Overcoming Metabolic Drug Resistance by Computer-Based Rational Design : Targeting DAPDC

     Metabolic enzymes, which catalyze essential biochemical transformations of abundant nutrients, have typically been overlooked in drug design campaigns. However, core metabolic enzymes are largely incompatible with traditional drug discovery strategies for reasons that originate in the physical chemistry of inhibition itself. Most enzyme inhibitors bind in the active site and compete directly with substrates to block activity. However, when a core metabolic enzyme is inactivated by a competitive inhibitor in vivo, enzymes upstream in the metabolic pathway continue to function and substrates of the targeted enzyme can accumulate to levels at which they out-compete the drug and reverse the inhibition. This phenomenon, referred to metabolic resistance, renders competitive inhibitors with high potency when tested against the purified enzyme in vitro are often far weaker or completely ineffective in the context of the full metabolic pathway of the intact organism.
     Inhibitors that block catalysis by binding to the enzyme/substrate complex (rather than the enzyme alone) are largely immune to metabolic resistance. Despite their tremendous advantages, uncompetitive inhibitors represent only a tiny fraction of current drugs. These types of inhibitors are often structurally dissimilar from the enzymatic substrates and products and they do not tend to be identified in high-throughput screens. We propose to leverage recent advances in our laboratories that will allow i) high-throughput in silico screening of synthetically-accessible molecules for those that bind to enzyme/substrate complexes ii) facile chemical synthesis of top-ranked hits, and iii) rapid biophysical testing to determine the strength and mode of inhibition. This novel drug design and testing pipeline will deliver exclusively uncompetitive inhibitors that are effectively competition-proof and can therefore completely block the activity of targeted metabolic enzymes in vitro and in vivo.      DAPDC (DiAminoPimelate DeCarboxylase) catalyzes the final step of lysine biosynthesis in bacteria, decarboxylating diaminopimelate to produce CO2 and L-lysine. Lysine is required for protein production and is an essential component of the bacterial cell wall. Abrogation of DAPC by genetic manipulation was shown to block bacterial infection, but the only small molecule inhibitors of DAPDC known to date are competitive substrate analogs, which are ineffective in vivo. Thus competition-proof inhibitors of DAPDC hold tremendous promise as new antimicrobials and antibiotic adjuvants.
Keywords : · DAPDC · Drug Resistance ·Computer-Based Rational Design · Competitive Inhibition
Key people involved in the project : Chris Wang (graduate student)
Key publications related to the project : coming soon!