scholarly journals Identification of Novel Chemical Entities for Mirk/Dyrk1B Receptor Using Molecular Modeling and Molecular Dynamic Approaches

2021 ◽  
Author(s):  
Ramar Vanajothi ◽  
Sundaresan Bhavaniramya ◽  
Muthu Umadevi ◽  
Rajendran Vijayakumar ◽  
Yaser E. Alqurashi ◽  
...  
Keyword(s):  
Cancer Prevention ◽  
3D Structure ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Major Health Problem ◽  
Antioxidant Genes ◽  
Dual Specificity ◽  
Pharmacokinetic Properties

Abstract Cancer is a major health problem worldwide and one of the leading death-causing diseases. Mirk (Minibrain-related kinase is a member of the dual-specificity tyrosine-phosphorylation-regulated kinase (Dyrk) family that is highly upregulated in various solid tumors and mediates cell survival including lung cancer. Mirk effectively increases the expression of a series of antioxidant genes, which scavenge the reactive oxygen species and stabilize the p27kip1 that maintain the viability of the quiescent cancer cell and also mediates the cell cycle and survival of cancer cells by influencing the MAPK/ERK signaling pathway. Hence, Mirk acts as a novel therapeutic target for cancer prevention. Owing to the unavailability of the three-dimensional structure of Mirk, in the present study, we have modeled the 3D structure of Mirk, based on the crystal structure of Dyrk1a as a template, and subsequently used it as a target for virtual screening and molecular docking against a small molecule database. Based on the visual inspection, four best hits such as Chembridge_ID 7768949, 7771055, 7758866, and 7764195 have high binding affinity, good docking score, and pharmacokinetic properties were shortlisted. Further, the dynamic stability of lead molecules with modeled Mirk/Dyrk1B was evaluated using 10 ns molecular dynamics simulation approach. The four hit molecules exhibited good and stable binding complex in the binding pocket of the target protein. Collectively the finding of this study suggested that the identified molecules may serve as potential effective anti-cancer inhibitors for cancer prevention.

scholarly journals Discovery of Novel Inhibitors for Nek6 Protein through Homology Model Assisted Structure Based Virtual Screening and Molecular Docking Approaches

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
P. Srinivasan ◽  
P. Chella Perumal ◽  
A. Sudha
Keyword(s):  
Virtual Screening ◽  
Cell Cycle Progression ◽  
Three Dimensional ◽  
Homology Model ◽  
Mitotic Cell ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Relationship Of

Nek6 is a member of the NIMA (never in mitosis, gene A)-related serine/threonine kinase family that plays an important role in the initiation of mitotic cell cycle progression. This work is an attempt to emphasize the structural and functional relationship of Nek6 protein based on homology modeling and binding pocket analysis. The three-dimensional structure of Nek6 was constructed by molecular modeling studies and the best model was further assessed by PROCHECK, ProSA, and ERRAT plot in order to analyze the quality and consistency of generated model. The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. Two lead compounds (Binding database ID: 15666, 18602) were retrieved through structure-based virtual screening and induced fit docking approaches as novel Nek6 inhibitors. Hence, we concluded that the potential compounds may act as new leads for Nek6 inhibitors designing.

MODELING OF THREE DIMENSIONAL STRUCTURE OF HUMAN ALPHA-FETOPROTEIN COMPLEXED WITH DIETHYLSTILBESTROL: DOCKING AND MOLECULAR DYNAMICS SIMULATION STUDY

2012 ◽  
Vol 10 (02) ◽  
pp. 1241012 ◽  
Author(s):  
ALEXANDER A. TERENTIEV ◽  
NURBUBU T. MOLDOGAZIEVA ◽  
OLGA V. LEVTSOVA ◽  
DMITRY M. MAXIMENKO ◽  
DENIS A. BOROZDENKO ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Site ◽  
Simulation Study ◽  
Md Simulation ◽  
Hydrophobic Interactions ◽  
3D Structure ◽  
Three Dimensional ◽  
Alpha Fetoprotein ◽  
Dynamics Simulation ◽  
Dimensional Structure

