From Structure – Based to Knowledge – Based Drug Design Through X-Ray Protein Crystallography: Sketching Glycogen Phosphorylase Binding Sites

Abstract

The knowledge derived from the three-dimensional structure of a macromolecular receptor either in the native form or in complex with different ligands has given new insights to the development of improved drug candidates contributing to the drug development pipeline. The structure-based drug design approach has been tested on a number of macromolecular targets implicated in various diseases such as hypertension, glaucoma, HIV and influenza. This approach has also been employed for the development of new antidiabetic agents targeting glycogen phosphorylase (GP), an enzyme that modulates glucose levels in blood circulation. The key role of x-ray protein crystallography in the structure-based inhibitor design process is presented by the case of rabbit muscle GP (RMGPb) that shares increased homology with the liver isoenzyme. The properties of the allosteric binding sites of RMGPb are revealed by filing the interactions formed upon binding of characteristic functional groups and documenting the changes induced in the residues lining the site of interest.

Glucopyranosylidene-spiro-iminothiazolidinone, a new bicyclic ring system: Synthesis, derivatization, and evaluation for inhibition of glycogen phosphorylase by enzyme kinetic and crystallographic methods

“…Liver and muscle isoforms of GP have been thoroughly characterized, the structural features of the proteins and the binding sites are well known and have been surveyed, 14,15 therefore these enzymes are ideal targets for rational and structure-based inhibitor design.…”

“…14,15,17 The evolution of some glucose based compounds leading to the first low micromolar inhibitor of GP is exemplified in Chart 1 by compounds A-C. Thus, introduction of an acylamino type substituent in the β-anomeric position of A to give B resulted in enhanced binding by more than one order of magnitude.…”

N-(4-Substituted-benzoyl)-N′-(β-d-glucopyranosyl)ureas as inhibitors of glycogen phosphorylase: Synthesis and evaluation by kinetic, crystallographic, and molecular modelling methods

“…This could be exploited for the design of more potent inhibitors of enzyme activity coupling the knowledge derived from each complex structure with geometric 640 algorithms. 25 The compounds 15, 25-32 were docked into the Bzurea and 2-Nap-urea crystal structure of the glycogen phosphorylase, respectively. The binding affinity of the highest ranked docked poses was predicted by the LIAISON program (LiaScore) and correlated with experimentally measured K i values of the studied inhibitors.…”

Synthesis of 2-(β-d-glucopyranosyl)-5-(substituted-amino)-1,3,4-oxa- and -thiadiazoles for the inhibition of glycogen phosphorylase

“…These studies contribute to an extension of SAR related to interactions of inhibitors in the b-channel of the enzyme which can accommodate aglycons of the glucose analogue compounds and is lined with amino acid side chains of mixed character. 16 …”