A5064772179- Enzyme Structure and Function
- Computational Drug Discovery Methods
- Chemical Reaction Mechanisms
- GABA and Rice Research
- Protein Structure and Dynamics
- Metal-Organic Frameworks: Synthesis and Applications
- Chemical Synthesis and Analysis
- Cyclopropane Reaction Mechanisms
- Free Radicals and Antioxidants
- Molecular spectroscopy and chirality
- DNA and Nucleic Acid Chemistry
- Photochemistry and Electron Transfer Studies
- Chemical Synthesis and Reactions
- Antimicrobial Peptides and Activities
- Monoclonal and Polyclonal Antibodies Research
- Analytical Chemistry and Chromatography
- Mass Spectrometry Techniques and Applications
- Catalytic C–H Functionalization Methods
- Synthesis and biological activity
- Mesoporous Materials and Catalysis
- Cholinesterase and Neurodegenerative Diseases
- Click Chemistry and Applications
- thermodynamics and calorimetric analyses
- Axial and Atropisomeric Chirality Synthesis
- Nanoplatforms for cancer theranostics
Istanbul Technical University
2010-2025
Orient-Institut Istanbul
2017
Boğaziçi University
2000-2004
Centre National de la Recherche Scientifique
2002-2004
Laboratoire de Chimie Théorique
2002-2004
Université de Lorraine
2002-2004
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug not confirmed so far for regular treatment. An important target is the main protease (M
Microvascular surgery plays a crucial role in reconnecting micrometer-scale vessel ends. Suturing remains the gold standard technique for small vessels; however, suturing collapsed lumen of microvessels is challenging and time-consuming, with risk misplaced sutures leading to failure. Although multiple solutions have been reported, emphasis has predominantly on resolving challenges related arteries rather than veins, none proven superior. In this study, we introduce an innovative solution...
RAS mutations occur in about 30% of human cancers, leading to enhanced signaling and tumor growth. KRAS is the most commonly mutated oncogene tumors, especially lung, pancreatic, colorectal cancers. Direct targeting difficult due its highly conserved sequence; but, complex with guanine nucleotide exchange factor Son Sevenless (SOS) 1 promises an attractive target for inhibiting RAS-mediated signaling. Here, we first revealed putative allosteric binding sites SOS1, KRASG12C-SOS1 complex,...
In the present study, we have modelled nucleophilic attack of water and a hydroxyl anion on carbonyl carbon succinimide derivative leading to aspartate aspartic acid. Calculations been carried out at B3LYP/6-31 +G* level in vacuum. The IEF-PCM methodology has used carry single point calculations solution. neutral medium, hydrolysis is facilitated by presence polar continuum, whereas basic medium environment hinders succinimide. deltaH degrees deltaS values for cyclization reactions acid...
The hydrolysis of a succinimide derivative in alkali and neutral media has been studied at the B3LYP/6-31+G* level. Stepwise concerted mechanisms have considered vacuum. Both also solution by means integral equation formalism-polarizable continuum model with single point calculation. In basic medium, stepwise mechanism consists bond cleavage subsequent rotation hydroxyl group that require 8.6 3.0 kcal/mol, respectively. For same barrier is 9.8 kcal/mol. facilitated presence polar continuum,...
Abstract The mechanism of ring–chain–ring tautomerization and the prominent effect solvent environment have been computationally investigated in an effort to explain enantiomeric interconversion observed 2‐oxazolidinone derivatives, heterocyclic analogues biphenyl atropisomers, which were isolated as single stable enantiomers potential be used axially chiral catalysts. This study has shed light on identity intermediate species involved process well catalytic polar protic solvents. These...
The density functional theory method at the B3LYP/6-31G(d) level of is used to determine mechanism [3+2] cycloaddition and cyclopropanation reactions 1,3-dioxepine derivatives with dimethyldiazomalonate (DMDM) in presence a copper(I) catalyst. dynamics catalytic have been elucidated, it found that reaction proceeds via stepwise pathway due copper. experimental product distribution for DMDM 4,5-dihydro-2-methyl-1,3-dioxepine 4,7-dihydro-2-methyl-1,3-dioxepine Cu(I) catalyst has also...
In this study, quantum mechanical calculations have been performed to elucidate the mechanism and enantioselectivity in rhodium-catalyzed 1,4-conjugate addition reaction of a series aryl groups electron-deficient 4,4,4-trifluoro-1-phenyl-2-buten-1-one presence (S)-BINAP. Conjugate unsubstituted, o-CH3, p- o-Cl substituted phenyl were considered explain steric electronic effects on mechanism. The activation energy difference between benzene o-toluene-substituted systems (8.1 kcal/mol for R...
We have investigated the pairs of rotational isomers for six 3-(o-aryl)-5-methyl-rhodanines (Z = H, F, Cl, Br, OH, and CH3) using NMR spectroscopy density functional theory (DFT) calculations. Electron topological NBO analysis has demonstrated importance non-covalent interactions, characterised by (3, -1) bond critical points (BCPs), between oxygen sulfur atoms on thiazolidine ring with aryl substitutents in stabilizing transition states. The energetic activation barriers to rotation also...
The bismuth nitrate-promoted disproportionative condensation of indoles with cyclohexanone in one pot, to yield C3-cyclohexyl substituted and 1,3-di(1<italic>H</italic>-indol-3-yl)benzene derivatives is reported for the first time.
The inactivation mechanism of γ-aminobutyric acid aminotransferase (GABA-AT) in the presence γ-vinyl-aminobutyric acid, an anti-epilepsy drug, has been studied by means theoretical calculations. Density functional theory methods have applied to compare three experimentally proposed mechanisms (Silverman et al., J. Biol. Chem., 2004, 279, 363). All calculations were performed at B3LYP/6-31+G(d,p) level theory. Single point solvent carried out water, integral equation formalism-polarizable...
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug not confirmed so far for regular treatment. An important target is the main protease (Mpro), which plays a major role in replication of virus. In this study, Gaussian residue...
Pyridoxal 5-phosphate (PLP), the phosphorylated and oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with ϵ-amino group lysine residue PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase enzyme that degrades GABA to succinic semialdehyde, while reduction concentration in brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for inactivation GABA-AT are synthesized extensively cases where...
The pyridoxal 5-phosphate (PLP) cofactor is a significant organic molecule in medicinal chemistry. It often found covalently bound to lysine residues proteins form PLP dependent enzymes. An example of this family enzymes γ-aminobutyric acid aminotransferase (GABA-AT) which responsible for the degradation neurotransmitter GABA. Its inhibition or inactivation can be used prevent reduction GABA concentration brain source several neurological disorders. As test case enzymes, we have performed...
Deamidation plays an important role in biochemical phenomena such as aging. The of the n + 1 residue on deamidation asparagine (asparagine being nth residue) three pentapeptide chains (GGNGG, GGNMG and GGNIG) has been analysed with hybrid computational tools. Potentials mean force at 300 K were calculated from MD/replica exchange simulations using weighted histogram analysis (WHAM) explicit water. snapshots clustered taking into account requirements plausible mechanisms, tautomerisation side...
The relationship between the deamidation mechanism and catalytic activity of triosephoshate isomerase has been studied with a QM/MM method where AM1/AMBER parametrization was used. considered in this study is compared to that previously described for dipeptide model vacuum using density functional theory. present focuses on determining whether ligand-induced proceeds via an intrasubunit or intersubunit transmission conformational change. Our calculations have shown that, although binding...
Abstract We study the structural fluctuations of triosephosphate isomerase (TIM) by an elastic model, namely, Gaussian network model (GNM), to identify a coupled motions in allosteric communication between its deamidation and catalytic sites, promoting for activity. For this, three TIM structures have been studied: one crystal structure two designed describe different putative models reaction taking place at subunit interface. The mapped on functional properties; then differences relation...
Controlled release of corticosteroids may lead to higher bioavailability the drugs and a dosage control. Here, we investigate suitability framework MIL-101 (Cr) as drug carrier for controlled five with different therapeutic potencies, namely Desoximethasone Clobetasol Propionate (strong), Methylprednisolone Triamcinolone Acetonide (medium), Hydrocortisone Valerate (weak). First, employ Grand Canonical Monte Carlo (GCMC) simulations calculate storage capacity host be around 1000 mg drug/g...