title: Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor.
abstract: Protein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments.
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: David C
authors.initials: DC
authors.lastname: Fry
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Charles
authors.initials: C
authors.lastname: Wartchow
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Bradford
authors.initials: B
authors.lastname: Graves
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Janson
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Christine
authors.initials: C
authors.lastname: Lukacs
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Ursula
authors.initials: U
authors.lastname: Kammlott
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Charles
authors.initials: C
authors.lastname: Belunis
authors.affiliation: Roche Diagnostics GmbH , Nonnenwald 2, Penzberg 82377, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Palme
authors.affiliation: Roche Glycart AG , Wagistrasse 18, Schlieren CH-8952, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Klein
authors.affiliation: Roche Research Center , 340 Kingsland Street, Nutley, New Jersey 07110, United States.
authors.forename: Binh
authors.initials: B
authors.lastname: Vu
keywords: MDM2; Nutlin; binding affinity; p53; protein−protein interaction inhibitor