Molecular docking and structure-based virtual screening studies of potential drug target,CAAX prenyl proteases,of Leishmania donovani

Targeting CAAX prenyl proteases of Leishmania donovani can be a good approach towards developing a drug molecule against Leishmaniasis. We have modeled the structure of CAAX prenyl protease I and II of L. donovani, using homology modeling approach. The structures were further validated using Ramachandran plot and ProSA. Active site prediction has shown difference in the amino acid residues present at the active site of CAAX prenyl protease I and CAAX prenyl protease II. The electrostatic potential surface of the CAAX prenyl protease I and II has revealed that CAAX prenyl protease I has more electropositive and electronegative potentials as compared CAAX prenyl protease II suggesting significant difference in their activity. Molecular docking with known bisubstrate analog inhibitors of protein farnesyl transferase and peptidyl (acyloxy) methyl ketones reveals significant binding of these molecules with CAAX prenyl protease I, but comparatively less binding with CAAX prenyl protease II. New and potent inhibitors were also found using structure-based virtual screening. The best docked compounds obtained from virtual screening were subjected to induced fit docking to get best docked configurations. Prediction of drug-like characteristics has revealed that the best docked compounds are in line with Lipinski’s rule. Moreover, best docked protein–ligand complexes of CAAX prenyl protease I and II are found to be stable throughout 20 ns simulation. Overall, the study has identified potent drug molecules targeting CAAX prenyl protease I and II of L. donovani whose drug candidature can be verified further using biochemical and cellular studies.     

Cutting edge: the nucleotide receptor P2X7 contains multiple protein- and lipid-interaction motifs including a potential binding site for bacterial lipopolysaccharide

The nucleotide receptor P2X7 has been shown to modulate LPS-induced macrophage production of numerous inflammatory mediators. Although the C-terminal portion of P2X7 is thought to be essential for multiple receptor functions, little is known regarding the structural motifs that lie within this region. We show here that the P2X7 C-terminal domain contains several apparent protein-protein and protein-lipid interaction motifs with potential importance to macrophage signaling and LPS action. Surprisingly, P2X7 also contains a conserved LPS-binding domain. In this report, we demonstrate that peptides derived from this P2X7 sequence bind LPS in vitro. Moreover, these peptides neutralize the ability of LPS to activate the extracellular signal-regulated kinases (ERK1, ERK2) and to promote the degradation of the inhibitor of kappaB-alpha isoform (IkappaB-alpha) in RAW 264.7 macrophages. Collectively, these data suggest that the C-terminal domain of P2X7 may directly coordinate several signal transduction events related to macrophage function and LPS action.     

Nonparametric approach to multitrait selection for yield in groundnut (Arachis hypogaea L.)

Summary Eight characters related to nitrogen fixation and pod development measured 30 days after flowering were evaluated for their correct grading of the relative yield performance of 17 genetically diverse lines of groundnut (Arachis hypogaea L.). Each line was assigned a high or low yield status based on its pod yield, shelling percentage, and 100-kernel weight. Seventeen character combinations were examined for their relative merit in correct identification of the yield status of lines. The character sets, nitrogenase activity alone or in combination with nitrogen percent or shoot weight identified the status of 77% of lines correctly. The extent to which various characters accounted for the variation in pod yield was also checked by multiple regression analysis. While the character combination, nitrogen percent plus leaf area explained 75% of variation in pod yield, nodule mass, nitrogenase activity, and leaf area occurred in some other combinations that explained yield variation to a lesser extent. These analyses point to the profitability of involving crop physiological traits such as leaf area and nitrogen percent in selecting for relative yield performance in groundnut.IARI Regional Station, Tutikandi, Simla 171004, IndiaNational Research Center for Groundnut, Timbawadi, Junagadh 362015, India     

“Thioureidopeptide”: Novel Synthon for the Synthesis of <Emphasis Type="Italic">N,N′, N″</Emphasis>-Trisubstituted Guanidinopeptide Mimics

The synthesis of N ^α-protected N,N′,N″-trisubstituted guanidinopeptide mimic molecules suitably decorated in peptide backbone has been delineated in one pot employing HgCl₂ as a desulphurizing agent. Chiral N ^α -protected thioureidopeptide esters were employed as synthons for the synthesis of title molecules. The protocol is simple and the reaction conditions employed were mild, amenable to the amino acid chemistry.     

微生物合成纳米银的一般方法及产物性质鉴定与生产应用

纳米银具有独特的理化性质,在化学、医药等领域应用广泛,但使用化学和物理法生产纳米银毒性较强且污染严重,因此,微生物法成为了一种可供替代的绿色生产技术。近年来,微生物法合成纳米银的报道逐渐增多,对其反应条件和产物性质的研究趋于成熟,纳米银也开始与多个应用领域相结合。归纳现有微生物合成方法的规律,阐述产物的性质及应用,比较其与传统材料的优势与不足,将有助于推动微生物与纳米技术的结合与进步。基于国内外学者的报道和本课题组所开展的相关研究,本文对微生物法合成纳米银的一般检验手段和功能鉴定方法进行综述,并就纳米银的应用展开设想与讨论,以期为微生物法合成纳米银的深入研究和优化改进提供参考。     

