How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a...

Area of Science:

• Biochemistry
• Enzyme kinetics
• Drug discovery

Background:

• N-myristoyltransferase (NMT) enzymes are crucial drug targets.
• Achieving selective inhibition of related NMT isoforms is challenging due to conserved active sites.

Purpose of the Study:

• To elucidate the molecular mechanisms driving selective inhibition of N-myristoyltransferase.
• To establish a framework for designing selective enzyme inhibitors for proteins with conserved binding sites.

Main Methods:

• Utilized a combination of computational modeling and experimental techniques.
• Investigated N-myristoyltransferase from two distinct organisms as a model system.
• Performed virtual screening to identify selective inhibitor candidates.

Main Results:

• Identified two distinct mechanisms for selective inhibition: altered side-chain flexibility and competitive water molecule displacement.
• Observed that side-chain flexibility changes can confer selectivity even for residues not directly interacting with ligands.
• Discovered that interfering with specific water molecule binding can also lead to selective inhibition.
• Successfully identified three hit compounds with the desired selectivity profile through virtual screening.

Conclusions:

• Selective enzyme inhibition can be achieved through diverse mechanisms beyond direct ligand-binding site interactions.
• The findings provide a practical guideline for assessing and exploiting selectivity-determining features in protein targets.
• This knowledge facilitates the rational design of highly selective inhibitors for enzymes with conserved active sites.