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.     

Phytochemical Characterization of Olea europaea L. Cultivars of Cilento National Park (South Italy) through NMR-Based Metabolomics

Olea europaea germplasm is constituted by a huge number of cultivars, each one characterized by specific features. In this context, endemic cultivars evolved for a very long period in a precise local area, developing very specific traits. These characteristics include the production and accumulation of phytochemicals, many of which are also responsible for the nutraceutical value of the drupes and of the oils therefrom. With the aim of obtaining information on the phytochemical profile of drupes of autochthonous cultivars of Cilento, Vallo di Diano and Alburni National Park, a metabolomics-based study was carried out on 19 selected cultivars. Multivariate data analysis of ¹H-NMR data and 2D NMR analyses allowed the rapid identification of metabolites that were qualitatively and/or quantitatively varying among the cultivars. This study allowed to identify the cultivars Racioppella, Guglia, Pizzulella, Oliva amara, and Racioppa as the richest in health-promoting phenolic compounds. Furthermore, it showed a significant variability among the different cultivars, suggesting the possibility of using metabolic fingerprinting approaches for cultivar differentiation, once that further studies aimed at assessing the influence of growing conditions and environmental factors on the chemical profiles of single cultivars are carried out.     

An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects

The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by¹H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.     

Fluorescent Phthalocyanine-Encapsulated Bovine Serum Albumin Nanoparticles: Their Deployment as Therapeutic Agents in the NIR Region

In recent times, researchers have aimed for new strategies to combat cancer by the implementation of nanotechnologies in biomedical applications. This work focuses on developing protein-based nanoparticles loaded with a newly synthesized NIR emitting and absorbing phthalocyanine dye, with photodynamic and photothermal properties. More precisely, we synthesized highly reproducible bovine serum albumin-based nanoparticles (75% particle yield) through a two-step protocol and successfully encapsulated the NIR active photosensitizer agent, achieving a good loading efficiency of 91%. Making use of molecular docking simulations, we confirm that the NIR photosensitizer is well protected within the nanoparticles, docked in site I of the albumin molecule. Encouraging results were obtained for our nanoparticles towards biomedical use, thanks to their negatively charged surface (−13.6 ± 0.5 mV) and hydrodynamic diameter (25.06 ± 0.62 nm), favorable for benefitting from the enhanced permeability and retention effect; moreover, the MTT viability assay upholds the good biocompatibility of our NIR active nanoparticles. Finally, upon irradiation with an NIR 785 nm laser, the dual phototherapeutic effect of our NIR fluorescent nanoparticles was highlighted by their excellent light-to-heat conversion performance (photothermal conversion efficiency 20%) and good photothermal and size stability, supporting their further implementation as fluorescent therapeutic agents in biomedical applications.     

Enantioselective analysis of venlafaxine and its active metabolites: A review on the separation methodologies

Venlafaxine (VFX) is a serotonin and norepinephrine reuptake inhibitor chiral drug used in therapy as an antidepressant in the form of a racemate consisting of R‐ and S‐VFX. The two enantiomers of VFX exhibit different pharmacological activities: R‐VFX inhibits both norepinephrine and serotonin synaptic reuptake, whereas S‐VFX inhibits only the serotonin one. R‐ and S‐VFX are metabolized in the liver to the respective R‐ and S‐O‐desmethylvenlafaxine (ODVFX), R‐ and S‐N‐desmethylvenlafaxine (NDVFX), and R‐ and S‐N,O‐didesmethylvenlafaxine (NODVFX). The pharmacological profile of ODVFX is close to that of VFX, whereas the other two chiral metabolites (NDVFX and NODVFX) have lower affinity for the receptor sites. The pharmacokinetics of the VFX enantiomers appear stereoselective, including the metabolism process. In the past 20 years, several studies describing the enantioselective analysis of R‐ and S‐VFX in pharmaceutical formulations and its chiral metabolites in biological matrices were published. These methods encompass liquid chromatography coupled with UV detection, mass spectrometry, or tandem mass spectrometry, and capillary electrophoresis. This paper reviews the published methods used for the determination of the individual enantiomers of VFX and its chiral metabolites in different matrices.     

