Preferred Language
Articles
/
bijps-1604
A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
...Show More Authors

Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

Scopus Crossref
View Publication Preview PDF
Quick Preview PDF
Publication Date
Fri Nov 01 2024
Journal Name
Journal Of Kufa Legal And Political Science
The legal system of mandatory mediation as a mean of setting disputes Comparative analytical study
...Show More Authors

The mediation system is based on settling the dispute amicably through the intervention of a third party by bringing views closer away from the judiciary, which is an amicable way to settle disputes, which disputants resort to voluntarily, but some Western legislation has begun to impose resorting to mediation to settle disputes compulsorily, to take advantage of its advantages, get rid of the disadvantages of resorting to the judiciary in some disputes, and relieve pressure on the courts.

Publication Date
Fri Sep 25 2020
Journal Name
International Journal Of Drug Delivery Technology
Synthesis, Antibacterial, and Molecular Docking Study of Novel 2-Chloro-8-Methoxy-3-Aryl-[1,3] Benzoxazine Derivatives using Vilsmeier Reagent
...Show More Authors

Reducing of ethyl 4-((2-hydroxy-3-methoxybenzylidene)amino)benzoate (1) afford ethyl 4-((2-hydroxy-3-methoxybenzyl)amino)benzoate (2). Reaction of this compound with Vilsmeier reagent affords novel 2-chloro-[1,3] benzoxazine ring (3). The corresponding acid hydrazide of compound 3 was synthesized from reaction of compound (3) with hydrazine hydrate. Newly series of hydrazones (5a–i) were synthesized from reaction of acid hydrazide with various aryl aldehydes. Antibacterial activity of the hydrazones was secerned utilizing gram-negative and gram-positive bacteria. Compound (5b) and (5c) exhibited significant antibacterial ability against both gram-negative and gram-positive bacteria, while the compounds (5a) showed mild antibacteri

... Show More
View Publication Preview PDF
Scopus (3)
Scopus Crossref
Publication Date
Thu Jul 02 2020
Journal Name
International Journal Of Drug Delivery Technology
Synthesis, Antibacterial and Molecular Docking Study of Novel 2-Chloro-8-Methoxy-3-Aryl-[1,3] Benzoxazine Derivatives Using Vilsmeier Reagen
...Show More Authors

Reducing of ethyl 4-((2-hydroxy-3-methoxybenzylidene)amino)benzoate (1) afford ethyl 4-((2-hydroxy-3-methoxybenzyl) amino)benzoate (2). Reaction of this compound with Vilsmeier reagent affords novel 2-chloro-[1,3] benzoxazine ring (3). The corresponding acid hydrazide of compound 3 was synthesized from reaction of compound (3) with hydrazine hydrate. Newly series of hydrazones(5a–i) were synthesized from reaction of acid hydrazide with various aryl aldehydes. Antibacterial activity of the hydrazones wassecerned utilizing gram-negative and gram-positive bacteria. Compound (5b) and (5c) exhibited significant antibacterial ability against both gram-negative and gram-positive bacteria, while the compounds(5a) showed mild antibacterial activit

... Show More
Publication Date
Wed Aug 28 2024
Journal Name
World Academy Of Sciences Journal
Serum angiopoietin‑1 as a biomarker of missed miscarriage
...Show More Authors

View Publication
Scopus Crossref
Publication Date
Fri May 18 2018
Journal Name
Thesis
The Arabian killifish (Aphanius dispar) as a novel model for mycophysiological studies.
...Show More Authors

Abstract Candida albicans is a commensal fungal pathogen that grows in yeast and hyphal forms in the human gut. C. albicans causes mucosal and cutaneous diseases that can result in significant mortality following systematic infections and it also exhibits drug resistance. Zebrafish have been an excellent model to investigate C. albicans infections because of their transparency and the availability of many transgenic lines. However, there is a limitation in using zebrafish as a model because the fish embryos cannot survive at 37°C therefore it is not suitable for studying Candida infections at physiological relevant human body temperature. In this thesis, the normal embryonic development of Arabian killifish (A. dispar) is investigated, rev

