High-throughput development of bacterial PROTACs
Lead Research Organisation:
University of Oxford
Department Name: Pharmacology
Abstract
Antimicrobial resistance (AMR) is one of the most serious threats to global health, potentially making life-saving medical advances such as surgery and chemotherapy so dangerous as to be impractical. Even diseases of old age such as neurodegeneration may become a lessening priority if AMR compromises medical procedures and curtails life expectancy. The challenge of AMR is exacerbated by a scarce pipeline of new antibiotics and it is widely appreciated that new molecules with novel mechanisms of action are urgently needed.
Bifunctional molecules have seen an explosion of research interest in human diseases; however, use in AMR is lacking. Proteolysis-targeting chimeras (PROTACs) recruit target proteins to the proteasome machinery for degradation. PROTACs have advantages over traditional inhibitors: activity does not require complete target occupancy meaning one bifunctional molecule can degrade multiple target protein molecules; and a longer duration of action can be achieved as target synthesis is required to recover function. We have recently shown for the first time that the E. coli periplasmic protease DegP can degrade functional beta-lactamase enzyme TEM116, and have synthesised ligands for both DegP and beta-lactamases. In addition, we have established a platform for automated PROTAC synthesis to rapidly generate bacterial PROTACs to explore structure-activity relationships.
The aim of this project is therefore to develop bacterial PROTAC degraders of antibiotic resistance enzymes. This will be achieved through the following objectives:
1. SAR optimisation of DegP and bet-lactamase ligands
2. Modification of bacterial PROTACs linker lengths for degradation of TEM116 in bacterial lysates,
3. Optimisation of cell penetration, profiling for degradation of other beta-lactamases, and demonstration of proof-of-concept degradation of TEM116 in intact bacteria
The potential applications and benefits of this project are broad. Firstly, this will provide a new series of molecules with a novel mechanism of action to sensitize resistant bacteria to beta-lactam antibiotics, primed for continued translation. Secondly, this opens a new area of research where existing antibiotics may be converted to bacterial PROTACs to partner with new or existing antibiotics to prolong lifetime, and where target degradation may produce enhanced effects compared to resistance enzyme inhibitors. Thirdly, the automated synthesis platform for high-throughput PROTAC generation may accelerate development of PROTACs for other diseases.
Bifunctional molecules have seen an explosion of research interest in human diseases; however, use in AMR is lacking. Proteolysis-targeting chimeras (PROTACs) recruit target proteins to the proteasome machinery for degradation. PROTACs have advantages over traditional inhibitors: activity does not require complete target occupancy meaning one bifunctional molecule can degrade multiple target protein molecules; and a longer duration of action can be achieved as target synthesis is required to recover function. We have recently shown for the first time that the E. coli periplasmic protease DegP can degrade functional beta-lactamase enzyme TEM116, and have synthesised ligands for both DegP and beta-lactamases. In addition, we have established a platform for automated PROTAC synthesis to rapidly generate bacterial PROTACs to explore structure-activity relationships.
The aim of this project is therefore to develop bacterial PROTAC degraders of antibiotic resistance enzymes. This will be achieved through the following objectives:
1. SAR optimisation of DegP and bet-lactamase ligands
2. Modification of bacterial PROTACs linker lengths for degradation of TEM116 in bacterial lysates,
3. Optimisation of cell penetration, profiling for degradation of other beta-lactamases, and demonstration of proof-of-concept degradation of TEM116 in intact bacteria
The potential applications and benefits of this project are broad. Firstly, this will provide a new series of molecules with a novel mechanism of action to sensitize resistant bacteria to beta-lactam antibiotics, primed for continued translation. Secondly, this opens a new area of research where existing antibiotics may be converted to bacterial PROTACs to partner with new or existing antibiotics to prolong lifetime, and where target degradation may produce enhanced effects compared to resistance enzyme inhibitors. Thirdly, the automated synthesis platform for high-throughput PROTAC generation may accelerate development of PROTACs for other diseases.
