Total free energy analysis of fully hydrated proteins

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

QSAR modelling, molecular docking, molecular dynamic and ADMET prediction of pyrrolopyrimidine derivatives as novel Bruton's tyrosine kinase (BTK) inhibitors

In recent years, there has been a focus on developing and discovering novel Bruton's tyrosine kinase (BTK) inhibitors, as they offer an effective treatment strategy for B-cell malignancies. BTK plays a crucial role in B cell receptor (BCR)-mediated activation and proliferation by regulating downstream factors such as the NF-κB and MAP kinase pathways. To address this challenge and propose potential therapeutic options for B-cell lymphomas, researchers conducted 2D-QSAR and ADMET studies on pyrrolopyrimidine derivatives that act as inhibitors of the BCR site in cytochrome b. These studies aim to improve and identify new compounds that could serve as more potent potential BTK inhibitors, which would lead to the identification of new drug candidates in this field. In our study, we used 2D-QSAR (multiple linear regression, multiple nonlinear regression, and artificial neural networks), molecular docking, molecular dynamics, and ADMET properties to investigate the potential of 35 pyrrolopyrimidine derivatives as BTK inhibitors. A molecular docking study and molecular dynamics simulations of molecule 13 over 10 ns revealed that it establishes multiple hydrogen bonds with several residues and exhibits frequent stability throughout the simulation period. Based on the results obtained by molecular modeling, we proposed six new compounds (Pred1, Pred2, Pred3, Pred4, Pred5, and Pred6) with highly significant predicted activity by MLR models. A study based on the in silico evaluation of the predicted ADMET properties of the new candidate molecules is strongly recommended to classify these molecules as promising candidates for new anticancer agents specifically designed to target Bruton's tyrosine kinase (BTK) inhibition.

Energy-entropy multiscale cell correlation method to predict toluene-water log P in the SAMPL9 challenge

The energy-entropy multiscale cell correlation (EE-MCC) method is used to calculate toluene-water log P values of 16 drug molecules in the SAMPL9 physical properties challenge. EE-MCC calculates the free energy, energy and entropy from molecular dynamics (MD) simulations of the water and toluene solutions. Specifically, MCC evaluates entropy by partitioning the system into cells of correlated atoms at multiple length scales and further partitioning the local coordinates into energy wells, yielding vibrational and topographical terms from the energy-well sizes and probabilities. The log P values calculated by EE-MCC using three 200 ns MD simulations have a mean average error of 0.82 and standard error of the mean of 0.97 versus experiment, which is comparable with the best methods entered in SAMPL9. The main contribution to log P is from energy. Less polar drugs have more favourable energies of transfer. The entropy of transfer consists of increased solute vibrational and conformational terms in toluene due to weaker interactions, fewer solute positions in the larger-molecule solvent, reduced water vibrational entropy, negligible change in toluene vibrational entropy, and gains in solvent orientational entropy. The solvent entropy contributions here may be slightly underestimated because software limitations and statistical fluctuations meant that only the first shell could be included while averaged over the whole solution. Nonetheless, such issues will be addressed in future software to offer a general method to calculate entropy directly from MD simulation and to provide molecular understanding or guide system design.