Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators

Protein–protein
interactions (PPIs) are known to play an
essential role between the neuronal calcium sensor 1 (NCS-1) and the
guanine exchange factor Ric8a to regulate synapse function, emerging
as a druggable interface for synaptopathies such as the fragile X
syndrome (FXS). Recently, the phenothiazine FD44 has been identified
as an inhibitor of this PPI, decreasing the abnormally high synapse
number and enhancing associative learning in a FXS animal model. Here,
we have integrated advanced experimental and computational studies
to obtain important structural insights into Drosophila NCS-1/FD44 recognition to understand the basis of its affinity and
specificity and generate improved PPI regulators. This has allowed
the identification of a new small drug-like molecule, IGS-1.76, which
efficiently inhibits the human NCS-1/Ric8a complex with improved binding
potency. The crystal structure of the Drosophila NCS-1/IGS-1.76
complex demonstrates that the new inhibitor, although chemically different
from FD44, shares the same mechanism of action and constitutes a new
hit candidate for FXS.