Molecular design and validation of halogen bonding orthogonal to hydrogen bonding in breast cancer MDM2-peptide complex.

Peptide therapeutics has been raised as an attractive approach for the treatment of breast cancer by targeting the oncogenic protein MDM2 that inactivates p53 tumor suppressor. Here, we performed molecular design of halogen bonding orthogonal to hydrogen bonding at the complex interface of MDM2 protein with its cognate peptide ligand to improve the peptide binding affinity and specificity. Crystal structure analysis, high-level quantum chemistry (QC) calculations and combined quantum mechanics/molecular mechanics (QM/MM) modeling revealed that halogen substitution at position 3 of the benzene moiety of peptide Phe3 residue can constitute a putative halogen bonding, which is shown to be geometrically perpendicular to and energetically independent of a native hydrogen bonding that share a common carbonyl oxygen acceptor. The designed halogen bonding was then validated by surface plasmon resonance (SPR) assays, that is, substitution with bromine at position 3 can considerably improve peptide affinity by ∼4-fold, but the peptide binding does not change substantially upon the bromine substitution at other positions of the Phe3 benzene moiety (the negative controls that are theoretically unable to form the halogen bonding), indicating that the orthogonal molecular interaction (OMI) system between the designed halogen bonding and native hydrogen bonding can co-work well at the complex interface of MDM2 protein with its halogenated peptide ligands.