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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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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.

 

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Publication Date
Wed Jun 10 2015
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
New Schiff Base Derived From Folic Acid and 3- Aminoacetophenone and its Metal Complexes with Some Transition Metals and Evaluation of Their Biological Activity
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The ligand [Potassium (E)-(4-(((2-((1-(3-aminophenyl) ethylidene) amino)-4-oxo-1,4- dihydropteridin-6-yl) methyl) amino)benzoyl)-L-glutamate] was prepared from the condensation reaction of folic acid with (3-aminoacetophenone) through Schiff reaction to give a new Schiff base ligand [H2L]. The ligand [H2L] was characterized by elemental analysis CHN, atomic absorption (A.A), (FT-I.R.), (U.V.-Vis), TLC, E.S. mass (for spectroscopes), molar conductance, and melting point. The new Schiff base ligand [H2L], reacts with Mn(II), Co(II), Ni(II), Cu(II), Cr(III) and Cd(II) metal ions and (2-aminophenol), (metal : derivative ligand : 2-aminophenol) to give a series of new mixed complexes in the general formula:- K3[M2(HL)(HA)2], (where M=Mn(II) and

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Publication Date
Sun Dec 27 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Isolation, Structural Characterization and Identification of Major Constituents in Ephedra foliata Naturally Growing in Iraq by TLC, GC-MS and UPLC-ESI-MS/MS
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Abstract:

   The aerial part of Ephedra foliata Family Ephedraceae have long been used in traditional medicine and now Ephedra species have medicinal, ecological, and commercial value. The variety of pharmacological actions of this plant is due to its chemical constituents. Ephedrine and
related alkaloids; are the newly potential medicinal value of Ephedra supplements for weight loss or performance improvement. Other pharmacological actions like antibacterial and antifungal effects of the phenolic acid compounds, the immunosuppressive action of the polysaccharides, and the antitumor action of flavonoids. The genus of this plant wildly distributed t

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Publication Date
Sat Mar 01 2025
Journal Name
Water, Air, & Soil Pollution
Adsorptive Performance of High Surface Area Date Palm Bunch Activated Carbon Towards Methyl Violet and Fuchsin Basic Dyes Removal: Thermochemical Activation And Statistical Optimization
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Herein, date palm (Phoenix dactylifera) bunch (DPB) waste was transformed into activated carbon (DPAC) adsorbent by using microwaveinduced ZnCl2 activation for 15 min at a power of 600 W. Several analytical methods were used to explain the physicochemical parameters of DPBAC including XRD, pHpzc, BET, SEM–EDX, and FTIR. Afterwards, the adsorptive performance of DPBAC was thoroughly investigated for the removal of two structurally different organic dyes namely methyl violet (MV) and fuchsin basic (FB). The key adsorption parameters, including the dose of DPBAC (A: 0.02–0.06 g), the solution pH (B: 4–10), and the contact time (C: 2–20 min) were statistically optimized using the Box-Behnken design with response surface methodology (RSM

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Publication Date
Mon Dec 20 2021
Journal Name
Baghdad Science Journal
Synthesizing, Structuring, and Characterizing Bioactivities of .Cr(III), La(III), and Ce(III) .Complexes with Nitrogen, Oxygen .and Sulpher donor bidentate Schiff base ligands
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Two Schiff bases, namely, 3-(benzylidene amino) -2-thioxo-6-methyl 2,5-dihydropyrimidine-4(3H)-one (LS])and 3-(benzylidene amino)-6-methyl pyrimidine 4(3H, 5H)-dione(LA)as chelating ligands), were used to prepare some complexes of Cr(III), La(III), and Ce(III)] ions. Standard physico-chemical procedures including metal analysis M%, element microanalysis (C.H.N.S) , magnetic susceptibility, conductometric measurements, FT-IR and UV-visible Spectra were used to identify Metal (III) complexes and  Schiff bases (LS) and (LA). According to findings, a [Cr(III) complex] showed six coordinated octahedral geometry, while [La(III), and Ce(III) complexes]were structured with coordination number seven.  Schiff's bases a

