A single glycine residue at the entrance to the first membrane-spanning domain of the gamma-aminobutyric acid type A receptor beta(2) subunit affects allosteric sensitivity to GABA and anesthetics

Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule

Ligand-protein docking has been developed and used in facilitating new drug discoveries. In this approach, docking single or multiple small molecules to a receptor site is attempted to find putative ligands. A number of studies have shown that docking algorithms are capable of finding ligands and binding conformations at a receptor site close to experimentally determined structures. These algorithms are expected to be equally applicable to the identification of multiple proteins to which a small molecule can bind or weakly bind. We introduce a ligand-protein inverse-docking approach for finding potential protein targets of a small molecule by the computer-automated docking search of a protein cavity database. This database is developed from protein structures in the Protein Data Bank (PDB). Docking is conducted with a procedure involving multiple-conformer shape-matching alignment of a molecule to a cavity followed by molecular-mechanics torsion optimization and energy minimization on both the molecule and the protein residues at the binding region. Scoring is conducted by the evaluation of molecular-mechanics energy and, when applicable, by the further analysis of binding competitiveness against other ligands that bind to the same receptor site in at least one PDB entry. Testing results on two therapeutic agents, 4H-tamoxifen and vitamin E, showed that 50% of the computer-identified potential protein targets were implicated or confirmed by experiments. The application of this approach may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity of a drug or drug candidate. Proteins 2001;43:217-226.

Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule

Ligand-protein docking has been developed and used in facilitating new drug discoveries. In this approach, docking single or multiple small molecules to a receptor site is attempted to find putative ligands. A number of studies have shown that docking algorithms are capable of finding ligands and binding conformations at a receptor site close to experimentally determined structures. These algorithms are expected to be equally applicable to the identification of multiple proteins to which a small molecule can bind or weakly bind. We introduce a ligand-protein inverse-docking approach for finding potential protein targets of a small molecule by the computer-automated docking search of a protein cavity database. This database is developed from protein structures in the Protein Data Bank (PDB). Docking is conducted with a procedure involving multiple-conformer shape-matching alignment of a molecule to a cavity followed by molecular-mechanics torsion optimization and energy minimization on both the molecule and the protein residues at the binding region. Scoring is conducted by the evaluation of molecular-mechanics energy and, when applicable, by the further analysis of binding competitiveness against other ligands that bind to the same receptor site in at least one PDB entry. Testing results on two therapeutic agents, 4H-tamoxifen and vitamin E, showed that 50% of the computer-identified potential protein targets were implicated or confirmed by experiments. The application of this approach may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity of a drug or drug candidate. Proteins 2001;43:217-226.

Design, docking, and evaluation of multiple libraries against multiple targets

We present a general approach to the design, docking, and virtual screening of multiple combinatorial libraries against a family of proteins. The method consists of three main stages: docking the scaffold, selecting the best substituents at each site of diversity, and comparing the resultant molecules within and between the libraries. The core "divide-and-conquer" algorithm for side-chain selection, developed from an earlier version (Sun et al., J Comp Aided Mol Design 1998;12:597-604), provides a way to explore large lists of substituents with linear rather than combinatorial time dependence. We have applied our method to three combinatorial libraries and three serine proteases: trypsin, chymotrypsin, and elastase. We show that the scaffold docking procedure, in conjunction with a novel vector-based orientation filter, reproduces crystallographic binding modes. In addition, the free-energy-based scoring procedure (Zou et al., J Am Chem Soc 1999;121:8033-8043) is able to reproduce experimental binding data for P1 mutants of macromolecular protease inhibitors. Finally, we show that our method discriminates between a peptide library and virtual libraries built on benzodiazepine and tetrahydroisoquinolinone scaffolds. Implications of the docking results for library design are explored.

Mechanism of action of general anaesthetics--new information from molecular pharmacology

Major progress in our understanding of the mechanisms of anaesthesia has been made during the past year. Several key advances in defining very specific sites of action on ligand-gated ion channels have been described. Furthermore, new techniques have become available for addressing the identification of binding sites and transduction mechanisms on these receptors. The discovery that anaesthetics affect a recently identified family of potassium channels could also lead to major new findings in the next few years.

Nitrous oxide and xenon increase the efficacy of GABA at recombinant mammalian GABA(A) receptors

We investigated the interactions between recombinant gamma-aminobutyric acid receptor complex (GABA(A)R) and nitrous oxide (N(2)O) or xenon (Xe). Human embryonic kidney cells (HEK 293) were transfected with rat cDNA for alpha(1)beta(2)gamma(2L) or for alpha(1)beta(2) recombinant GABA(A)R subunits. Patch clamp techniques were used in the whole-cell mode to evaluate the effect of N(2)O and Xe on GABA-induced currents. A piezo-driven "liquid filament switch" was used for fast application. Both N(2)O (100%, 29.2 mM) and Xe (100%, 3.9 mM) reversibly increased GABA-induced currents through the alpha(1)ss(2)gamma(2L) and the alpha(1)beta(2) GABA(A)R channels. The potentiating effect of N(2)O or Xe on peak currents was prominent at small GABA concentrations (10(-7) to 10(-5) M). The addition of N(2)O or Xe increased the efficacy of GABA (10(-7) to 10(-3) M). Both N(2)O and Xe significantly decreased the risetime((10%-90%)) of the currents elicited by small GABA concentrations. At the concentrations used, neither N(2)O nor Xe had an intrinsic effect. We conclude that, similar to other anesthetics, both N(2)O and Xe increase the efficacy of GABA at the GABA(A)R and enhance inhibitory GABAergic synaptic transmission.

Barbiturates inhibit K(+)-evoked noradrenaline and dopamine release from rat striatal slices--involvement of voltage sensitive Ca(2+) channels

The cellular target site(s) for anaesthetic action remain unclear. In rat striatal slices we have previously demonstrated that K(+)-evoked noradrenaline (NA) and dopamine (DA) release is mediated predominantly via P/Q-type voltage sensitive Ca(2+) channels (VSCC). Using this model of Ca(2+) dependent transmitter release we have evaluated the effects of anaesthetic and non-anaesthetic barbiturates. Rat brain striatal slices were incubated in the absence and presence of barbiturate for 10 min at 37 degrees C. The slices were then incubated for 6 min with 40 mM KCl. All anaesthetic barbiturates produced a concentration-dependent inhibition of K(+)-evoked NA and DA release. Non-anaesthetic barbiturate, barbituric acid was ineffective. The pIC(50) for NA and DA release (thiopental: 4.90+/-0.13 and 5.00+/-0.10, pentobarbital: 4.39+/-0.07 and 4.43+/-0.14, phenobarbital: 3.85+/-0.08 and 3.59+/-0.10, respectively) correlated with lipid solubility (NA: r(2)=0.999, DA: r(2)=0.987). We therefore suggest that barbiturates inhibit catecholamine release via an interaction with P/Q VSCC further implicating this channel in anaesthetic action.