Structural Insight into Anaphase Promoting Complex 3 Structure and Docking with a Natural Inhibitory Compound.

Background: Anaphase promoting complex (APC) is the biggest Cullin-RING E3 ligase and is very important in cell cycle control; many anti-cancer agents target this. APC controls the onset of chromosome separation and mitotic exit through securin and cyclin B degradation, respectively. Its APC3 subunit identifies the APC activators-Cdh1 and Cdc20.

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study.

Background: Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se.

Computational and nonglycosylated systems: a simpler approach for development of nanosized PEGylated proteins.

Cysteine PEGylation includes several steps, and is difficult to manage in practice. In the current investigation, the cysteine PEGylation of erythropoietin analogs was examined using computational and nonglycosylated systems to define a simpler approach for specific PEGylation. Two model analogs (E31C and E89C) were selected for PEGylation based on lowest structural deviation from the native form, accessibility, and nucleophilicity of the free thiol group.

Growth inhibition of MDA-MB-231 cell line by peptides designed based on uPA.

Interaction between urokinase-type plasminogen activator (uPA) and its receptor (uPAR) plays an important role in the progression of numerous cancer types including breast cancer by promoting tumor initiating, proliferation, invasion and metastasis. Hence, disruption of this interaction inhibits their downstream cascades and subsequently tumor growth. For this, we created two series of 8 and 10 amino acids linear peptides, derived from uPA binding region to target uPAR and studied the inhibition of proliferation in MDA-MB-231 cell line.

SDRL: a sequence-dependent protein side-chain rotamer library.

Since the introduction of the first protein side-chain rotamer library (RL) almost half a century ago, RLs have been components of many programs and algorithms in structural bioinformatics. Based on the dependence of side-chain dihedral angles on the local backbone, three types of RLs have been identified: backbone-independent, secondary-structure-dependent and backbone-dependent. In all previous studies, the effect of sequence specificity on side-chain conformational preferences was neglected.

Design, synthesis and biological evaluation of novel anti-cytokine 1,2,4-triazine derivatives.

A series of 16 novel 1,2,4-triazine derivatives bearing hydrazone moiety (7a-7p) have been designed, synthesized and evaluated for their activity to inhibit IL-1β and TNF-α production. All compounds are reported for the first time. The chemical structures of all compounds were confirmed by spectroscopic methods and elemental analyzes.

Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers.

Due to the increasing number of protein structures with unknown function originated from structural genomics projects, protein function prediction has become an important subject in bioinformatics. Among diverse function prediction methods, exploring known 3D-motifs, which are associated with functional elements in unknown protein structures is one of the most biologically meaningful methods. Homologous enzymes inherit such motifs in their active sites from common ancestors.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory.

Biochemical characterization of two recombinant ferredoxin reductases from Alcanivorax borkumensis SK2.

Alcanivorax borkumensis strain SK2 is a cosmopolitan oil-degrading oligotrophic marine γ-proteobacterium that exclusively uses petroleum hydrocarbons as sources of carbon and energy. Its ubiquity and unusual physiology suggest its global importance in the removal of hydrocarbons from polluted marine systems. The genome of A.

Immunological evaluation of predicted linear B-cell epitopes of human CD20 antigen.

The importance of B-lymphocyte-restricted differentiation antigen Bp35 (CD20) as a target for immunotherapeutic depletion of B cells is irrefutable. Several anti-human CD20 (anti-hCD20) monoclonal antibodies are expressed at different stages of development. However, resistance to anti-CD20 therapy has made the search for new alternatives imperative.

Phenylimino-2H-chromen-3-carboxamide derivatives as novel small molecule inhibitors of β-secretase (BACE1).

The inhibition of β secretase (BACE1) is potentially important approach to treatment of Alzheimer disease (AD). A novel series of 4-bromophenyl piperazine derivatives coupled to the phenylimino-2H-chromen-3-carboxamide scaffold were investigated as BACE1 inhibitors in this study. Docking study suggested that the phenyl-imino group of the scaffold establishes favorable π-π stacking interaction with side chain of Phe108 of flap pocket.

Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.

Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.

Prediction of the Human EP1 Receptor Binding Site by Homology Modeling and Molecular Dynamics Simulation.

The prostanoid receptor EP1 is a G-protein-coupled receptor (GPCR) known to be involved in a variety of pathological disorders such as pain, fever and inflammation. These receptors are important drug targets, but design of subtype specific agonists and antagonists has been partially hampered by the absence of three-dimensional structures for these receptors. To understand the molecular interactions of the PGE2, an endogen ligand, with the EP1 receptor, a homology model of the human EP1 receptor (hEP1R) with all connecting loops was constructed from the 2.

Design, modeling, and expression of erythropoietin cysteine analogs in Pichia pastoris: improvement of mean residence times and in vivo activities through cysteine-specific PEGylation.

In this study, the low-cost production of recombinant human erythropoietin cysteine analogs (Cys-rhEPOs) from Pichia pastoris and the potential to increase their serum residency and in vivo activity through cysteine-specific PEGylation were investigated. Three-dimensional structures of several Cys-rhEPOs were generated using homology modeling, and three stable Cys-rhEPOs were selected on the basis of model stability in molecular dynamics simulation and surface accessibility of the inserted cysteine. cDNAs encoding Cys-rhEPOs were constructed by site-directed mutagenesis and expressed as secreted proteins in flask cultures of P.

