Molecular Modelling of Multi-Drug Resistance Transporters

Abstract

Drug efflux is an important mechanism of drug resistance. It is mediated by transmembrane proteins called efflux transporters, which utilise either a primary source of energy (e.g. ATP), or a secondary source (e.g. electrochemical potential difference across the membrane), to extrude toxic substances, including therapeutic drugs, out of the cell. One family of efflux transporters that are frequently associated with drug resistance is the ATP-binding cassette (ABC) superfamily. They utilise energy gained from ATP hydrolysis to transport substrates either into the cell (import) or out of the cell (export) and are subsequently divided into two functional groups, the importers and the efflux transporters (also known as efflux pumps). Two ABC efflux transporters that are implicated in tolerance to antimicrobial drugs are PfMDR1 and PatA/PatB. PfMDR1 is protein expressed in the eukaryotic protist Plasmodium falciparum, the most important of the species that cause malaria. Malaria is a devastating disease killing millions of people every year in tropical and subtropical areas. Polymorphisms within the pfmdr1 gene are found to confer resistance to several first-line drugs against malaria. Similarly, PatA/PatB is a heterodimeric efflux transporter of the pathogenic bacterium Streptococcus pneumoniae, which is a leading cause of illness in young children, older people and individuals with debilitating medical conditions. Several strains of S. pneumoniae have been isolated during the last decades that show susceptibility to the frequently prescribed drugs, including fluoroquinolones. Overexpression of PatA/PatB transporter has been recently connected to fluoroquinolone resistance.This project aimed to model in silico the 3D structure of PfMDR1 and PatA/PatB, as a potential first stage in drug design. Atomistic models of the full-length transporters in the outward-facing conformation were build, using a combination of comparative modelling and ab initio structure prediction. Emphasis was given to the nucleotide binding domains (NBDs), with a special focus on the ATP-binding site, which is the most promising receptor site for future design of transporter modulators. Structural information available for other homologous proteins was utilised to model backbone and side-chain conformations in the most accurate way. The resulting models showed great robustness, and a large cavity was traced at the interface of the two NBDs , which can potentially facilitate a wide range of drug-like compounds.

Date of Award	31 Dec 2011
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Jeffrey Penny (Supervisor) & Andrew Mcbain (Supervisor)