Computational Modeling of Human Serum Albumin Binding of Per- and Polyfluoroalkyl Substances Employing QSAR, Read-Across, and Docking

Article Mathematical & Computational Biology

The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification

Davide Chicco et al.

Summary: Binary classification commonly utilizes machine learning and computational statistics, with ROC AUC serving as the standard metric. However, ROC AUC has flaws and limitations. The Matthews correlation coefficient (MCC) should replace ROC AUC as the standard statistic for binary classification in all scientific studies.

BIODATA MINING (2023)

Add to Collection

Article Environmental Sciences

Critical new insights into the binding of poly- and perfluoroalkyl substances (PFAS) to albumin protein

Jessica L. Alesio et al.

Summary: This study critically analyzed three common models for analyzing the binding of PFAS to bovine serum albumin and found that the Hill equation highlighted a unique relationship between binding cooperativity and the number of fluorinated carbons, with PFOA exhibiting the greatest binding cooperativity. Additionally, the results obtained by fluorescence quenching were compared to those obtained by equilibrium dialysis, confirming the significance of steric limitations in PFAS binding. Van der Waals volume was found to best describe the steric limitations observed by fluorescence quenching.

CHEMOSPHERE (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood-Brain Barrier Permeability

Andrea Mauri et al.

Summary: Quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) are techniques used to relate molecular features to endpoints. Alvascience software suite provides tools for predicting endpoints for untested molecules, including data curation with alvaMolecule, feature generation with alvaDesc, model building and validation with alvaModel, and deployment with alvaRunner. The predictive models in a real case scenario have high accuracy above 0.8.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Add to Collection

Review Environmental Sciences

Per- and Polyfluoroalkyl Substance Toxicity and Human Health Review: Current State of Knowledge and Strategies for Informing Future Research

Suzanne E. Fenton et al.

Summary: Reports on the impacts of per- and polyfluoroalkyl substances (PFAS) on the environment and human health have increased substantially in peer-reviewed literature. Epidemiological studies have shown associations between exposure to specific PFAS and various health effects, and further research is needed to understand differences in responses between sexes, species, and life stages. More contemporary approaches such as read-across, molecular dynamics, and protein modeling are proposed to accelerate the development of toxicity information on PFAS, as well as the need for precaution to protect human health given the known effects of certain PFAS compounds.

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY (2021)

Add to Collection

Article Chemistry, Multidisciplinary

Computational Analysis of the Binding Mechanism of GenX and HSA

Jeannette Delva-Wiley et al.

Summary: GenX, an alternative to PFOS, has been detected in water sources and air in certain regions of the United States, impacting human health and binding to the protein HSA. Researchers identified four binding sites of GenX on the HSA protein through docking and molecular dynamics simulation.

ACS OMEGA (2021)

Add to Collection

Article Engineering, Environmental

Rapid Characterization of Human Serum Albumin Binding for Per- and Polyfluoroalkyl Substances Using Differential Scanning Fluorimetry

Thomas W. Jackson et al.

Summary: This study optimized a novel thermal denaturation assay to evaluate the thermal stability changes of HSA in the presence of various PFAS, revealing the protein-binding properties of most PFAS and providing a new method for understanding the structure and protein-binding properties of these chemicals.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2021)

Add to Collection

Article Environmental Sciences