Mark P Thomas | PubMed Health

PubMed2006

Protein structures in virtual screening: a case study with CDK2.

The influence of protein structure on the successful reproduction of known ligand poses by high-throughput docking programs is rarely discussed. Two commonly used programs, Glide and GOLD, were used to dock a set of CDK2 inhibitors of known bound pose into 20 different CDK2 structures. The numbers of docked poses that reproduced the known pose are reported. Depending on the program and protein structure, 0.3%-96.2% of the ligands docked with the correct pose. Although it is not possible to say that any one structure is "the best" for virtual screening, there are some structures that are clearly better than others. The main determinants of this are the volume of the binding site into which the ligands are docked and the exact orientation of the residues forming the binding site.

Binding Sites↗

PubMed2006

Structure-based discovery and optimization of potential cancer therapeutics targeting the cell cycle.

Progress has been made recently in the structure-based optimization of novel cell cycle antitumor therapeutics based on cyclin-dependent kinase (CDK) inhibition. A novel inhibitor series based on the 2-amino-4-heteroaryl-pyrimidine scaffold was discovered using the LIDAEUS high-throughput docking methodology, and was subsequently optimized for CDK2 potency through information provided by crystallographic complex structures. A computational study of CDK4 inhibitors led to the incorporation of selectivity determinants into a pyrimidine pharmacophore to generate isoform-specific inhibitors. In addition, molecules from the inhibitor series have been crystallized in complex structures with both monomeric inactive CDK2 and an active complex of CDK2 bound to cyclin A or E. This crystallization revealed that significant differences exist in the affinity of the inhibitors for active and inactive states of CDK2. Information on differences in affinity facilitates the prediction of experimental binding of inhibitors and allows for the further development of structure-guided design.

Antineoplastic Agents↗

PubMed2003

Suppression of L-type voltage-gated calcium channel-dependent synaptic plasticity by ethanol: analysis of miniature synaptic currents and dendritic calcium transients.

Intoxicating concentrations of ethanol inhibit N-methyl-d-aspartate (NMDA) receptor-dependent long-term potentiation, an interaction thought to underlie a major component of the central nervous system actions of ethanol. Another form of synaptic potentiation involving activation of L-type dihydropyridine-sensitive voltage-gated calcium channels (VGCCs) has been described, but very little information concerning ethanol effects on VGCC-dependent synaptic potentiation is available. Here, we assessed ethanol effects on VGCC-dependent synaptic potentiation using whole cell patch-clamp recordings of alpha-amino-3-hydroxy-5-methyl-4-soxazolepropionic acid (AMPA) receptor-mediated miniature excitatory postsynaptic currents (mEPSCs) in area CA1 of the rat hippocampus. No potentiation was observed in artificial cerebrospinal fluid containing 2 to 3 mM Ca2+, but marked potentiation of mEPSCs was consistently observed in 4 mM Ca2+ and with patch pipettes containing an ATP-regenerating system. This potentiation was insensitive to the NMDA receptor antagonist DL-2-amino-5-phosphonovaleric acid, whereas it was completely blocked the L-type VGCC antagonist nifedipine. Potentiation was also blocked dose dependently by bath application of ethanol (25-75 mM), which had no effect on baseline mEPSC amplitude or frequency. The synaptic potentiation involved enhancement of both presynaptic and postsynaptic components because significant increases in both the frequency and amplitude of AMPA mEPSCs were observed. Ethanol inhibition of VGCC-dependent synaptic potentiation seemed to occur at the induction step because both the increases in mEPSC frequency and amplitude were affected. To address that question more directly, we used fluorescent imaging of synaptically evoked dendritic calcium events, which displayed a similarly marked ethanol sensitivity. Thus, ethanol modulates fast excitatory synaptic transmission by inhibiting the induction of an NMDA receptor-independent form of synaptic potentiation observed at excitatory synapses on central neurons.

Animals↗