Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications

The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field.

DOCKING AND MD SIMULATIONS OF THE INTERACTION OF THE POTASSIUM-SPARING DIURETIC AGENT AMILORIDE WITH THE hASIC1a CHANNEL USING A HOMOLOGY MODEL

The interaction of the K+ -sparing agent amiloride — a synthetic chlorinated pyrimidine derivative — with the hASIC1a ion channel is investigated here along homology modeling of the pore region (using the crystal structure of the cASIC1 channel as a template and the known sequence of hASIC1a), automated docking (using the NMR solution structure of amiloride and its conjugated acid, refined by computations), and molecular dynamics simulations. This represents the first modeling and computational chemistry of the pore region of ASIC/DEG/ENaCs/FaNaCh channels. The results agree with the putative amiloride binding site for alphaENaC channel chimeras once the amiloride free base is considered, while its conjugated acid — in contrast with literature beliefs — is poorly scored on a nearby protein pocket. Different protonation conditions of the pore region are irrelevant because histidine residues are far from the binding sites. Mapping the amino acids of the homology model closest to amiloride can have heuristic value in stimulating in silico search of new pore-blocking agents, experimental studies of ASIC channels themselves, and development of code for constant-pH MD simulations.

COMPUTER SIMULATIONS OF THE INTERACTION OF CIGUATOXIN 3C, BREVENAL AND ent-BREVENAL LADDER POLYETHERS WITH A HOMOLOGY MODEL OF THE VOLTAGE-GATED Kv1.5 POTASSIUM CHANNEL

The interaction of ladder polyethers of marine origin, like ciguatoxin 3C and brevenal, as well as hypothetic ent-brevenal, with the human voltage-gated Kv1.5 potassium ion channel is investigated in this work using homology modeling, automated docking, and energy scoring from molecular dynamics (MD) simulations. A 3D homology model of the pore region of the Kv1.5 channel, previously developed from the 2.9 Å resolution crystal structure of the mammalian Kv1.2 channel — which has a very similar pore sequence — is used here. While ciguatoxin 3C did not enter the pore, both brevenal and ent-brevenal were found into the pore, the latter one with the best score. Binding is attended by notable strain in the ligands, and the corresponding energy increase was evaluated for ent-brevenal by self consistent field (SCF) and density functional theory (DFT) procedures. Egress of ent-brevenal from the pore, as a microscopical reversal of the ingress, was investigated by a smart form of biased MD simulations. While this study indicates ample room and attractive interactions for both brevenal and its enantiomer into the pore, whether these molecules will be found to inhibit voltage-gated potassium ion currents depends upon the barriers in the real system to access the pore, with their thermodynamic and kinetic requirements.

Total synthesis of gambierol

The total synthesis of gambierol has been achieved utilizing an oxiranyl anion strategy in an iterative manner. Synthetic highlights of this route include direct carbon-carbon formation on epoxides, sulfonyl-assisted 6-endo cyclization, and expansion reaction of tetrahydropyranyl rings to oxepanes to forge the polycyclic architecture of the target molecule.

Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin-1 with ASIC1a channels using a homology model

The interaction of the tarantula toxin PcTx1 with the hASIC1a ion channel is investigated here along homology modeling (using the crystal structure of the cASIC1 channel as a template and the known sequence of hASIC1a), automated docking (using the NMR solution structure of PcTx1), and molecular dynamics simulations (taking into account proton-binding sites), in what represents the first modeling and computational chemistry in the whole family of ASIC/DEG/ENaCs/FaNaCh channels. The results agree with binding and electrophysiological data for the interaction of mutant (125)I-PcTx1Y(N) with rASIC1a chimeras and PcTx1 itself with hASIC1a chimeras. They go even farther by revealing that only two hASIC1a subunits can be directly involved in the binding, to which four domains - instead of the only two identified by the experiments - participate. Mapping the closest lying amino acids of the homology model and PcTx1 can have heuristic value in stimulating ideas, software, and experimentation.