Breaking the Barrier: Mapping protein interactions in the bacterial outer membrane as targets for new antimicrobials
Lead Research Organisation:
University of Leeds
Department Name: Astbury Centre
Abstract
Across human history, bacteria have been responsible for a huge burden of disease and mortality that only lessened with the discovery of vaccination and antibiotics. We now face a rising tide of antimicrobial resistance, and are experiencing a slow-moving pandemic of hospital-acquired infections by drug-resistant bacteria. Alongside better prevention, control, and surveillance, there is an urgent need to identify new targets against which we can develop new antibiotic drugs. Of particular concern are the Gram-negative group of bacteria. Of the five microorganisms identified as urgent threats by the US Centres for Disease Control, three are Gram-negative bacteria, and while there are worryingly few new antibiotics in trials, even fewer target Gram-negative bacteria.
Membranes, and the proteins associated with them, constitute the majority of current drug targets across multiple disease areas, largely because membranes are the basis for much compartmentalisation and communication in and between cells. Gram-negative bacteria have a unique, additional, protective outer membrane (OM) that shields the bacterium from its environment. The OM is a major barrier to toxins and antibiotics, and is critical for bacterial growth, virulence, pathogenesis, and the formation of biofilms (which are important for establishing many infections). All biological membranes have two leaflets of amphipathic lipid molecules (typically phospholipids) that form a bilayer, and the lipids in each leaflet are different (asymmetric). The bacterial OM is perhaps the most striking example of membrane asymmetry in biology, with an inner leaflet dominated by phospholipids (as in normal membranes), and an outer leaflet dominated by lipopolysaccharide molecules (which are unique to the bacterial membrane). Integral outer membrane proteins (OMPs), which all have a barrel-shaped structure, have thus evolved to fold and function in a different environment to proteins in other membranes: they experience a very rigid membrane because the lipopolysaccharide clumps together. Furthermore, they don't move around very much in the membrane, and their conformations and interactions are dictated by interactions with other proteins and lipopolysaccharide that are missing in other membranes, but essential for bacterial growth and survival.
The OM is thus a fascinating environment that could provide a rich source of new targets for antibacterial interventions. In this MRC programme grant, we will integrate functional and structural studies on the bacterial OM, with the latest innovations in protein structure (and protein interaction) prediction, and in our ability to design new proteins that can bind target proteins. Working in the test tube and with whole bacterial cells, we will learn how OMPs naturally fold up and become embedded within the outer membrane, how they interact with each other and with LPS molecules when they're in that membrane, and how these interactions affect the ways proteins work and how bacteria grow. Ultimately, we want to use these discoveries to illuminate new ways of killing bacteria, or at least weakening their defences so that other drugs can kill them. A programme grant is essential because it will allow us to build a talented team that can work together to make discoveries at a pace and scale that would be impossible via individual, smaller project grants, and it will allow us to place the UK at the forefront of this vital area of research.
Membranes, and the proteins associated with them, constitute the majority of current drug targets across multiple disease areas, largely because membranes are the basis for much compartmentalisation and communication in and between cells. Gram-negative bacteria have a unique, additional, protective outer membrane (OM) that shields the bacterium from its environment. The OM is a major barrier to toxins and antibiotics, and is critical for bacterial growth, virulence, pathogenesis, and the formation of biofilms (which are important for establishing many infections). All biological membranes have two leaflets of amphipathic lipid molecules (typically phospholipids) that form a bilayer, and the lipids in each leaflet are different (asymmetric). The bacterial OM is perhaps the most striking example of membrane asymmetry in biology, with an inner leaflet dominated by phospholipids (as in normal membranes), and an outer leaflet dominated by lipopolysaccharide molecules (which are unique to the bacterial membrane). Integral outer membrane proteins (OMPs), which all have a barrel-shaped structure, have thus evolved to fold and function in a different environment to proteins in other membranes: they experience a very rigid membrane because the lipopolysaccharide clumps together. Furthermore, they don't move around very much in the membrane, and their conformations and interactions are dictated by interactions with other proteins and lipopolysaccharide that are missing in other membranes, but essential for bacterial growth and survival.
The OM is thus a fascinating environment that could provide a rich source of new targets for antibacterial interventions. In this MRC programme grant, we will integrate functional and structural studies on the bacterial OM, with the latest innovations in protein structure (and protein interaction) prediction, and in our ability to design new proteins that can bind target proteins. Working in the test tube and with whole bacterial cells, we will learn how OMPs naturally fold up and become embedded within the outer membrane, how they interact with each other and with LPS molecules when they're in that membrane, and how these interactions affect the ways proteins work and how bacteria grow. Ultimately, we want to use these discoveries to illuminate new ways of killing bacteria, or at least weakening their defences so that other drugs can kill them. A programme grant is essential because it will allow us to build a talented team that can work together to make discoveries at a pace and scale that would be impossible via individual, smaller project grants, and it will allow us to place the UK at the forefront of this vital area of research.
Technical Summary
Gram-negative bacteria are pervasive in Nature and responsible for a huge burden of disease and mortality. Despite this, and the fact that they have been identified by CDC/WHO as urgent threats, very few new antibiotics are in the pipeline targeted at Gram-negative (GN) bacteria. GN bacteria have a unique outer membrane (OM) that is a barrier to toxins/antibiotics, and is required for growth, virulence, pathogenesis, and biofilm formation. While membranes typically have asymmetry between the leaflets of lipids that form the bilayer, the bacterial OM is uniquely asymmetric. It has an inner leaflet dominated by phospholipids, and an outer leaflet dominated by lipopolysaccharides (LPS) that are highly negatively charged and strong activators of host immunity. The OM is very high in protein, and reliant on currently poorly understood protein-protein and protein:LPS interactions for its integrity. Integral outer membrane proteins (OMPs) have thus evolved to fold/function in a very different environment to proteins in other bilayers.
Given these evolutionary differences, the OM is a fascinating environment that could provide a rich source of new targets for antibacterials. In this MRC programme, we will integrate functional/structural studies on the OM, with innovations in protein structure prediction, and the design of proteins that can bind target proteins. Working both in vitro and in vivo, we will reveal the determinants of OMP folding into the OM, how OMPs interact with each other and with LPS, and how these interactions affect OMP function and bacterial viability. Ultimately we want to use these discoveries to discover small molecules and design protein binders, that are diagnostic, bactericidal or least weaken bacterial defences for the action of other drugs.
Given these evolutionary differences, the OM is a fascinating environment that could provide a rich source of new targets for antibacterials. In this MRC programme, we will integrate functional/structural studies on the OM, with innovations in protein structure prediction, and the design of proteins that can bind target proteins. Working both in vitro and in vivo, we will reveal the determinants of OMP folding into the OM, how OMPs interact with each other and with LPS, and how these interactions affect OMP function and bacterial viability. Ultimately we want to use these discoveries to discover small molecules and design protein binders, that are diagnostic, bactericidal or least weaken bacterial defences for the action of other drugs.