The Crucial Role of Sb2F10 in the Chemical Synthesis of F2

The purely chemical synthesis of fluorine is a spectacular reaction which for more than a century had been believed to be impossible. In 1986, it was finally experimentally achieved, but since then this important reaction has not been further studied and its detailed mechanism had been a mystery. The known thermal stability of MnF₄ casts serious doubts on the originally proposed hypothesis that MnF₄ is thermodynamically unstable and decomposes spontaneously to a lower manganese fluoride and F₂. This apparent discrepancy has now been resolved experimentally and by electronic structure calculations. It is shown that the reductive elimination of F₂ requires a large excess of SbF₅ and occurs in the last reaction step when in the intermediate [SbF₆][MnF₂][Sb₂F₁₁] the addition of one more SbF₅ molecule to the [SbF₆]⁻ anion generates a second tridentate [Sb₂F₁₁]⁻ anion. The two tridentate [Sb₂F₁₁]⁻ anions then provide six fluorine bridges to the Mn atom thereby facilitating the reductive elimination of the two fluorine ligands as F₂.     

Tumor Carbohydrate Associated Antigen Analogs as Potential Binders for Siglec-7

We investigated two recently synthesized and characterized sialyl derivatives, bearing the Neu5Ac-α-(2-6)-Gal epitope, as promising binders for Siglec-7, an inhibitory Siglec mainly found on natural killer cells. A variety of sialoglycan structures can be recognized by Siglec-7 with implications in the modulation of immune responses. Notably, overexpression of sialylated glycans recognized by Siglec-7 can be associated with the progression of several tumors, including melanoma and renal cell carcinoma. NOE-based NMR techniques, including Saturation Transfer Difference and transferred-NOESY NMR, together with molecular docking and dynamic simulations were combined to shed light on the molecular basis of Siglec-7 recognition of two conformationally constrained Sialyl-Tn antigen analogs. We, therefore, identify the ligands epitope mapping and their conformational features and propose 3D models accurately describing the protein-ligand complexes. We found that the binding site of Siglec-7 can accommodate both synthetic analogs, with the sialic acid mainly involved in the interaction. Moreover, the flexibility of Siglec-7 loops allows a preferred accommodation of the more rigid compound bearing a biphenyl moiety at position 9 of the sialic acid that contributed to the interaction to a large extent. Our findings provided insights for developing potential novel high affinity ligands for Siglec-7 to hinder tumor evasion.     

On a New Class of Systems of Generalized Quasi-Variational Inequalities

We introduce new types of systems of generalized quasi-variational inequalities and we prove the existence of the solutions by using results of pair equilibrium existence for free abstract economies. We consider the fuzzy models and we also introduce the random free abstract economy and the random equilibrium pair. The existence of the solutions for the systems of quasi-variational inequalities comes as consequences of the existence of equilibrium pairs for the considered free abstract economies.     

Deformations of permutation representations of Coxeter groups

The permutation representation afforded by a Coxeter group W acting on the cosets of a standard parabolic subgroup inherits many nice properties from W such as a shellable Bruhat order and a flat deformation over ?[q] to a representation of the corresponding Hecke algebra. In this paper we define a larger class of “quasiparabolic” subgroups (more generally, quasiparabolic W-sets), and show that they also inherit these properties. Our motivating example is the action of the symmetric group on fixed-point-free involutions by conjugation.     

Counting Shi Regions with a Fixed Separating Wall

Athanasiadis introduced separating walls for a region in the extended Shi arrangement and used them to generalize the Narayana numbers. In this paper, we fix a hyperplane in the extended Shi arrangement for type A and calculate the number of dominant regions which have the fixed hyperplane as a separating wall; that is, regions where the hyperplane supports a facet of the region and separates the region from the origin.