Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions for the Design of p53 Mutant Y220C Rescue Drugs.
Many oncogenic mutants of the tumor suppressor p53 are conformationally unstable, including the frequently occurring Y220C mutant. We have previously developed several small-molecule stabilizers of this mutant. One of these molecules, PhiKan083, 1-(9-ethyl-9H-carbazole-3-yl)-N-methylmethanamine, binds to a mutation-induced surface crevice with a KD = 150 μM, thereby increasing the melting temperature of the protein and slowing its rate of aggregation. Incorporation of fluorine atoms into small molecule ligands can substantially improve binding affinity to their protein targets. We have, therefore, harnessed fluorine-protein interactions to improve the affinity of this ligand. Step-wise introduction of fluorines at the carbazole ethyl anchor, which is deeply buried within the binding site in the Y220C-PhiKan083 complex, led to a 5-fold increase in affinity for a 2,2,2-trifluoroethyl anchor (ligand efficiency of 0.3 kcal mol(-1) atom(-1)). High-resolution crystal structures of the Y220C-ligand complexes combined with quantum chemical calculations revealed favorable interactions of the fluorines with protein backbone carbonyl groups (Leu145 and Trp146) and the sulfur of Cys220 at the mutation site. Affinity gains were, however, only achieved upon trifluorination, despite favorable interactions of the mono- and difluorinated anchors with the binding pocket, indicating a trade-off between energetically favorable protein-fluorine interactions and increased desolvation penalties. Taken together, the optimized carbazole scaffold provides a promising starting point for the development of high-affinity ligands to reactivate the tumor suppressor function of the p53 mutant Y220C in cancer cells.
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.
Matthias R
MR
Bauer
Department of Chemistry, School of Life Sciences, University of Sussex , Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom.
Rhiannon N
RN
Jones
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.
Matthias G J
MG
Baud
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.
Rainer
R
Wilcken
Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Frank M
FM
Boeckler
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.
Alan R
AR
Fersht
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.|Department of Chemistry, School of Life Sciences, University of Sussex , Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom.|German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany.|Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.
Andreas C
AC
Joerger
Department of Chemistry, School of Life Sciences, University of Sussex , Falmer, Brighton, East Sussex BN1 9QJ, United Kingdom.
John
J
Spencer
D001703:Biophysics; D018360:Crystallography, X-Ray; D015195:Drug Design; D005461:Fluorine / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009154:Mutation; D011789:Quantum Theory; D013455:Sulfur / Q000737:chemistry*; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry* / Q000235:genetics
D016159:Tumor Suppressor Protein p53; D005461:Fluorine; D013455:Sulfur