... Show More
Publication Date
Fri May 12 2023
Journal Name
Bulletin Of The Chemical Society Of Ethiopia
SYNTHESIS, CHARACTERIZATION, ANTIMICROBIAL STUDIES, AND MOLECULAR DOCKING STUDIES OF TRANSITION METAL COMPLEXES FORMED FROM A BENZOTHIAZOLE-BASED AZO LIGAND
...Show More Authors

The azo ligand obtained from the diazotization reaction of 2-aminobenzothiazole and 4- nitroaniline yielded a novel series of complexes with Co(II), Ni(II), Cu(II), and Zn(II) ions. The complexes were investigated using spectral techniques such as UV-Vis, FT-IR, 1H and 13C NMR spectroscopic analyses, LC-MS and atomic absorption spectrometry, electrical conductivity, and magnetic susceptibility. The molar ratio of the synthesized compounds was determined using the ligand exchange ratio, which revealed the metal-ligand ratios in the isolated complexes were 1:2. The synthesized complexes were tested for antimicrobial activity against S. aureus, E. coli, C. albicans, and C. tropicalis bacterial species. Additionally, their binding affinities we

... Show More
Publication Date
Wed Dec 15 2021
Journal Name
Abstract And Applied Analysis
Dynamical Behaviors of a Fractional-Order Three Dimensional Prey-Predator Model
...Show More Authors

In this paper, the dynamical behavior of a three-dimensional fractional-order prey-predator model is investigated with Holling type III functional response and constant rate harvesting. It is assumed that the middle predator species consumes only the prey species, and the top predator species consumes only the middle predator species. We also prove the boundedness, the non-negativity, the uniqueness, and the existence of the solutions of the proposed model. Then, all possible equilibria are determined, and the dynamical behaviors of the proposed model around the equilibrium points are investigated. Finally, numerical simulations results are presented to confirm the theoretical results and to give a better understanding of the dynami

... Show More
View Publication
Scopus (8)
Crossref (6)
Scopus Crossref
Publication Date
Thu Feb 01 2024
Journal Name
Russian Journal Of Bioorganic Chemistry
Synthesis, Characterization of Formazan Derivatives from Isoniazid and Study Their Antioxidant Activity and Molecular Docking
...Show More Authors

Objective: Synthesis, Characterization of formazan derivatives and studies the antioxidant activity of prepared compounds and molecular docking. Methods: In this study, formazan compounds (III–XIV) were produced by combining Schiff base compounds (I), (II) with diazonium salts resulting from reactions of different aromatic amines with sodium nitrate in the presence of Con.HCl at 0–5°C. When isonicotinic acid hydrazide reacts with (N,N-dimethylbenzaldehyde, 4-hydroxy-3-methoxybenzaldehyde) in the presence glacial acetic acid as a solvent Schiff base compounds are created. Results: The prepared compounds were identified by FT-IR, 1H NMR, 13C NMR, then the antioxidant activity of the derivatives and molecular docking were studied. D

... Show More
View Publication
Scopus (2)
Scopus Clarivate Crossref
Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Institutional Performance Assessment using a model of the European Foundation for Quality Management (EFQM) A case study at an organization
...Show More Authors

The study aims to use the European Excellence Model (EFQM) in assessing the institutional performance of the National Center for Administrative Development and Information Technology in order to determine the gap between the actual reality of the performance of the Center and the standards adopted in the model, in order to know the extent to which the Center seeks to achieve excellence in performance to improve the level of services provided and the adoption of methods Modern and contemporary management in the evaluation of its institutional performance.

The problem of the study was the absence of an institutional performance evaluation system at the centre whereby weaknesses (areas of improvement) and st

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Nov 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A Suggested Model for Using a Students Attendance Management Information Systems/ A Case Study In Lebanese French University/ Erbil
...Show More Authors

This study aims to design unified  electronic information system to manage students attendance in Lebanese French university/Erbil, as a system that simplifies the process of entering and counting the students absence, and generate absence reports to expel students who passed  the acceptable limit of being absent, and by that we can replace the traditional way of  using papers to count absence,  with  a complete electronically system for managing students attendance, in a way that makes the results accurate and unchangeable by the students.

            In order to achieve the study's objectives, we designed an information syst

... Show More
View Publication Preview PDF
Crossref