Protein-x of hepatitis B virus in interaction with CCAAT/enhancer-binding protein α (C/EBPα)--an in silico analysis approach.

Background: Even though many functions of protein-x from the Hepatitis B virus (HBV) have been revealed, the nature of protein-x is yet unknown. This protein is well-known for its transactivation activity through interaction with several cellular transcription factors, it is also known as an oncogene. In this work, we have presented computational approaches to design a model to show the structure of protein-x and its respective binding sites associated with the CCAAT/enhancer-binding protein α (C/EBPα).

Computational evaluation of some indenopyrazole derivatives as anticancer compounds; application of QSAR and docking methodologies.

A computational procedure was performed on some indenopyrazole derivatives. Two important procedures in computational drug discovery, namely docking for modeling ligand-receptor interactions and quantitative structure activity relationships were employed. MIA-QSAR analysis of the studied derivatives produced a model with high predictability.

Exploring a model of a chemokine receptor/ligand complex in an explicit membrane environment by molecular dynamics simulation: the human CCR1 receptor.

The seven transmembrane helices G-protein-coupled receptors (GPCRs) form one of the largest superfamilies of signaling proteins found in humans. Homology modeling, molecular docking, and molecular dynamics (MD) simulation were carried out to construct a reliable model for CCR1 as one of the GPCRs and to explore the structural features and the binding mechanism of BX471 as one of the most potent CCR1 inhibitors. In this study, BX471 has been docked into the active site of the CCR1 protein.

Design, modeling, expression, and chemoselective PEGylation of a new nanosize cysteine analog of erythropoietin.

Background: Recombinant human erythropoietin (rhEPO) is considered to be one of the most pivotal pharmaceutical drugs in the market because of its clinical application in the treatment of anemia-associated disorders worldwide. However, like other therapeutic proteins, it does not have suitable pharmacokinetic properties for it to be administrated at least two to three times per week. Chemoselective cysteine PEGylation, employing molecular dynamics and graphics in in silico studies, can be considered to overcome such a problem.

Rubredoxin reductase from Alcanivorax borkumensis: expression and characterization.

Oil pollution is an environmental problem of increasing importance. Alcanivorax borkumensis, with a high potential for biotechnological applications, is a key marine hydrocarbonoclastic bacterium and plays a critical role in the bioremediation of oil-polluted marine systems. In oil degrading bacteria, the first step of alkane degradation is catalyzed by a monooxygenase.

Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation.

In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed to construct a 3D model of CCR5. For this procedure, the X-ray crystal structure of bovine rhodopsin (1F88A) at 2.

QSAR analysis for some diaryl-substituted pyrazoles as CCR2 inhibitors by GA-stepwise MLR.

Quantitative relationships between calculated molecular structure and 26 diaryl-substituted pyrazoles CCR2 inhibitors were investigated by GA-stepwise multiple linear regression. In multiple linear regression analysis, the quantitative structure-activity relationship models were constructed by grouping descriptors and also dual selection of variables using genetic algorithm and stepwise selection methods from each group of the pool of all calculated descriptors. The accuracy of the proposed multiple linear regression model was demonstrated using the following evaluation techniques: cross-validation, validation through an external test set, and Y-randomization.

Application of partial least squares and radial basis function neural networks in multivariate imaging analysis-quantitative structure activity relationship: study of cyclin dependent kinase 4 inhibitors.

The detailed application of multivariate image analysis (MIA) method for the evaluation of quantitative structure activity relationship (QSAR) of some cyclin dependent kinase 4 inhibitors is demonstrated. MIA is a type of data mining methods that is based on data sets obtained from 2D images. The purpose of this study is to construct a relationship between pixels of images of investigated compounds as independent and their bioactivities as a dependent variable.

Molecular interaction of human serum albumin with paracetamol: spectroscopic and molecular modeling studies.

The interaction between paracetamol and human serum albumin (HSA) under physiological conditions has been investigated by fluorescence, circular dichroism (CD) and docking. Fluorescence data revealed that the fluorescence quenching of HSA by paracetamol was the result of the formed complex of HSA-paracetamol, and the binding constant (K(a)) and binding number obtained is 1.3 x 10(4) at 298 K and 2, respectively for the primary binding site.

A theory of mode of action of azolylalkylquinolines as DNA binding agents using automated flexible ligand docking.

Azolylalkylquinolines (AAQs) are a family of quinolines with varying degrees of cytotoxic activity (comparable or moderately superior to adriamycin in some cases) developed in the past decade in our group where their exact mode of action is still unclear. In this study the most probable DNA binding mode of AAQs was investigated employing a novel flexible ligand docking approach by using AutoDock 3.0.

An in vitro evaluation of human DNA topoisomerase I inhibition by Peganum harmala L. seeds extract and its beta-carboline alkaloids.

Purpose: Peganum harmala L. (Zygophyllaceae) seeds extract is one of the main components of an ethnobotanical preparation used in the treatment of neoplasms in Iran. Cytotoxic effects of P.