Exploring the energy-coupling factor (ECF) transporters as a novel antibiotic target

ATP-binding cassette (ABC) transporters use the free energy obtained from the hydrolysis of ATP to transport small molecules or macromolecules across biological membranes. Numerous ABC transporter functions are essential for life. The recently discovered ECF class of prokaryotic ABC proteins bind the substrate (vitamins and other micronutrients) in the membrane via an integral membrane protein (the S-component). The S-component associates with the ECF, consisting of a second integral membrane protein and two ATP-binding domains, to form a functional ABC transporter. The ECF-type ABC transporters are essential for the growth of Gram-positive and some Gram-negative pathogens, making them validated drug targets for the development of novel antibacterials. The S-components are accessible from the outside of the cell and attractive targets for inhibition of the transporters by small molecules, and therefore for inactivation of the pathogenic bacteria. 

We focussed our attention on the thiamine-specific S-component ThiT to gain a better understanding of the structural factors that lead to the nanomolar affinity. Systematic modification of the central aromatic ring as well as the pyrimidinyl ring by SBDD has led to a synthetically more easily accessible and versatile thiamine analogue (Kd = 3.96 ± 1.48 nM), which is a convenient starting point to grow into the unoccupied pocket. In addition, we have started to see some movement of the L1 loop for the benzyl derivative of thiamine 3. We adopted SBDD in a true de novo sense and inspired by the software KRIPO to grow 4 into an adjacent, unoccupied pocket and interfere with the L1 loop and identified binders with comparable affinities to our thiamine analogues; the fact that the affinity did not increase and that we could not cocrystallise them suggest that this pocket appears to be flexible, making traditional SBDD particularly challenging and that they are starting to interfere with the L1 loop, thereby disrupting the crystal packing. 

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Anna Hirsch

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