Contamination, bioaccumulation mechanism, detection, and control of human norovirus in bivalve shellfish: A review

M Yang, F Zhao, L Tong, S Wang… - Critical Reviews in Food …, 2022 - Taylor & Francis
Human norovirus (HuNoV) is a major foodborne pathogen that causes acute viral
gastroenteritis, and bivalve shellfish are one of the main carriers of HuNoV transmission. A …

Dimethoxyindoles based thiosemicarbazones as multi-target agents; synthesis, crystal interactions, biological activity and molecular modeling

M Yıldız, M Bingul, Y Zorlu, MF Saglam, M Boga… - Bioorganic …, 2022 - Elsevier
Alzheimer's disease (AD) is known as one of the most devastating neurodegenerative
disease diagnosed for the old-aged people and cholinesterase inhibitors (ChEI) can be …

Accurate binding free energy method from end-state MD simulations

E Akkus, O Tayfuroglu, M Yildiz… - Journal of Chemical …, 2022 - ACS Publications
Herein, we introduce a new strategy to estimate binding free energies using end-state
molecular dynamics simulation trajectories. The method is adopted from linear interaction …

Synthesis and molecular modeling studies of naphthazarin derivatives as novel selective inhibitors of α-glucosidase and α-amylase

Ş Abadan, MF Saglam, MS Koca, M Bingul… - Journal of Molecular …, 2023 - Elsevier
Diabetes mellitus is known as one of the most life-threatening diseases and has attracted
the attention of medicinal chemists. The design and synthesis of novel potential candidates …

Synthesis of 7-azaindole based carbohydrazides and 1, 3, 4-oxadiazoles; antioxidant activity, α-glucosidase inhibition properties and docking study

S Izgi, IF Sengul, E Şahin, MS Koca, F Cebeci… - Journal of Molecular …, 2022 - Elsevier
In this current work, 7-azaindole based 1, 3, 4-oxadiazoles have been successfully prepared
by treatment of 3-(hydrazonomethyl)-7-azaindole with the different acyl chlorides or acetic …

Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations

A Kocak, M Yildiz - Journal of Molecular Graphics and Modelling, 2022 - Elsevier
Androgen receptors (AR) are the primary drug target in prostate cancer (PCa). There are
several drugs developed against its activity for prostate cancer treatment, but cancer cells …

Revisiting MMPBSA by adoption of MC-based surface area/volume, ANI-ML potentials, and two-valued interior dielectric constant

E Akkus, O Tayfuroglu, M Yildiz… - The Journal of Physical …, 2023 - ACS Publications
Here, we report the accuracy improvements of molecular mechanics Poisson–Boltzmann
surface area (MMPBSA) calculations by adoption of ANI-ML potentials in replacement of MM …

Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study

U Uzuner, E Akkus, A Kocak… - Journal of Biomolecular …, 2024 - Taylor & Francis
The COVID-19 pandemic has caused havoc around the globe since 2019 and is considered
the largest global epidemic of the twentieth century. Although the first antiviral drug …

Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses

GS Hansman, G Kher, AD Svirina, JRH Tame… - Journal of …, 2024 - journals.asm.org
Human norovirus was discovered more than five decades ago and is a widespread cause of
outbreaks of acute gastroenteritis. There are no approved vaccines or antivirals currently …

Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro

IN Zengin, MS Koca, O Tayfuroglu, M Yildiz… - Journal of Computer …, 2024 - Springer
Here, we introduce the use of ANI-ML potentials as a rescoring function in the host–guest
interaction in molecular docking. Our results show that the “docking power” of ANI potentials …