Can MM‐PBSA calculations predict the specificities of protein kinase inhibitors?

An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.     

Conformational studies of tertiary oligo-m-benzanilides and oligo-p-benzanilides in solution

A series of oligo-m- and p-benzanilides were made and their conformations in solution were studied by NMR. In most cases, conformational mixtures were observed as soon as three or more monomers were incorporated into the oligomer. Some crystal structures were obtained, which indicated that helical conformations were adopted in the solid state.     

Ab Initio rovibrational spectrum of the NaH2 + ion–quadrupole complex

The electronic and rovibrational structure of (¹A₁) NaH₂ ⁺ has been investigated using a relativistically-corrected, all-electron coupled-cluster with singles, doubles and perturbative triples (CCSD(T)) ansatz. For the electronic ground state this ansatz yielded equilibrium Na–H bond lengths (R _e ) of 2.4208 Å and an equilibrium H–Na–H bond angle (θ_e) of 17.8°. An analytical potential energy surface (PES) was embedded in the rovibrational Hamiltonian. The PES was constructed using 118 CCSD(T) points and exhibited a residual error of 1.2 cm^?1. The rovibrational Hamiltonian was diagonalised using variational techniques. The vibrational and rovibrational eigenvectors were assigned using a configuration weight scheme in terms of normal modes and the Mulliken assignment scheme, respectively. For the ground vibrational state of (¹A₁) NaH₂ ⁺, the vibration-averaged bond lengths 〈R〉 and angle 〈θ〉 were 2.4995 Å and 17.1°, respectively. The ab initio (¹A₁) NaH₂ ⁺ PES yielded a dissociation energy (D ₀) value of 10.3 kJ mol^?1, which is in excellent agreement with the experimental value of 10.3 ± 0.8 kJ mol^?1 (Bushnell et al. in J Phys Chem 98:2044, 1994). An analytical dipole moment surface was constructed using 90 CCSD(T) points. Rovibrational spectra of (¹A₁) NaH₂ ⁺, (¹A′) NaHD⁺ and (¹A₁) NaD₂ ⁺ for v ≤ 10, J ≤ 5 were constructed using rovibrational transition moment matrix elements calculated in a novel manner that employs the analytical dipole moment surface (DMS). The rovibrational structure of the Na⁺–H₂ v _HH = 1 ← v _HH = 0 band was calculated and compared to that of Li⁺–H₂.