It has been long experimentally demonstrated that human alpha-fetoprotein (HAFP) has an ability to bind immobilized estrogens with the most efficiency for synthetic estrogen analog — diethylstilbestrol (DES). However, the question remains why the human AFP (HAFP), unlike rodent AFP, cannot bind free estrogens. Moreover, despite the fact that AFP was first discovered more than 50 years ago and is presently recognized as a "golden standard" among onco-biomarkers, its three-dimensional (3D) structure has not been experimentally solved yet. In this work using MODELLER program, we generated 3D model of HAFP on the basis of homology with human serum albumin (HSA) and Vitamin D–binding protein (VTDB) with subsequent molecular docking of DES to the model structure and molecular dynamics (MD) simulation study of the complex obtained. The model constructed has U-shaped structure in which a cavity may be distinguished. In this cavity the putative estrogen-binding site is localized. Validation by RMSD calculation and with the use of PROCHECK program showed good quality of the model and stability of extended region of four alpha-helical structures that contains putative hormone-binding residues. Data extracted from MD simulation trajectory allow proposing two types of interactions between amino acid residues of HAFP and DES molecule: (1) hydrogen bonding with involvement of residues S445, R452, and E551; (2) hydrophobic interactions with participation of L138, M448, and M548 residues. A suggestion is made that immobilization of the hormone using a long spacer provides delivery of the estrogen molecule to the binding site and, thereby, facilitates interaction between HAFP and the hormone.

scholarly journals Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

2013 ◽  
Vol 288 (23) ◽  
pp. 16460-16475 ◽  
Author(s):  
Linda J. Olson ◽  
Ramiro Orsi ◽  
Solana G. Alculumbre ◽  
Francis C. Peterson ◽  
Ivan D. Stigliano ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Mannose Residue ◽  
Glucosidase Ii ◽  
Mannose 6 Phosphate ◽  
First Time ◽  
Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

scholarly journals Generalized predictive model of estimation of inhibition of muscarinic receptors M1-M5

2020 ◽  
Vol 3 (3) ◽  
pp. e00129
Author(s):  
A.V. Mikurova ◽  
V.S. Skvortsov ◽  
V.V. Grigoryev
Keyword(s):  
Predictive Model ◽  
Muscarinic Receptors ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Regression Equations ◽  
Energy Characteristics ◽  
Value Prediction ◽  
M3 Receptor ◽  
The Mean

A general predictive model for assessing the inhibition constant (K<sub>i</sub>) value of human acetylcholine muscarinic receptors M1-M5 by potential ligands has been constructed. We used information on the three-dimensional structure of human M1, M2, M4, and M5 receptors, as well as a model of the M3 receptor constructed according to homology based on the structure of the rat M3 receptor. A set of complexes of known inhibitors with the target receptor constructed by means of molecular docking, was selected using an additional option: the coincidence of the spatial position of 4 pharmacophore points of a tested inhibitor and tiotropium, for which the position in the crystal structure was known. For five types of M receptors 199 complexes with known K<sub>i</sub> values were selected. Based on the data obtained during molecular dynamics simulation of these complexes by means of the MM-PBSA/MM-GBSA methods, their energy characteristics were calculated. They were used as independent variables in linear regression equations for pK<sub>i</sub> value prediction. The R<sup>2</sup> prediction for the generalized equation was 0.7, and the mean prediction error was 0.55 logarithmic units with a range for pK<sub>i</sub>=4.7.

scholarly journals Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca

2021 ◽  
Author(s):  
Patrick Brendan Timmons ◽  
Chandralal M Hewage
Keyword(s):  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Peptide Sequence ◽  
Helical Conformation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Anticancer Activities ◽  
American Bullfrog ◽  
Α Helix

Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defense peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-d3 mixture. The structure is defined by an α-helix that spans between Ile6-Ala26, and a cyclic disulphide bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide's interactions with sodium dodecyl sulphate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its α-helical conformation between residues Ile6-Ala26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.