Altered LV inotropic reserve and mechanoenergetics early in the development of heart failure

To test the hypothesis that alterations in left ventricular (LV) mechanoenergetics and the LV inotropic response to afterload manifest early in the evolution of heart failure, we examined six anesthetized dogs instrumented with LV micromanometers, piezoelectric crystals, and coronary sinus catheters before and after 24 h of rapid ventricular pacing (RVP). After autonomic blockade, the end-systolic pressure-volume relation (ESPVR), myocardial O(2) consumption (MVO(2)), and LV pressure-volume area (PVA) were defined at several different afterloads produced by graded infusions of phenylephrine. Short-term RVP resulted in reduced preload with proportionate reductions in stroke work and the maximum first derivative of LV pressure but with no significant reduction in baseline LV contractile state. In response to increased afterload, the baseline ESPVR shifted to the left with maintained end-systolic elastance (E(es)). In contrast, after short-term RVP, in response to comparable increases in afterload, the ESPVR displayed reduced E(es) (P < 0.05) and significantly less leftward shift compared with control (P < 0.05). Compared with the control MVO(2)-PVA relation, short-term RVP significantly increased the MVO(2) intercept (P < 0.05) with no change in slope. These results indicate that short-term RVP produces attenuation of afterload-induced enhancement of LV performance and increases energy consumption for nonmechanical processes with maintenance of contractile efficiency, suggesting that early in the development of tachycardia heart failure, there is blunting of length-dependent activation and increased O(2) requirements for excitation-contraction coupling, basal metabolism, or both. Rather than being adaptive mechanisms, these abnormalities may be primary defects involved in the progression of the heart failure phenotype.     

Computational exploration of polymorphisms in 5-hydoxytryptamine 5-HT₁A and 5-HT₂A receptors associated with psychiatric disease

The huge polymorphic data have been prioritized towards a specific disease based on sequence and structure homology tools to a large extent. In this study, we have explored the potential non-synonymous Single Nucleotide Polymorphism (nsSNP) in serotonin (5-HT) receptors involved in psychotic syndromes and their response pathway. The most damaging point mutations were screened from 12 classes of serotonin receptors comprising 7743 variants. In 5HT(1A) receptor, two alleles were found to be highly deleterious located at ligand binding extracellular-2 and one at intracellular loop-3 domains. Similarly, we found two alleles predicted to be highly damaging in 5HT(2A) residing at N and C-Terminal domains. The above alleles were further confirmed based on their flexibility and stability difference using the molecular dynamic simulation analysis. Integrating these results appeared promising for being able to filter out potential non-synonymous Single Nucleotide Polymorphisms for neuropsychiatric disorders.     

A Coupled Experiment-finite Element Modeling Methodology for Assessing High Strain Rate Mechanical Response of Soft Biomaterials

This study offers a combined experimental and finite element (FE) simulation approach for examining the mechanical behavior of soft biomaterials (e.g. brain, liver, tendon, fat, etc.) when exposed to high strain rates. This study utilized a Split-Hopkinson Pressure Bar (SHPB) to generate strain rates of 100-1,500 sec^-1. The SHPB employed a striker bar consisting of a viscoelastic material (polycarbonate). A sample of the biomaterial was obtained shortly postmortem and prepared for SHPB testing. The specimen was interposed between the incident and transmitted bars, and the pneumatic components of the SHPB were activated to drive the striker bar toward the incident bar. The resulting impact generated a compressive stress wave (i.e. incident wave) that traveled through the incident bar. When the compressive stress wave reached the end of the incident bar, a portion continued forward through the sample and transmitted bar (i.e. transmitted wave) while another portion reversed through the incident bar as a tensile wave (i.e. reflected wave). These waves were measured using strain gages mounted on the incident and transmitted bars. The true stress-strain behavior of the sample was determined from equations based on wave propagation and dynamic force equilibrium. The experimental stress-strain response was three dimensional in nature because the specimen bulged. As such, the hydrostatic stress (first invariant) was used to generate the stress-strain response. In order to extract the uniaxial (one-dimensional) mechanical response of the tissue, an iterative coupled optimization was performed using experimental results and Finite Element Analysis (FEA), which contained an Internal State Variable (ISV) material model used for the tissue. The ISV material model used in the FE simulations of the experimental setup was iteratively calibrated (i.e. optimized) to the experimental data such that the experiment and FEA strain gage values and first invariant of stresses were in good agreement.     

Higher frequency of dicentrics and micronuclei in peripheral blood lymphocytes of cancer patients

The presence of dicentric chromosome (DC) and micronuclei (MN) frequency in the peripheral blood lymphocytes of 25 cancer patients prior to chemo and radiotherapy and 21 healthy volunteers were studied. The overall DC and MN showed significantly higher frequency compared to those obtained in normal healthy volunteers (p<0.0001). However, among 25 patients only 15 showed a higher frequency of DC aberration, nine patients showed the presence of minutes (M) and seven patients showed chromatid breaks (ChB). The reasons for the higher frequency of aberration observed in these cancer patients are discussed in this paper.