Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.

This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one of 10 base pairs in length, are measured and characterized by isothermal titration calorimetry (ITC) as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔG) is large and unfavorable.

Dual Effect of Secondary Solutes on Binding Equilibria: Contributions from Solute-Reactant Interactions and Solute-Water Interactions.

This study examines the role of water in binding equilibria with a special focus on secondary solutes (cosolutes) that influence the equilibrium but are not constituents of the final product. Using a thermodynamic framework that includes an explicit term for the release of water molecules upon binding, this investigation reveals how solutes may alter equilibria by changing the activity of the reactants, reflected in Δ°, and by changing the chemical potential of the solvent, reflected in Δ. The framework is applied to four experimental binding systems that differ in the degree of electrostatic contributions.

Sulfoglycodendrimer Therapeutics for HIV-1 and SARS-CoV-2.

Hexavalent sulfoglycodendrimers (SGDs) are synthesized as mimics of host cell heparan sulfate proteoglycans (HSPGs) to inhibit the early stages in viral binding/entry of HIV-1 and SARS-CoV-2. Using an HIV neutralization assay, the most promising of the seven candidates are found to have sub-micromolar anti-HIV activities. Molecular dynamics simulations are separately implemented to investigate how/where the SGDs interacted with both pathogens.