No abstract

Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational “anchor extension” methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC50 values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.

The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l- and d-amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.

The elastic properties, elastic anisotropy, and thermodynamic properties of the lately synthesized orthorhombic FeB4 at high pressures are investigated using first-principles density functional calculations. The calculated equilibrium parameters are in good agreement with the available experimental and theoretical data. The obtained normalized volume dependence of high pressure is consistent with the previous experimental data investigated using high-pressure synchrotron x-ray diffraction. The complete elastic tensors and crystal anisotropies of the FeB4 are also determined in the pressure range of 0–100 GPa. By the elastic stability criteria and vibrational frequencies, it is predicted that the orthorhombic FeB4 is stable up to 100 GPa. In addition, the calculated B/G ratio reveals that FeB4 possesses brittle nature in the range of pressure from 0 to 100 GPa. The calculated elastic anisotropic factors suggest that FeB4 is elastically anisotropic. By using quasi-harmonic Debye model, the compressibility, bulk modulus, the coefficient of thermal expansion, the heat capacity, and the Grüneisen parameter of FeB4 are successfully obtained in the present work.