Synthesis and inverse virtual screening of new bi-cyclic structures towards cancer-relevant cellular targets

Structural Chemistry - We report here synthetic approaches to access new classes of small molecules based on three heterocyclic scaffolds, i.e. 3,7-dihydropyrimido[4,5-d]pyridazine-4,8-dione,...     

Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self-Assembly

Iodination has long been employed as a successful labelling strategy to gain structural insights into proteins and other biomolecules via several techniques, including Small Angle X-ray Scattering, Inductively Coupled Plasma Mass Spectrometer (ICP-MS), and single-crystal crystallography. However, when dealing with smaller biomolecular systems, interactions driven by iodine may significantly alter their self-assembly behaviour. The engineering of amyloidogenic peptides for the development of ordered nanomaterials has greatly benefitted from this possibility. Still, to date, iodination has exclusively been applied to aromatic residues. In this work, an aliphatic bis-iodinated amino acid was synthesized and included into a custom pentapeptide, which showed enhanced fibrillogenic behaviour. Peptide single crystal X-ray structure and powder X-ray diffraction on its dried water solution demonstrated the key role of iodine atoms in promoting intermolecular interactions that drive the peptide self-assembly into amyloid fibrils. These findings enlarge the library of halogenated moieties available for directing and engineering the self-assembly of amyloidogenic peptides.     

A Stable Porphyrin Functionalized Graphite Electrode Used at the Oxygen Evolution Reaction Potential

Many researches have been devoted to rechargeable power generators that can store (but also release) energy. This availability is ensured through (e. g.) the oxygen evolution reaction (OER). However, (i) large values of the overpotentials and (ii) a progressive detriment of the anode (graphite) electrode limit the ultimate device. In view of enhancing the electrode performances, graphite was protected by following different strategies, which oblige to follow precise preparation protocols. Here, we prove that a thin layer of free-base porphyrin molecules is able to protect the underneath graphite electrode from detriment even if many (about 100) electrochemical cycles are performed.     

Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures

DNA G-quadruplexes (G4s) are key structures for the development of targeted anticancer therapies. In this context, ligands selectively interacting with G4s can represent valuable anticancer drugs. Aiming at speeding up the identification of G4-targeting synthetic or natural compounds, we developed an affinity chromatography-based assay, named G-quadruplex on Oligo Affinity Support (G4-OAS), by synthesizing G4-forming sequences on commercially available polystyrene OAS. Then, due to unspecific binding of several hydrophobic ligands on nude OAS, we moved to Controlled Pore Glass (CPG). We thus conceived an ad hoc functionalized, universal support on which both the on-support elongation and deprotection of the G4-forming oligonucleotides can be performed, along with the successive affinity chromatography-based assay, renamed as G-quadruplex on Controlled Pore Glass (G4-CPG) assay. Here we describe these assays and their applications to the screening of several libraries of chemically different putative G4 ligands. Finally, ongoing studies and outlook of our G4-CPG assay are reported.     

Chemometric Tools to Point Out Benchmarks and Chromophores in Pigments through Spectroscopic Data Analyses

Spectral preprocessing data and chemometric tools are analytical methods widely applied in several scientific contexts i.e., in archaeometric applications. A systematic classification of natural powdered pigments of organic and inorganic nature through Principal Component Analysis with a multi-instruments spectroscopic study is presented here. The methodology allows the access to elementary and molecular unique benchmarks to guide and speed up the identification of an unknown pigment and its recipe. This study is conducted on a set of 48 powdered pigments and tested on a real-case sample from the wall painting in S. Maria Delle Palate di Tusa (Messina, Italy). Four spectroscopic techniques (X-ray Fluorescence, Raman, Attenuated Total Reflectance and Total Reflectance Infrared Spectroscopies) and six different spectrometers are tested to evaluate the impact of different setups. The novelty of the work is to use a systematic approach on this initial dataset using the entire spectroscopic energy range without any windows selection to solve problems linked with the manipulation of large analytes/materials to find an indistinct property of one or more spectral bands opening new frontiers in the dataset spectroscopic analyses.     

Fractionation of HDPE on quench cooling

In a previous paper we discussed co-crystallization in a LDPE/HDPE blend using TREF and DSC. As part of that study it was observed that pure HDPE showed an unexpected fractionation behavior when quench crystallized in TREF. The overall peak broadened and two peaks appeared instead of the previously observed single peak for slow cooled HDPE.The development of two peaks was observed for all commercial HDPEs investigated, independent of their melting indices and densities. TREF and GPC were used in an attempt to evaluate the origin of the two HDPE components.The authors appreciate support from CAPES-BRAZIL (C.A.F.). Additional thanks go to Dr. G. W. Knight in Dow Chemical Company for kindly providing the polymer samples and performing the GPC analysis.     

