Rational redesign of a cation···π···π stacking at cardiovascular Fbw7–Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction

Molecular conversion of MIG6 hotspot-3 peptide from the nonbinder to a moderate binder of HER2 by rational design of an orthogonal interaction system at the HER2-peptide interface

Human epidermal growth factor receptor 2 (HER2) has been established as an approved druggable target for the treatment of patients with diverse gynecological tumors such as ovarian, cervical and breast cancers. The mitogen-inducible gene 6 (MIG6) protein is a negative regulator of HER2 signaling by using its Seg1 segment to disrupt the allosteric dimerization of HER2 kinase domain. Previous studies found that the Seg1 adopts three separated hotspots to interact with the HER2 dimerization interface, in which the third hotspot (H3) is located at the core region of the interface but its derived H3 peptide (356PKYVS360) and Tyr358Phe mutant (356PKFVS360) cannot bind effectively to the interface in an independent manner. In this study, we demonstrate that the H3 peptide can be converted from nonbinder to a moderate binder of HER2 by just adding an orthogonal noncovalent interaction system (X⋯O┄H) between a halogen bond (X⋯O) and a hydrogen bond (H┄O) involving peptide Phe358 residue and HER2 Val948/Trp951 residues. High-level calculations are utilized to rigorously characterize and rationally design the X⋯O┄H system, which is then optimized with different halogen atoms and at different substituting positions. It is revealed that there is a synergistic effect between the X⋯O and H┄O of the orthogonal interaction system; formation of the halogen bond can enhance the interaction strength of the hydrogen bond. In silico analysis and in vitro assay reach a consistence that Br-substitution at the m-position of peptide Phe358 phenyl moiety is the best choice that can render strong interaction for the X⋯O┄H system, which also makes the peptide 'bindable' to HER2 kinase domain, while F/Cl/I-substitution at the same position can only improve the peptide affinity moderately or modestly. In contrast, the Br-substitution at the o- and p-positions of peptide Phe358 phenyl moiety cannot define effective X⋯O┄H interaction and thus does not confer additional affinity to the HER2-peptide complex.

User-Friendly Quantum Mechanics: Applications for Drug Discovery

Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.