HT were synthesized. Exemplary ring systems include the 8-alkoxy-hexahydroindeno[1,2-c]pyrrole, 5-alkoxy-hexahydro-1H-indeno-[2,1-c]pyridine, and 9-alkoxy-hexahydro-1H-benz[e]isoindole systems. These couformationally restricted molecules demonstrated moderate stereospecificity in their interaction with the 5-HT_1A binding site, which was enhanced in compounds with larger nitrogen substituents. Appropriate choice of such derivatives led to highly potent compounds selective for 5-HT_1A sites compared with their activity at other 5-HT and/or adrenergic receptors. The pharmacological profile of compounds which appear to act as agonists at 5-HT_1A receptors in the central nervous system to lower blood pressure in animal models of hypertension is presented     

Computationally Design of Inhibitory Peptides Against Wnt Signaling Pathway: In Silico Insight on Complex of DKK1 and LRP6

Wnt signaling pathway plays a major role in the regulation of cell proliferation, migration, tissue homeostasis, tumor progression and cancer. This pathway can be antagonized by different proteins such as DKK proteins, which disrupt the initiatory complex (Frizzled–LRP6 complex). Therefore, interruption of its formation could be a promising strategy for the design of Low-density lipoprotein receptor-Related Protein 6 (LRP6) inhibitors. A computational study was conducted in order to assist in the design of inhibitory peptides against LRP6 as co-receptor of frizzled. Twelve fragments as peptide derivatives of natural ligand of LRP6 receptor (DKK1) were designed using the information from the analysis of the DKK1_C/LRP6 complex, hot spot residues and the secondary structure. These fragments were based on cys2 domain of DKK1. The designed peptides were energy minimized by molecular dynamics simulations in the presence and absence of LRP6 receptor and their binding affinities were investigated via molecular docking using ClusPro, HADDOCK and PRODIGY webservers. Finally, the stability and free energy of binding in peptides were calculated by FoldX software. The results showed that four designed peptides had the highest affinity (the interaction energy: ?10.2867, ?10.1388, ?7.94339 and ?7.57536 kcal/mol) to interact with the receptor which showed the most interacting residues and the lowest free energy of binding. Also, the RMSD, RMSF and RoG of the protein–peptide complex exhibited less structural fluctuations which can be linked to the stability of peptides associated to the receptor. These peptides may be considered as candidates for inhibiting Wnt signaling pathway through LRP6 receptor.     

A Novel Design of Multi-epitope Vaccine Against Helicobacter pylori by Immunoinformatics Approach

International Journal of Peptide Research and Therapeutics - Helicobacter pylori (H. pylori) is a gram-negative spiral bacterium that caused infections in half of the world’s population and...     

A Novel Multi-Epitopic Peptide Vaccine Candidate Against Helicobacter pylori: In-Silico Identification,Design, Cloning and Validation Through Molecular Dynamics

International Journal of Peptide Research and Therapeutics - Helicobacter pylori is a highly potential pathogen to colonize in the human stomach. This bacterial strain is now alarming serious...     

杂交水稻育种将迎来新时代

杂种优势是生物界一种普遍的现象,在许多作物中得到应用．杂交水稻自20世纪70年代开始在中国大规模种植,对于粮食生产具有举足轻重的作用．现有的“三系法”和“两系法”杂交育种技术对粮食增产贡献巨大,但它们的技术缺陷也非常明显．本文在总结已有杂交育种技术的操作流程及优缺点的基础上,阐述了利用智能不育杂交育种技术,实现隐性雄性核不育材料在杂交水稻中应用的技术流程．这种飞跃性技术的运用将推动杂交水稻的生产进入一个新的时代．     

Novel Strategies to Construct Complex Synthetic Vectors to Produce DNA Molecular Weight Standards

DNA molecular weight standards (DNA markers, nucleic acid ladders) are commonly used in molecular biology laboratories as references to estimate the size of various DNA samples in electrophoresis process. One method of DNA marker production is digestion of synthetic vectors harboring multiple DNA fragments of known sizes by restriction enzymes. In this article, we described three novel strategies—sequential DNA fragment ligation, screening of ligation products by polymerase chain reaction (PCR) with end primers, and “small fragment accumulation”—for constructing complex synthetic vectors and minimizing the mass differences between DNA fragments produced from restrictive digestion of synthetic vectors. The strategy could be applied to construct various complex synthetic vectors to produce any type of low-range DNA markers, usually available commercially. In addition, the strategy is useful for single-step ligation of multiple DNA fragments for construction of complex synthetic vectors and other applications in molecular biology field. Zhe Chen and Jianbing Wu contributed to this work equally.     

