ESR13: Fragment-based assessment of new antibiotic targets

Host: University of York, UK
Academic supervisors: Prof. dr. Peter O’Brien and Prof. dr. Rod Hubbard (University of York)
Researcher: Bas Lamoree

Download the full description of this project: ESR13: Fragment-based assessment of new antibiotic targets

Fragment-based assessment of new antibiotic targets

We are using the fragment-based approach to discover new antibiotics. Specifically, we are investigating new ways of targeting bacteria, by looking at a set of their DNA-replicating proteins: the bacterial replisome.

The bacterial replisome is a molecular machine made up of at least twelve essential components, including a DNA polymerase, an RNA polymerase, a nuclease, and three different ATPases, as well as other non-catalytic but structurally important proteins. These proteins form three main subcomplexes: the polymerase, the clamp loader, and the helicase. Structural details are known for these subcomplexes, but not for the active whole replisome complex. Instead, it is better characterized by the many different dynamic interactions between proteins during various stages of the catalytic cycle.

As the machine only works when all these components are present, inactivating one of them would lead to slow-down or arrest of DNA replication. Such inhibition of DNA replication can therefore happen in many ways. We have reconstituted the functional bacterial replisome in vitro and screened a fragment library against it. We found that fragments can target several known sites, while some fragments appear to act by unknown mechanisms. This demonstrates a novel way of working with fragments in a complex system.

The current project focuses on 1) using structural and functional experiments to optimize fragment screening hits against a protein-protein interaction in the helicase subcomplex, and 2) using covalent modification of the replisome to directly identify the sites of action of fragments with unknown mechanism.

Other projects

• ESR1: 3D Fragments with small aliphatic rings – David Hamilton
• ESR2: Novel 3D fragments – Hanna Francesca Klein
• ESR3: Warhead Library of Covalent Fragment Binders – Aaron Keeley
• ESR4: Development of FBLD techniques for Intrinsically Disordered Proteins – Darius Vagrys
• ESR5: Biophysics Based FBLD – Sébastien Keiffer
• ESR6: FBLD experimental methods – Edward Fitzgerald
• ESR7: Understanding PDE binding kinetics – Pierre Boronat
• ESR8: Virtual Screening of Fragment Libraries of Covalent Binders – Andrea Scarpino
• ESR9: Fragment evolution platform – chemical navigation – Moira Rachman
• ESR10: Fragment evolution platform – molecular simulations – Maciej Majewski
• ESR11: Fragment-based approaches to identify novel PPI inhibitors – Lorena Zara
• ESR12: Covalent fragments to activate industrial enzymes – Eleni Makraki
• ESR14: Targeting allosteric pockets with FBLD – Lena Münzker
• ESR15: Science, Business & Innovation in the pharmaceutical sciences – Angelo Kenneth Romasanta