Insights into the dynamic interactions of RNase a and osmolytes through computational approaches

Unveiling critical structural features for effective HDAC8 inhibition: a comprehensive study using quantitative read-across structure-activity relationship (q-RASAR) and pharmacophore modeling

Histone deacetylases constitute a group of enzymes that participate in several biological processes. Notably, inhibiting HDAC8 has become a therapeutic strategy for various diseases. The current inhibitors for HDAC8 lack selectivity and target multiple HDACs. Consequently, there is a growing recognition of the need for selective HDAC8 inhibitors to enhance the effectiveness of therapeutic interventions. In our current study, we have utilized a multi-faceted approach, including Quantitative Structure-Activity Relationship (QSAR) combined with Quantitative Read-Across Structure-Activity Relationship (q-RASAR) modeling, pharmacophore mapping, molecular docking, and molecular dynamics (MD) simulations. The developed q-RASAR model has a high statistical significance and predictive ability (Q2F1:0.778, Q2F2:0.775). The contributions of important descriptors are discussed in detail to gain insight into the crucial structural features in HDAC8 inhibition. The best pharmacophore hypothesis exhibits a high regression coefficient (0.969) and a low root mean square deviation (0.944), highlighting the importance of correctly orienting hydrogen bond acceptor (HBA), ring aromatic (RA), and zinc-binding group (ZBG) features in designing potent HDAC8 inhibitors. To confirm the results of q-RASAR and pharmacophore mapping, molecular docking analysis of the five potent compounds (44, 54, 82, 102, and 118) was performed to gain further insights into these structural features crucial for interaction with the HDAC8 enzyme. Lastly, MD simulation studies of the most active compound (54, mapped correctly with the pharmacophore hypothesis) and the least active compound (34, mapped poorly with the pharmacophore hypothesis) were carried out to validate the observations of the studies above. This study not only refines our understanding of essential structural features for HDAC8 inhibition but also provides a robust framework for the rational design of novel selective HDAC8 inhibitors which may offer insights to medicinal chemists and researchers engaged in the development of HDAC8-targeted therapeutics.

Development, Evaluation, and Molecular Dynamics Study of Ampicillin-Loaded Chitosan-Hyaluronic Acid Films as a Drug Delivery System

Periodontitis is an inflammatory periodontal disease defined by the progressive loss of tissues surrounding the tooth. Ampicillin is an antibiotic for managing and treating specific bacterial infections, including periodontitis. Periodontal pockets occur due to periodontal disease progression and act as a natural reservoir that is easily reachable for the insertion of a delivery system, and the amount of drug to be released has a major role in the efficiency of treatment of the disease. Polyelectrolyte complexes (PECs), particularly those based on chitosan and hyaluronic acid combinations, offer a promising avenue to overcome the challenges associated with drug delivery. These complexes are both biodegradable and biocompatible, making them an optimal choice for enabling targeted drug delivery. This study centers on developing and assessing the structure and dynamic attributes of a drug-PEC system encompassing ampicillin and chitosan-hyaluronic acid components, which represents a targeted drug delivery system to better alleviate the periodontitis. To achieve this goal, we conducted experiments including weight and drug content uniformity, swelling ındex, drug release %, FT-IR and SEM analyses, and atomistic molecular dynamics simulations on the drug PECs loaded with ampicillin with varying amounts of hyaluronic acid. All simulations and the experimental analysis suggested that increased HA amount resulted in an increase in drug release % and swelling index. The simulation outcomes provide insights into the nature of the drug and PEC interactions alongside transport properties such as drug diffusion coefficients. These coefficients offer valuable insights into the molecular behavior of ampicillin-PEC drug delivery systems, particularly in the context of their application in periodontitis treatment.