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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
New Tetra-dentate Schiff Base Ligand N2O2 and Its Complexes with Some of Metal Ions: Preparation, Identification, and Studying Their Enzymatic and Biological Activities
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In present work, new tetra-dentate ligand, titled 3,5-bis ((E)-5-Bromo-2-hydroxy benzylidene amino) benzoic acid (H3L), was prepared via an acid-catalyzed condensation process. New four metallic ligand complexes with Co(II), Ni(II), Cu(II) and Zn(II) ions, were also prepared from the refluxing of equivalent moles. Ligand's structure and its complexes; were confirmed by numerous characterization methods, including Ultraviolet-Visible, Infrared, Mass Spectrometer, 1H and 13C Nuclear Magnetic Resonance spectra, atomic absorption, magnetic moments, and molar conductivity measurements. The results of the spectroscopic analyzes proved that the prepared ligand acts as tetradentate bi-ionic ligand and it was bond

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Publication Date
Mon May 01 2023
Journal Name
Environmental Nanotechnology, Monitoring & Management
Photodegradation of tetracycline antibiotic by ternary recyclable Z-scheme g-C3N4/Fe3O4/Bi2WO6/Bi2S3 photocatalyst with improved charge separation efficiency: Characterization and mechanism studies
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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
Microwave Assisted Synthesis, Solution State, Spectral Studies and Theoretical Treatment of Pd(II) , Pt(IV) and Au(III) ions Complexes Containing 2-Benzamide Benzothiazole
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2-benzamide benzothiazole complexes of Pd(II) , Pt(IV) and Au(III) ions were prepared by microwave assisted radiation. The ligand and the complexes were isolated and characterized in solid state by using FT-IR, UV-Vis spectroscopy, flame atomic absorption, elemental analysis CHNS , magnetic susceptibility measurements , melting points and conductivity measurements. The nature of complexes in liquid state was studied by following the molar ratio method which gave results approximately identical to those obtained from isolated solid state; also, stability constant of the prepared complexes were studied and found that they were stable in molar ratio 1:1.The complexes have a sequar planner geometry except Pt(IV) complex has octahedral .

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Assessment <b></b>of Serum P53 Protein Level in Adult Patients with Acute Myeloid Leukemia in Correlation with Response to Treatment
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Background: Acute myeloid leukemia (AML) is an adult leukemia characterized by rapid proliferation of undifferentiated myeloid precursors, leading to bone marrow (BM) failure and impaired erythropoiesis. The p53 tumor suppressor protein regulates cell division and inhibits tumor development by preventing cell proliferation of altered or damaged DNA. It orchestrates various cellular reactions, including cell cycle arrest, DNA repair, and antioxidant properties. Objectives: To investigate the relationship of P53 serum level with hematological findings, remission, and survival status in de novo AML patients. Methods: This is a cross-sectional study that enrolled 63 newly diagnosed de novo AML patients, and 15 sex- and age-matched healt

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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
Mixed Ligand Complexes of quinoline-2-carboxylic acid and 4,4/-dimethyl-2,2/-bipyridyl with V(IV),Cr(III), Rh(III), Cd(II) and Pt(IV)
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A new mixed ligand complexes were prepared by reaction of quinoline -2-carboxylic acid (L1) and 4,4?dimethyl-2,2?-bipyridyl (L2) with V(IV),Cr(III), Rh(III), Cd(II) and Pt(IV) ions. These complexes were isolated and characterized by (FT-IR) and (UV-Vis) spectroscopy, elemental analysis, flame atomic absorption technique, thermogravimetric analysis, in addition to magnetic susceptibility and conductivity measurements. Most complexes were mononuclear and with octahedral geometry, except Cd (II) with tetrahedral geometry, and V (IV) with square pyramidal geometry. A theoretical treatment of the ligands and the prepared complexes in gas phase was done using two programs Hyperchem.8 and Gaussian program (GaussView Currently Available Versions (

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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
sw uobaghdad edu iqSynthesis and Characterization of Mn(II), Co(II), Ni(II), Cu(II), Zn(II), and Hg(II) Complexes with Symmetrical Schiff base
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New binuclear Mn(II), Co(II), Ni(II), Cu(II), Zn(II), and Hg(II) Complexes of N2S2 tetradentate or N4S2 hexadentate symmetric Schiff base were prepared by the condensation of butane-1,4-diylbis(2-amino ethylcarbamodithioate) with 3-acetyl pyridine. The complexes having the general formula [M2LCl4] (where L=butane-1,4-diyl bis (2-(z)-1-(pyridine-3-ylethylidene amino))ethyl carbamodithioate, M= Mn(II), Co(II), Ni(II), Cu(II), Zn(II), and Hg(II)), were prepared by the reaction of the mentioned metal salts and the ligand. The resulting binuclear complexes were characterized by molar conductance, magnetic susceptibility ,infrared and electronic spectral measurements. This study indicated that Mn(II), Ni(II) and Cu(II) complexes have octahedral g

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