Series of molecular dynamics simulations for 2-propanol-water mixtures, as a function of temperature (between freezing and room temperature) and composition ( = 0, 0.5, 0.1, and 0.2), have been performed for temperatures reported in the only available experimental structure study. It is shown that when the all-atom optimized potentials for liquid simulations interatomic potentials for the alcohol are combined with the TIP4P/2005 water model, then the near-quantitative agreement with measured X-ray data, in the reciprocal space, can be achieved. Such an agreement justifies detailed investigations of structural, energetic, and dynamic properties on the basis of simulation trajectories. Here, we focus on characteristics related to hydrogen bonds (HB): cluster-, and in particular, ring formation, energy distributions, and lifetimes of HB-s have been scrutinized for the entire system, as well as for the water and isopropanol subsystems. It is demonstrated that similar to ethanol-water mixtures, the occurrence of 5-membered-hydrogen-bonded rings are significant, particularly at higher alcohol concentrations. Concerning HB energetics, an intriguing double maximum appears on the alcohol-alcohol HB energy distribution function. HB lifetimes have been found significantly longer in the mixtures than they are in pure liquids.
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http://dx.doi.org/10.1021/acs.jpcb.9b05631 | DOI Listing |
Mol Biotechnol
December 2024
Unit of Scientific Research, Applied College, Qassim University, Buraydah, 52571, Saudi Arabia.
The Zika virus (ZIKV), an arbovirus within the Flavivirus genus, is associated with severe neurological complications, including Guillain-Barré syndrome in affected individuals and microcephaly in infants born to infected mothers. With no approved vaccines or antiviral treatments available, there is an urgent need for effective therapeutic options. This study aimed to identify new natural compounds with inhibitory potential against the NS2B-NS3 protease (PDB ID: 5LC0), an essential enzyme in viral replication.
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December 2024
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh.
This study investigated the potential genotoxic and carcinogenic effects of N-nitrosodimethylamine (NDMA), a hazardous compound found in ranitidine formulations that are used to treat excessive stomach acid. The study first examined the effects of NDMA-contaminated ranitidine formulation on Allium cepa root growth and mitotic activity. The results demonstrated dose-dependent decreases in both root growth and mitotic index indicating genotoxicity and cell division disruption.
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December 2024
Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Kyungbook, Republic of Korea.
Alanine racemase (Alr) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization between L- and D-alanine in bacteria. Owing to the potential interest in targeting Alr for antibacterial drug development, several studies have determined the structures of Alr from different species, proposing models for the reaction mechanism. Insights into its reaction dynamics may be conducive to a better understanding of the Alr reaction mechanism.
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December 2024
Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Thung Phayathai, Ratchathewi, Bangkok, 10400, Thailand.
Wnt signaling is a critical pathway implicated in cancer development, with Frizzled proteins, particularly FZD10, playing key roles in tumorigenesis and recurrence. This study focuses on the potential of repurposed FDA-approved drugs targeting FZD10 as a therapeutic strategy for nasopharyngeal carcinoma (NPC). The tertiary structure of human FZD10 was constructed using homology modeling, validated by Ramachandran plot and ProQ analysis.
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December 2024
College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
Drug-drug co-amorphous systems are a promising approach to improve the aqueous solubility of poorly water-soluble drugs. This study explores the combination of breviscapine (BRE) and matrine (MAT) form an amorphous salt, aiming to synergistically enhance the solubility and dissolution of BRE. In silico analysis of electrostatic potential and local ionization energy were conducted on BRE-MAT complex to predict the intermolecular interactions, and solvent-free energies were calculated using thermodynamic integration and density functional theory.
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