Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

Peptides are a rapidly growing class of therapeutics with various advantages over traditional small molecules, especially for targeting difficult protein–protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing bioactive cyclic topologies that go beyond natural l-amino acids. Here, we report a generalizable framework that exploits the computational power of Rosetta, in terms of large-scale backbone sampling, side-chain composition and energy scoring, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we developed two new inhibitors (PD-i3 and PD-i6) of programmed cell death 1 (PD-1), a key immune checkpoint in oncology. A comprehensive biophysical evaluation was performed to assess their binding to PD-1 as well as their blocking effect on the endogenous PD-1/PD-L1 interaction. Finally, NMR elucidation of their in-solution structures confirmed our de novo design approach.

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.     

Redox-Switchable Complexes Based on Nanographene-NHCs

A series of rhodium and iridium complexes with a N-heterocyclic carbene (NHC) ligand decorated with a perylene-diimide-pyrene moiety are described. Electrochemical studies reveal that the complexes can undergo two successive one-electron reduction events, associated to the reduction of the PDI moiety attached to the NHC ligand. The reduction of the ligand produces a significant increase on its electron-donating character, as observed from the infrared spectroelectrochemical studies. The rhodium complex was tested in the [3+2] cycloaddition of diphenylcyclopropenone and methylphenylacetylene, where it displayed a redox-switchable behavior. The neutral complex showed moderate activity, which was suppressed when the catalyst was reduced.     

A branch and cut algorithm for the hierarchical network design problem

The Hierarchical Network Design Problem consists of locating a minimum cost bi-level network on a graph. The higher level sub-network is a path visiting two or more nodes. The lower level sub-network is a forest connecting the remaining nodes to the path. We optimally solve the problem using an ad hoc branch and cut procedure. Relaxed versions of a base model are solved using an optimization package and, if binary variables have fractional values or if some of the relaxed constraints are violated in the solution, cutting planes are added. Once no more cuts can be added, branch and bound is used. The method for finding valid cutting planes is presented. Finally, we use different available test instances to compare the procedure with the best known published optimal procedure, with good results. In none of the instances we needed to apply branch and bound, but only the cutting planes.     

Understanding Chemical Reactivity in Extended Systems:Exploring Models of Chemical Softness in Carbon Nanotubes

Chemical reactivity towards electron transfer is captured by the Fukui function.However,this is not well defined when the system or its ions have degenerate or pseudo-degenerate ground states.In such a case,the first-order chemical response is not independent of the perturbation and the correct response has to be computed using the mathematical formalism of perturbation theory for degenerate states.Spatialpseudo-degeneracy is ubiquitous in nanostructures with high symmetry and totally extended systems.Given the size of these systems,using degenerate-state perturbation theory is impractical because it requires the calculation of many excited states.Here we present an alternative to compute the chemical response of extended systems using models of local softness in terms of the local density of states.The local softness is approximately equal to the density of states at the Fermi level.However,such approximation leaves out the contribution of inner states.In order to include and weight the contribution of the states around the Fermi level,a model inspired by the long-range behavior of the local softness is presented.Single wall capped carbon nanotubes(SWCCNT) illustrate the limitation of the frontier orbital theory in extended systems.Thus,we have used a C360 SWCCNT to test the proposed model and how it compares with available models based on the local density of states.Interestingly,a simple Hü ckel approximation captures the main features of chemical response of these systems.Our results suggest that density-of-states models of the softness along simple tight binding Hamiltonians could be used to explore the chemical reactivity of more complex system,such a surfaces and nanoparticles.     

A Diels-Alder reaction / oxa-Michael addition / acyloin rearrangement cascade on tropolonic substrates

We describe a novel pericyclic/anionic cascade reaction on tropolonic substrates that combines a Diels-Alder reaction, an oxa-Michael addition, and an acyloin rearrangement to afford tricyclic α-hydroxy-β-methoxyketones. Spectroscopic, crystallographic, and mechanistic studies indicate that the process requires stabilization of reaction intermediates through intramolecular H-bonding to take place, and suggest that the conjugate addition step involves a catalytic cycle with initial formation of an ammonium enolate and sustained by an alkoxide ion pair. Given the rich functionality and structural complexity generated in a single step, the process could be exploited in the preparation of natural product-like compound libraries.     

Acetylacetonate anchors for robust functionalization of TiO2 nanoparticles with Mn(II)-terpyridine complexes

A novel class of derivatized acetylacetonate (acac) linkers for robust functionalization of TiO2 nanoparticles (NPs) under aqueous and oxidative conditions is reported. The resulting surface adsorbate anchors are particularly relevant to engineering photocatalytic and photovoltaic devices since they can be applied to attach a broad range of photosensitizers and photocatalytic complexes and are not affected by humidity. Acac is easily modified by CuI-mediated coupling reactions to provide a variety of scaffolds, including substituted terpy complexes (terpy = 2,2':6,2'-terpyridine), assembled with ligands coordinated to transition-metal ions. Since Mn-terpy complexes are known to be effective catalysts for oxidation chemistry, functionalization with Mn(II) is examined. This permits visible-light sensitization of TiO2 nanoparticles due to interfacial electron transfer, as evidenced by UV-vis spectroscopy of colloidal thin films and aqueous suspensions. The underlying ultrafast interfacial electron injection is complete on a subpicosecond time scale, as monitored by optical pump-terahertz probe transient measurements and computer simulations. Time-resolved measurements of the Mn(II) EPR signal at 6 K show that interfacial electron injection induces Mn(II) --> Mn(III) photooxidation, with a half-time for regeneration of the Mn(II) complex of ca. 23 s.