PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking.

The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

The molecular basis of high-affinity binding of the antiarrhythmic compound vernakalant (RSD1235) to Kv1.5 channels.

Vernakalant (RSD1235) is an investigational drug recently shown to convert atrial fibrillation rapidly and safely in patients (J Am Coll Cardiol 44:2355-2361, 2004). Here, the molecular mechanisms of interaction of vernakalant with the inner pore of the Kv1.5 channel are compared with those of the class IC agent flecainide. Initial experiments showed that vernakalant blocks activated channels and vacates the inner vestibule as the channel closes, and thus mutations were made, targeting residues at the base of the selectivity filter and in S6, by drawing on studies of other Kv1.5-selective blocking agents. Block by vernakalant or flecainide of Kv1.5 wild type and mutants was assessed by whole-cell patch-clamp experiments in transiently transfected human embryonic kidney 293 cells. The mutational scan identified several highly conserved amino acids, Thr479, Thr480, Ile502, Val505, and Val508, as important residues for affecting block by both compounds. In general, mutations in S6 increased the IC50 for block by vernakalant; I502A caused an extremely local 25-fold decrease in potency. Specific changes in the voltage-dependence of block with I502A supported the crucial role of this position. A homology model of the pore region of Kv1.5 predicted that, of these residues, only Thr479, Thr480, Val505, and Val508 are potentially accessible for direct interaction, and that mutation at additional sites studied may therefore affect block through allosteric mechanisms. For some of the mutations, the direction of changes in IC50 were opposite for vernakalant and flecainide, highlighting differences in the forces that drive drug-channel interactions.

Quantitative association of bark beetles with pitch canker fungus and effects of verbenone on their semiochemical communication in Monterey pine forests in Northern Spain.

The association between 11 species of bark beetles (Coleoptera: Scolytinae) and one weevil (Coleoptera: Entiminae) with the pitch canker fungus, Fusarium circinatum Nirenberg and O'Donnell, was determined by crushing beetles on selective medium and histone H3 gene sequencing. Pityophthorus pubescens (Marsham) (25.00%), Hylurgops palliatus (Gyllenhal) (11.96%), Ips sexdentatus (Börner) (8.57%), Hypothenemus eruditus Westwood (7.89%), Hylastes attenuatus Erichson (7.40%), and Orthotomicus erosus (Wollaston) (2.73%) were found to carry the inoculum. In addition, the root weevil Brachyderes incanus L. (14.28%) had the second highest frequency of occurrence of the fungus. The responses of the insects to a range of verbenone doses were tested in field bioassays using funnel traps. Catches of P. pubescens, a species colonizing branch tips of live trees, were significantly reduced in a log-linear dose-dependent relationship. Catches of I. sexdentatus, an opportunistic species normally attacking fresh dead host material, were also gradually reduced with increasing verbenone dose. Catches of Tomicus piniperda L., O. erosus, Dryocoetes autographus (Ratzeburg), H. eruditus, Xyleborus dryographus (Ratzeburg), Hylastes ater (Paykull), Hylurgus ligniperda (F.), H. attenuatus, and B. incanus were not significantly affected by verbenone. The effects of verbenone were consistent with differences in host-age preference. Semiochemical disruption by verbenone in P. pubescens and I. sexdentatus could represent an integrated pest management strategy for the prevention of the spread of pitch canker disease between different stands. However, several species associated with F. circinatum were unaffected by verbenone, not supporting this compound for prevention of the establishment of potential vectors in Northern Spain.