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Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics.
J Chem Inf Model
January 2025
Department of Modeling and Informatics, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Potency optimization of macrocyclic peptides can include both modifying intermolecular interactions and modifying the conformational stability of the bioactive conformation. However, the number of possible modifications is vast. To identify modifications that enhance the stability of the binding conformations in a cost-effective manner, there is a need for a high-throughput in-silico method that scores the conformational stability of these modified molecules.
View Article and Find Full Text PDFHow Much Data Are Enough? Toward Statistically Robust Adhesion Experiments by Atomic Force Microscopy.
Langmuir
January 2025
Department of Physical Chemistry II, University of Bayreuth, Universitaetsstrasse 30, Bayreuth 95447, Germany.
Direct force measurements by atomic force microscopy (AFM) have become an indispensable analytical tool in the last decades. Force measurements have been widely used for adhesion measurements, often in combination with the colloidal probe technique. For the latter technique, a colloidal particle is attached to the end of an AFM cantilever, proving great flexibility in terms of colloid/surface interaction to be studied.
View Article and Find Full Text PDFRecalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry.
Anal Chem
January 2025
School of Molecular and Cellular Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K.
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to interrogate protein structure and dynamics. With the ability to study almost any protein without a size limit, including intrinsically disordered ones, HDX-MS has shown fast growing importance as a complement to structural elucidation techniques. Current experiments compare two or more related conditions (sequences, interaction partners, excipients, conformational states, etc.
View Article and Find Full Text PDFREACH assessment of humans exposed to chemicals indirectly via the environment: screening modeling in EUSES versus state of the science.
Integr Environ Assess Manag
January 2025
Henkel AG & Co KGaA, Düsseldorf, Germany.
The assessment of humans indirectly exposed to chemicals via the environment (HvE) is an assessment element of the Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH) regulation. The European Union System for the Evaluation of Substances (EUSES) is the default screening tool, aimed at prioritizing chemicals for further refinement/higher tier assessment. This review summarizes the approach used in EUSES, evaluates the state of the science in human exposure modeling via the environment, and identifies areas for further research to strengthen the confidence and applicability of EUSES for assessing HvE.
View Article and Find Full Text PDFComputational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.
Mol Pharm
January 2025
Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic.
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs not soluble in water, those with otherwise strong adverse effects, or very fragile ones such as nucleic acids. However, for the rational design of LNCs, a detailed understanding of the composition-structure-function relationships is missing.
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