3D Structure of Striations in the North Pacific

2021 ◽  
Author(s):  
YU ZHANG ◽  
YU PING GUAN ◽  
RUI XIN HUANG
Keyword(s):  
North Pacific ◽  
3D Structure ◽  
Three Dimensional ◽  
Vertical Plane ◽  
Dimensional Structure ◽  
The North ◽  
Layer Analysis ◽  
Fluid Potential ◽  
The North Pacific

AbstractOcean striations are composed of alternating quasi-zonal band-like flows; this kind of organized structure of currents be found in all world’s oceans and seas. Previous studies have mainly been focused on the mechanisms of their generation and propagation. This study uses the spatial high-pass filtering to obtain the three-dimensional structure of ocean striations in the North Pacific in both the z-coordinate and σ-coordinate based on 10-yr averaged SODA3 data. First, we identify an ideal-fluid potential density domain where the striations are undisturbed by the surface forcing and boundary effects. Second, using the isopycnal layer analysis, we show that on isopycnal surfaces the orientations of striations nearly follow the potential vorticity (PV) contours, while in the meridional-vertical plane the central positions of striations are generally aligned with the latitude of zero gradient of the relative PV. Our analysis provides a simple dynamical interpretation and better understanding for the role of ocean striations.

scholarly journals Electrostatics of Tau Protein by Molecular Dynamics

Biomolecules ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 116 ◽  
Author(s):  
Tarsila Castro ◽  
Florentina-Daniela Munteanu ◽  
Artur Cavaco-Paulo
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Microtubule Assembly ◽  
Interaction Sites ◽  
Disordered Protein ◽  
Fluid Environment ◽  
Function Relationship ◽  
Insight Into

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

scholarly journals Analysis of the three dimensional structure of the kidney glomerulus capillary network

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mark Terasaki ◽  
Jason Cory Brunson ◽  
Justin Sardi
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
The Body ◽  
Capillary Network ◽  
Dimensional Structure ◽  
Pixel Resolution ◽  
Longitudinal Splitting ◽  
Kidney Glomerulus ◽  
Minimum Number ◽  
Glomerular Size

AbstractThe capillary network of the kidney glomerulus filters small molecules from the blood. The glomerular 3D structure should help to understand its function, but it is poorly characterized. We therefore devised a new approach in which an automated tape collecting microtome (ATUM) was used to collect 0.5 μm thick serial sections from fixed mouse kidneys. The sections were imaged by scanning electron microscopy at ~ 50 nm/pixel resolution. With this approach, 12 glomeruli were reconstructed at an x–y–z resolution ~ 10 × higher than that of paraffin sections. We found a previously undescribed no-cross zone between afferent and efferent branches on the vascular pole side; connections here would allow blood to exit without being adequately filtered. The capillary diameters throughout the glomerulus appeared to correspond with the amount of blood flow within them. The shortest path (minimum number of branches to travel from afferent to efferent arterioles) is relatively independent of glomerular size and is present primarily on the vascular pole size. This suggests that new branches and longer paths form on the urinary pole side. Network analysis indicates that the glomerular network does not form by repetitive longitudinal splitting of capillaries. Thus the 3D structure of the glomerular capillary network provides useful information with which to understand glomerular function. Other tissue structures in the body may benefit from this new three dimensional approach.

scholarly journals Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk

Sequencing ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Amitava Moulick ◽  
Debashis Mukhopadhyay ◽  
Shonima Talapatra ◽  
Nirmalya Ghoshal ◽  
Sarmistha Sen Raychaudhuri
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Transcript Level ◽  
Copper Stress ◽  
Dimensional Structure ◽  
Functional Study ◽  
Plantago Ovata

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

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