Software Speeds Up Drug Development
Researchers develop novel method to predict the morphology of sugar coats on clinically relevant proteins within minutes. GlycoSHIELD, a new computational approach to study the sugar shields of proteins, is resource-reducing, time-efficient and user-friendly. It was developed in the frame of the Max Planck Society's Dioscuri Programme in a Polish-German cooperation project through international collaborations with researchers in France, Taiwan and Germany, including the MPCDF. where the interactive web-application has been developed and hosted. The study was recently published in Cell.
Proteins not only carry out the functions that are critical for the survival of cells, but also influence the development and progression of diseases. To understand their role in health and disease, researchers study the three-dimensional atomic structure of proteins using both experimental and computational methods. Over 75% of proteins present at the surface of our cells are covered by glycans. These sugar-like molecules form very dynamic protective shields around the proteins. However, the mobility and variability of the sugars make it difficult to determine how these shields behave, or how they influence the binding of drug molecules. Mateusz Sikora, the project leader and head of the Dioscuri Centre for Modelling of Posttranslational Modifications, and his team in Krakow and partners at the Max Planck Institute of Biophysics in Frankfurt am Main, Germany, have addressed this challenge by using computers, working together with scientists at Inserm in Paris, Academia Sinica in Tapei and the University of Bremen. Their powerful new algorithm GlycoSHIELD enables a fast but realistic modeling of the sugar chains present on protein surfaces. Reducing computing hours and therefore power consumption by several orders of magnitude compared to conventional simulation tools, GlycoSHIELD paves the path towards green computing. The scientists published their new method and its validation in the renowned journal Cell.(summary taken from the website of MPI of Biophysics, read more)
Further reading and references:
- GlycoSHIELD web application hosted by MPCDF
- Original publication: Tsai, Y.-X.; et al. (incl. K. Reuter, MPCDF). Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 187, pp. 1296 - 1311 (2024). DOI
Contacts:
Dr. Klaus Reuter, Max Planck Computing and Data Facility, Garching
Dr. Mateusz Sikora, Dioscuri Centre for Modelling of Posttranslational Modifications, Krakau