Rel Enzyme Modulators Targeting Persister Cells
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Solution Overview
Problem
The emergence of antibiotic-resistant bacteria, particularly those in a persistent state, poses a significant threat due to their resistance to conventional antibiotics, and the poor stability and aggregation of Rel enzymes during crystallization have hindered understanding of their molecular control mechanisms, necessitating innovative strategies to counteract these bacteria.
Innovation Solution
The elucidation of the structural changes in Rel enzymes upon ligand binding and the development of new screening methods to identify compounds that modulate Rel hydrolase and synthetase activities, allowing for the identification of compounds that steer Rel activity and counteract persister cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional antibiotics are used to treat bacterial infections, then rapidly dividing bacteria are eliminated, but persister cells survive and cause chronic infections
Solution Approach 1:
The invention extracts and targets the specific molecular mechanism (RelA/SpoT enzymes and ppGpp alarmone) that controls persister cell formation, separating this target from general bacterial growth processes. By specifically inhibiting the RelA/SpoT enzymes that synthesize and degrade ppGpp, the treatment selectively addresses persister cells without affecting rapidly dividing bacteria, thereby overcoming the limitation of conventional antibiotics that only target active growth.
Solution Approach 2:
Instead of targeting bacterial growth processes directly (as conventional antibiotics do), the invention inverts the approach by targeting the stress response mechanism (stringent response via ppGpp) that enables persistence. By modulating the alarmone system rather than growth processes, the treatment achieves the opposite effect: eliminating dormant persisters rather than active growers.
2Reliability
If RelA/SpoT enzymes are targeted to modulate ppGpp levels, then persister cell formation is reduced, but the bifunctional nature of these enzymes makes structural characterization difficult
Solution Approach 1:
The invention segments the bifunctional RelA/SpoT enzyme into its two distinct catalytic activities: ppGpp synthetase activity and ppGpp hydrolase activity. By developing separate screening assays and computational models for each function, the complex enzyme can be characterized and targeted independently for each activity, simplifying the structural and functional analysis despite the enzyme's dual functionality.
Solution Approach 2:
The invention uses computational molecular docking and virtual screening as intermediary tools to bridge the gap between the difficult-to-characterize bifunctional enzyme and potential inhibitors. These computational methods serve as mediators that can predict binding modes and affinities without requiring complete structural characterization, enabling drug discovery despite the enzyme's structural challenges.
3Productivity
If molecular docking and virtual screening are used to identify Rel modulators, then compound identification is accelerated, but computational resources and time are required for structure optimization
Solution Approach 1:
The invention performs preliminary computational screening and molecular docking on large compound libraries before wet-lab validation. By pre-filtering compounds in silico based on predicted binding affinity and properties, the approach identifies promising candidates early, reducing the number of compounds that require time-consuming experimental testing and optimization.
Solution Approach 2:
The invention replaces mechanical/wet-lab screening methods with computational molecular docking and virtual screening to identify and optimize Rel modulators. This substitution of computational methods for experimental methods accelerates the initial compound identification and optimization phases, allowing rapid evaluation of thousands of compounds in silico before proceeding to laboratory validation.
Data Source
AI summary
The present invention concerns screening methods to identify compounds that regulate activity of RSH enzymes such as Rel, and specifically Rel synthetase and/or Rel hydrolase activity. Also intended are compounds that interact and regulate Rel synthetase and/or hydrolase activity. These compounds are valuable to target persister cells not affected by traditional antibiotics.