PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules

Area of Science:

• Biochemistry
• Computational Chemistry
• Structural Biology

Background:

• Many enzymes lack elucidated catalytic mechanisms despite available structural data.
• Reactivity descriptors, derived from electronic structure, can predict and explain chemical processes in biological systems.

Purpose of the Study:

• Introduce PRIMoRDiA (Macromolecular Reactivity Descriptors Access) software for calculating reactivity descriptors in large biosystems.
• Demonstrate the software's efficiency and accuracy in handling large quantum chemistry output files.

Main Methods:

• PRIMoRDiA employs efficient and accurate methods for processing large output files from quantum chemistry packages.
• The software calculates reactivity descriptors for enzymatic systems and analyzes molecular interactions.

Main Results:

• PRIMoRDiA successfully calculated reactivity descriptors for various enzymatic systems, highlighting their utility in biological studies.
• The software demonstrated potential for large-scale applications and aided in depicting interactions between SARS-CoV-2 main protease and an inhibitor.

Conclusions:

• PRIMoRDiA is a valuable tool for elucidating enzyme mechanisms and predicting reactivity in large biological systems.
• The software facilitates the study of enzyme function and the development of potential inhibitors, including for SARS-CoV-2.