Design of Multiepitope Vaccine Construct Against Non-typhoidal Salmonellosis and its Characterization Using Immunoinformatics Approach

International Journal of Peptide Research and Therapeutics - Non-typhoidal salmonellosis (NTS) is a food-borne zoonotic disease of human and veterinary importance. Besides enteric infections, most...     

Design,Synthesis, Cytotoxic Screening and Molecular Docking Studies of Novel Hybrid Thiosemicarbazone Derivatives as Anticancer Agents

Thiosemicarbazones have been the focus of scientists owing to their broad clinical anticancer range. Herein, A Series of new thiosemicarbazone derivatives 5 – 9 were synthesized and confirmed through the use of different spectroscopic techniques along with elemental analysis. The in vitro cytotoxic activity of compounds 5 – 9 against MCF-7 and A549 cell lines and normal breast cells were assessed. Several compounds were found to be active. The most active compound 7 caused MCF-7 cell cycle arrest at G1/ S phases; and induced apoptosis at the pre-G1 phase. The apoptosis-inducing activity of compound 7 was proofed by the elevation of caspase 3/7 activity and also by up-regulation of the expression of Bax and p53 proteins together with the down-regulation of the expression of the Bcl-2 protein. It also had a strong inhibitory effect topoisomerase IIβ enzyme. Molecular Docking study revealed that the synthesized compounds had good docking scores compared to the standard drug Etoposide towards the topoisomerase IIβ protein (3QX3). Overall, these findings confirmed that the new thiosemicarbazone derivatives could aid in the development of promising cancer drug candidates.     

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.     

Molecular Design of Interfacial Modifiers for Polymer‐Inorganic Hybrid Solar Cells

The heterojunction of poly(3‐hexylthiophene) (P3HT) and TiO₂ in hybrid solar cells is systematically engineered with four cyanoacrylic acid‐containing conjugated molecules with various lowest unoccupied molecular orbital (LUMO) levels, WL‐1 to WL‐4, which are prepared by the formylation of thiophene derivatives in a Vilsmeier–Haack reaction, followed by treatment with cyanoacetic acid. The optical characteristics, redox properties, and intrinsic dipole moments of these interfacial modifiers (IMs) are examined using UV‐vis spectrophotometry, cyclic voltammetry, and density functional theory calculations. Using cyanoacrylic acid as a terminal anchoring group in IMs increases the electron affinity in regions close to the titania surface and forms a molecular dipole that is orientated away from the TiO₂ surface, enabling both open‐circuit voltage (V_OC) and short‐circuit current density to be increased simultaneously. Photovoltaic measurements demonstrate that V_OC increases with the dipole moment of IMs along the molecular backbone. Moreover, the external quantum efficiency (EQE) spectra display a bimodal distribution, revealing that both IMs and P3HT contribute to the photocurrent. The EQE at 570 nm is identified as characteristic of P3HT. More importantly, the LUMO of the IMs decisively determines the dissociation efficiency of P3HT excitons. The device based on P3HT/WL‐4/TiO₂ exhibits the highest power conversion efficiency of 2.87%.     

Design and Formulation Technique of a Novel Drug Delivery System for Azithromycin and its Anti-Bacterial Activity Against Staphylococcus aureus

Azithromycin, an important member of the azalide subclass is effective against both Gram-positive and Gram-negative organisms. Certain physicochemical properties of the drug like poor water solubility and relatively low bioavailability of 37% due to incomplete absorption after ingestion, aroused the need for the development of a novel drug delivery system to enhance the solubilization potential and antibacterial activity against Staphylococcus aureus at a very low concentration. Cinnamon oil (Cinnamonum zeylanicum)-based microemulsion system formulated using non-ionic surfactant, Tween 20, and water was characterized. The drug-incorporated system F4 (oil to surfactant ratio of 1:4 (v/v)) showed enhanced solubilization of the drug, droplet diameter of 5–8 nm, and a good thermodynamic stability. The effect of surfactant concentration exhibited a negative correlation with droplet size diameter and turbidity and a positive correlation with stability and viscosity. The system was investigated for its antibacterial activity that demonstrated a significantly higher activity at a minimum concentration (4 μg/ml) of the novel drug-loaded system in comparison with the conventional formulation (128 μg/ml). Examination through scanning electron microscopy analysis further confirmed a considerable morphologic variation due to alteration in the membrane permeability of the microemulsion-treated system. The small droplet size of the microemulsion system and the antibacterial property of cinnamon oil, together, accounts clearly for the enhanced efficacy of the new formulated system F4 and not just azithromycin alone. Staining with acridine orange/ethidium bromide dyes as examined through fluorescence microscopy also substantiated with the results of membrane permeability of bacteria. Thus, our study discloses a potential oral drug delivery system of azithromycin with improved biocompatibility.     

