Integrative modeling of experimentally unapproachable drug targets: the case of Staphylococcus aureus? beta-lactam sensor MecR1

ABRIATA, L.A.; AYDIN, D.; BELLUZO, B.S.; LLARRULL, L.I.; DAL PERARO, M.

Lausana

Simposio; Structure-based drug discovery symposium; 2015

Many proteins stand as attractive targets for drug design given their roles in disease processes, but are very hard to study from structural perspectives. Yet, their functions can often be studied through biochemical experiments and their structures be modeled through approaches that integrate sparse experimental data including partial structures and lower resolution hints about residue-residue contacts, transmembrane topology, shape, etc. plus sequence-based predictions, homology modeling, computational simulations, and general knowledge about protein chemistry.Here we have integrated varied sources of information and predictions to model MecR1, a protein that regulates the expression of a transpeptidase enzyme resistant to clinical concentrations of beta-lactams in Staphylococcus aureus. Activation of this transpeptidase extends the weaponry that staphylococci employ to overcome therapies with beta-lactam antibiotics, a very important problem in clinic.MecR1 consists of a periplasmic penicillin-binding domain of known structure, and a transmembrane metallopeptidase domain that complicates its purification in the laboratory despite efforts by several groups, thus precluding structural studies that could give molecular insights into the mechanism that triggers resistance upon beta-lactam binding and complicating the interpretation of several pieces of biochemical evidences. Our model of full MecR1 based on homology modeling, residue coevolution, a new topology mapping of the transmembrane domain, and NMR data about its interactions with the sensor domain, as well as molecular dynamics simulations of the sensor domain, provide explanations to several biochemical observations, lead to new experimental hypotheses now being tested through biochemical experiments, and advance possible functional mechanisms.