A Carbocationic Triarylmethane-Based Porous Covalent Organic Network

A thermally stable carbocationic covalent organic network (CON), named RIO-70 was prepared from pararosaniline hydrochloride, an inexpensive dye, and triformylphloroglucinol in solvothermal conditions. This nanoporous organic material has shown a specific surface area of 990 m² g⁻¹ and pore size of 10.3 Å. The material has CO₂ uptake of 2.14 mmol g⁻¹ (0.5 bar), 2.7 mmol g⁻¹ (1 bar), and 6.8 mmol g⁻¹ (20 bar), the latter corresponding to 3 CO₂ molecules adsorbed per pore per sheet. It is shown to be a semiconductor, with electrical conductivity (σ) of 3.17×10⁻⁷ S cm⁻¹, which increases to 5.26×10⁻⁴ S cm⁻¹ upon exposure to I₂ vapor. DFT calculations using periodic conditions support the findings.     

2-Mercaptomethyl-thiazolidines use conserved aromatic–S interactions to achieve broad-range inhibition of metallo-β-lactamases

Infections caused by multidrug resistant (MDR) bacteria are a major public health threat. Carbapenems are among the most potent antimicrobial agents that are commercially available to treat MDR bacteria. Bacterial production of carbapenem-hydrolysing metallo-β-lactamases (MBLs) challenges their safety and efficacy, with subclass B1 MBLs hydrolysing almost all β-lactam antibiotics. MBL inhibitors would fulfil an urgent clinical need by prolonging the lifetime of these life-saving drugs. Here we report the synthesis and activity of a series of 2-mercaptomethyl-thiazolidines (MMTZs), designed to replicate MBL interactions with reaction intermediates or hydrolysis products. MMTZs are potent competitive inhibitors of B1 MBLs in vitro (e.g., K_i = 0.44 μM vs. NDM-1). Crystal structures of MMTZ complexes reveal similar binding patterns to the most clinically important B1 MBLs (NDM-1, VIM-2 and IMP-1), contrasting with previously studied thiol-based MBL inhibitors, such as bisthiazolidines (BTZs) or captopril stereoisomers, which exhibit lower, more variable potencies and multiple binding modes. MMTZ binding involves thiol coordination to the Zn(ii) site and extensive hydrophobic interactions, burying the inhibitor more deeply within the active site than d/l-captopril. Unexpectedly, MMTZ binding features a thioether–π interaction with a conserved active-site aromatic residue, consistent with their equipotent inhibition and similar binding to multiple MBLs. MMTZs penetrate multiple Enterobacterales, inhibit NDM-1 in situ, and restore carbapenem potency against clinical isolates expressing B1 MBLs. Based on their inhibitory profile and lack of eukaryotic cell toxicity, MMTZs represent a promising scaffold for MBL inhibitor development. These results also suggest sulphur–π interactions can be exploited for general ligand design in medicinal chemistry.

Metallo-β-lactamases (MBLs) are major culprits of resistance to carbapenems in bacteria. A series of thiazolidines are potent MBL inhibitors, restoring the activity of carbapenems. Metal binding and sulphur–π interactions are key to inhibition.     

Driving Organic Nanocrystals Dissolution Through Electrochemistry

We have recently discussed how organic nanocrystal dissolution appears in different morphologies and the role of the solution pH in the crystal detriment process. We also highlighted the role of the local molecular chemistry in porphyrin nanocrystals having comparable structures: in water-based acid solutions, protonation of free-base porphyrin molecules is the driving force for crystal dissolution, whereas metal (Zn^II) porphyrin nanocrystals remain unperturbed. However, all porphyrin types, having an electron rich π-structure, can be electrochemically oxidized. In this scenario, a key question is: does electrochemistry represent a viable strategy to drive the dissolution of both free-base and metal porphyrin nanocrystals? In this work, by exploiting electrochemical atomic force microscopy (EC-AFM), we monitor in situ and in real time the dissolution of both free-base and metal porphyrin nanocrystals, as soon as molecules reach the oxidation potential, showing different regimes according to the applied EC potential.     

The Glycolytic Pathway as a Target for Novel Onco-Immunology Therapies in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal forms of human cancer, characterized by unrestrained progression, invasiveness and treatment resistance. To date, there are limited curative options, with surgical resection as the only effective strategy, hence the urgent need to discover novel therapies. A platform of onco-immunology targets is represented by molecules that play a role in the reprogrammed cellular metabolism as one hallmark of cancer. Due to the hypoxic tumor microenvironment (TME), PDA cells display an altered glucose metabolism—resulting in its increased uptake—and a higher glycolytic rate, which leads to lactate accumulation and them acting as fuel for cancer cells. The consequent acidification of the TME results in immunosuppression, which impairs the antitumor immunity. This review analyzes the genetic background and the emerging glycolytic enzymes that are involved in tumor progression, development and metastasis, and how this represents feasible therapeutic targets to counteract PDA. In particular, as the overexpressed or mutated glycolytic enzymes stimulate both humoral and cellular immune responses, we will discuss their possible exploitation as immunological targets in anti-PDA therapeutic strategies.