A Hybrid Computational Method for the Discovery of Novel Reproduction-Related Genes

Uncovering the molecular mechanisms underlying reproduction is of great importance to infertility treatment and to the generation of healthy offspring. In this study, we discovered novel reproduction-related genes with a hybrid computational method, integrating three different types of method, which offered new clues for further reproduction research. This method was first executed on a weighted graph, constructed based on known protein-protein interactions, to search the shortest paths connecting any two known reproduction-related genes. Genes occurring in these paths were deemed to have a special relationship with reproduction. These newly discovered genes were filtered with a randomization test. Then, the remaining genes were further selected according to their associations with known reproduction-related genes measured by protein-protein interaction score and alignment score obtained by BLAST. The in-depth analysis of the high confidence novel reproduction genes revealed hidden mechanisms of reproduction and provided guidelines for further experimental validations.     

In Vitro Characterization of Novel Protegrin-1 Analogues Against Neoplastic Cells

Even with the great advances in cancer therapies, cancer remains the major cause of death worldwide. The use of high doses of anti-cancer chemotherapeutic drugs eventually causes the inevitable damage in non-neoplastic cells. New, selective, and more effective drugs are therefore urgently required to fight cancer. In this study, the anticancer activity of new peptide analogues (P1 and P2) derived from natural peptide, protegrin-1 (PG-1) were evaluated against human breast carcinoma cell lines (MCF-7) and human non-neoplastic mammary epithelial cell lines (MCF-10A), human hepatocellular carcinoma cells (HepG2) and Vero cells. The CC₅₀ values of cancer cells were significantly lower (P < 0.01) compared to non-neo-plastic cells after treating with P1 and P2 analogues. The analogues of PG-1 showed lower percentage of Lactate Dehydrogenase release (P < 0.001) from non-neoplastic cells compared to cancer cells and low haemolytic potential (P < 0.001) compared to PG-1. The P1 and P2 analogues were shown to be able to induce cancer cell senescence and apoptosis in a p53-dependent pathway which in turn, induced caspase activities and subsequent cell death. Overall, these results suggested that designing shorter peptides, as well as altering the number and position of positive charged residues in P1 and P2 analogues resulted in reduction of their toxicity to non-neoplastic cells and increased selectivity towards cancer cells. Increased selectivity also suggests its potential use to be developed as delivery vectors in the design of chemotherapeutic anticancer drugs.     

Harnessing Bioinformatic Approaches to Design Novel Multi-epitope Subunit Vaccine Against Leishmania infantum

International Journal of Peptide Research and Therapeutics - Kala-azar or visceral leishmaniasis (VL) is the most important vector-borne protozoan disease and a life-threatening problem in the...     

小鼠新分泌蛋白基因mBolA1的克隆与鉴定

采用生物信息学工具预测与实验相结合的方法得到了一个新的小鼠分泌蛋白基因mBolA1。该基因定位于染色体3F2,cDNA全长为730bp,编码137个氨基酸的蛋白,该蛋白含有一个保守的BolA结构域,等电点为9.05。用RT-PCR方法从鼠的混合cDNA库中克隆到mBolA1。Western blot实验表明mBolA1能从瞬转的COS 7细胞中分泌到细胞培养液中。亚细胞定位显示mBolA1定位于细胞浆,且与高尔基体不共定位,提示它是个非经典分泌途径的分泌蛋白。RT PCR显示mBolA1在组织中广泛表达。它的具体功能有待进一步研究。     

Computational Design and Analysis of a Multi-epitope Against Influenza A virus

International Journal of Peptide Research and Therapeutics - Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed....