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New αIIbβ3 variants in 28 Turkish Glanzmann patients; structural hypothesis for complex activation by residues variation...

Published in Platelets

Glanzmann thrombasthenia (GT) is a rare autosomal recessive bleeding disorder characterized by impaired platelet aggregation due to defects in integrin αIIbβ3, a fibrinogen receptor. Platelet phenotypes and allelic variations in 28 Turkish GT patients are reported. Platelets αIIbβ3 expression was evaluated by flow cytometry. Sequence analyzes of IT...

Integration of advanced methods and models to study drug absorption and related processes: An UNGAP perspective.

This collection of contributions from the European Network on Understanding Gastrointestinal Absorption-related Processes (UNGAP) community assembly aims to provide information on some of the current and newer methods employed to study the behaviour of medicines. It is the product of interactions in the immediate pre-Covid period when UNGAP members...

Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies.

Published in Saudi journal of biological sciences

The inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) and papain-like protease (PLpro) prevents viral multiplications; these viral enzymes have been recognized as one of the most favorable targets for drug discovery against SARS-CoV-2. In the present study, we screened 225 phytocompounds present in 28 d...

Strong reduction of thermal conductivity of WSe2 with introduction of atomic defects

Published in Nanotechnology

The thermal conductivities of pristine and defective single-layer tungsten diselenide (WSe2) are investigated by using equilibrium molecular dynamics method. The thermal conductivity of WSe2 increases dramatically with size below a characteristic of ~5 nm and levels off for broader samples and reaches a constant value of ~2 W/mK. By introducing ato...

Computational study reveals substituted benzimidazole derivatives' binding selectivity to PI3Kδ and PI3Kγ.

Published in Journal of molecular modeling

Phosphatidylinositol 3-kinase (PI3K) is a key regulatory kinase in the PI3K/AKT/mTOR signaling pathway, which is involved in the regulation of cell proliferation, differentiation, apoptosis, and angiogenesis. Class IA PI3K isoforms γ and δ share a highly homologous ATP binding site and are distinguished by only a few residues around the binding sit...

Multi-conformational frame from molecular dynamics as a structure-based pharmacophore model for mapping, screening and i...

Published in Journal of biomolecular structure & dynamics

Despite intensive research on clinical and molecular factors, the development of antidiabetic drugs in the last few decades is decelerating and as a result, the number of drugs approved by the US FDA is reduced. Hence, there is a persistent need for the innovative development of novel anti-diabetic drugs. Recent studies have provided ample proof th...

Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential: Molecular docking, MD...

Published in Saudi journal of biological sciences

In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to ...

Assessment of the reactivity and hydration of Portland cement clinker phases from atomistic simulation: A critical revie...

Over the last decade, atomistic simulations were increasingly employed to describe cementitious materials properties. As a complement to experimental measurements, they have improved our understanding of anhydrous and hydrated phases. This article reviews most of the principal investigations based on density functional theory, molecular dynamics, a...

Nicotinic receptors: From protein allostery to computational neuropharmacology

We propose an extension and further development of the Monod-Wyman-Changeux model for allosteric transi- tions of regulatory proteins to brain communications and specifically to neurotransmitters receptors, with the nicotinic acetylcholine receptor (nAChR) as a model of ligand-gated ion channels. The present development of- fers an expression of th...

A molecular dynamics and docking study to screen anti-cancer compounds targeting mutated p53.

Published in Journal of biomolecular structure & dynamics

The p53 gene is mutated in greater than 50% of several human cancers including bladder urothelial carcinoma, lung adenocarcinoma, colorectal carcinoma, and oral cancer. Mutations in the p53 gene occur predominantly in the DNA-binding domain causing loss of function and accumulation of dysfunctional p53 protein in tumors by hetero-oligomerization wi...