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Glutamatergic system plays an important role in mammals CNS functioning. Positive allosteric modulators (PAMs) of AMPA receptors (one of types of ionotropic glutamate receptors) have a significant influence on learning and memory consolidation. It is also shown in experiments that the intensive ion currents caused by such modulators and further postsynaptic membrane depolarization launch the mechanism of gene expression responsible for the synthesis of NGF (nerve growth factor) and BDNF (brain-derived neurotrophic factor). Thus the drugs having this mechanism of action could be efficient for the treatment of neurodegenerative diseases. The negative allosteric modulators of another important type of ionotropic glutamate receptors, NMDA receptors, could serve as neuroprotectors restricting the excessive calcium influx into neurons. In this report the techniques are considered for computer-aided design of AMPA and NMDA receptor modulators based on new scaffolds as well as approaches to their synthesis and the results of physiological activity studies. New modulators were found with a unique combination of properties including picomolar activity and low toxicity.