Modelling of ligand–receptor interactions: ab-initio and DFT calculations of solvent reaction field effects on methylated ammonium–π and –acetate complexes

Dynamacophore model for breast cancer estrogen receptor alpha as an effective lead generation screening technique

Regardless to overwhelming quantum of cancer research worldwide, there are few drugs on the market to treat disease conditions. This is owing to multiple process inferences of drug targets in integrated pathways for invasion, growth, and metastasis. Over the past years, the death rate due to breast cancer has been increasing, that set the stage for improved better treatment. Therefore, there is a persistent and vital demand for innovative development of drugs to treat breast cancer. Many studies have reported that more than 60% of breast cancers are Estrogen receptor-α (ERα)-positive tumours and a key transcription factor, Estrogen receptor-α (ERα) was believed to promote proliferation of breast cancer cells. In this study, 150 ns of molecular dynamics was performed for protein-ligand complex to retrieve the potential stable conformations. The most populated dynamics cluster of 4-Hydroxytamoxifen intact with active site amino acid was selected to generate dynamacophore model (dynamic pharmacophore). Further, internal model validation with AU-ROC values ∼0.93 indicate the best model to screen library. The refined hits are funnelled in pharmacokinetics/dynamics, CDOCKER molecular docking, MM-GBSA and density functional theory to identify the promising ERα ligand candidates.Communicated by Ramaswamy H. Sarma.

Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method

Free energy perturbation (FEP) calculations using the Amber 95 force field and the TIP3P water model were carried out to evaluate the solvation free energy of deoxyribonucleoside triphosphates in aqueous solution. Solvation free energies of -307.5, -311.5, -314.1, and -317.0 kcal/mol were calculated for the (Mg x dTTP)2-, (Mg x dATP)2-, (Mg x dCTP)2-, and (Mg x dGTP)2- complexes, respectively. Structural origins of the relative solvation free energies of deoxyribonucleoside phosphates were examined by calculating the contribution of the interaction of the base moiety with its surroundings. We showed that for each nucleobase the magnitude of this contribution is unaffected by substituting the 5'-OH group of the corresponding nucleoside with the charged mono- or triphosphate groups. This free energy contribution was further decomposed into the sum of free energies originating from the interactions of the base with itself, its substituent, water, and Na+ ions. Although the sum of these components was nearly constant over a wide range of solutes the individual free energy constituents varied significantly. Furthermore, this decomposition showed a high degree of additivity. Computational conditions necessary for obtaining additive free energy decomposition for the systems studied here within the framework of the FEP method included the use of a single mutation pathway and a subdivision of the FEP protocol into 51 or more windows.

Influence of the Water Molecule on Cation−π Interaction: Ab Initio Second Order Møller−Plesset Perturbation Theory (MP2) Calculations

The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.