Studi sui metalloenzimi come bersaglio per l’attività farmacobiologica: HIV-1 integrasi e anidrasi carbonica

The aim of this thesis is to better understand the complex relationships that occur between metalloenzymes and their ligands, especially inhibitors. Two targets, such as HIV-1 Integrase (IN) and Carbonic Anidrase (CA), were selected and explored. IN is an Mg(II)/Mn(II) -containing enzyme, whereas CA is a Zn(II)-enzyme. The work is structured and detailed into three main chapters. Chapter one discusses about a molecular and functional study of a series of clinically developed IN inhibitors, strictly related to the b-diketo acid (DKAs) class of compounds, that belong to the family of IN strand transfer inhibitors (INSTIs). Starting from the hypothesis to identify a common pharmacophore amongst them, the chapter attempts to elucidate how the metal-chelating properties can influence the activity of these compounds. Moreover, an extensive investigation of metal complexation as a suitable strategy in the IN drug design was performed. In chapter two, which deals with CA, two different projects are presented. The first one describes how new inhibitors of CA (isozyme II) have been discovered by using a complete Virtual Screening (VS) approach. The second part reports on the design and the preparation, as well as modelling studies and enzymatic inhibitory activity, of a series of original photoprobes, as useful tools to be used in the Photoaffinity Labelling (PAL) procedure, to elucidate enzyme interactions of the sulfonamide class of CAII inhibitors. In the third chapter, a retrospective structural analysis on a series of 4-benzylidene-2-(2- hydroxybenzoyl)-5-methyl-2,4-dihydro-3H-pyrazol-3-one, previously reported as IN inhibitors, as well as an alternative versatile synthetic approach for their preparation are presented and discussed

Targeted nanoparticles for the delivery of novel bioactive molecules to pancreatic cancer cells

Pancreatic cancer (PaCa) is a multifaceted disorder with an extremely poor prognosis. There is an urgent need to identify new and safe drugs as well as to develop novel tumor-targeted controlled release systems for effective treatment of late stage and resistant PaCa. Active targeting via the inclusion of specific ligands on the nanoparticles (NPs) is envisioned to provide a powerful therapeutic strategy. Herein, we present a study on the design and the development of novel DFCencapsulated biocompatible polymeric NPs, functionalized with peptides to selectively bind to Plec-1 (PTP), or densely decorated by low molecular weight organic molecules as alternative targeting ligands (2-ABA), and evaluated a) the impact on ligand binding and b) the in vitro antiproliferative efficacy against a panel of PaCa cells

The "Click-tail approach" for the design and synthesis of novel carbonic anhydrase inhibitors

The Carbonic Anhydrases (CAs) are a family of zinc enzymes deputed to the interconversion of carbonic dioxide to hydrogen carbonate. Herein, we report on a sustainable modular strategy, also called "clicktail approach", used to obtain two series of 4-(4-substituted-lH-l,2,3-triazol-lyl) benzenesulfonamides. Design and synthesis strategies, x-ray derived CA-ligand binding mode and enzyme-based inhibition results will be presented

Searching for novel carbonic anhydrase inhibitors: from virtual screening to the lab bench

Carbonic Anhydrases (CAs) are zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate both in prokaryotes and eukaryotes. In this context, Computer Aided Drug Design strategies have emerged as powerful tools in the modern drug discovery paradigm. In particular, using ligand- and pharmacophore-based virtual screening approaches, we identified novel chemical entities with original chemotypes, that showed an interesting and selective inhibitory activity in nanomolar/low micromolar range toward CA I and CAII, isoforms. Herein, we present the hit-to-lead optimization process for these prototypes

Investigation of furo[2,3-h]- and pyridazino[3,4-f]cinnolin-3-ol scaffolds as substrates for the development of novel HIV-1 integrase inhibitors

With the aim to develop novel HIV-1 integrase inhibitors, we obtained a set of condensed ring systems based on the furo[2,3-h]cinnolin-3(2H)-one and pyridazino[3,4-f]cinnolin-3-ol scaffolds bearing a potential chelating pharmacophore, which can be involved in the inhibition mechanism of the enzyme. Herein, we report the design, synthesis, structural investigation and preliminary biological results of these heteroaromatic systems

Inhibition of ?±-class cytosolic human carbonic anhydrases I II IX and XII and ?²-class fungal enzymes by carboxylic acids and their derivatives: New isoform-I selective nanomolar inhibitors

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Design and synthesis of bis-amide and hydrazide-containing derivatives of malonic acid as potential HIV-1 integrase inhibitors

HIV-1 integrase (IN) is an attractive and validated target for the development of novel therapeutics against AIDS. In the search for new IN inhibitors, we designed and synthesized three series of bis-amide and hydrazide-containing derivatives of malonic acid. We performed a docking study to investigate the potential interactions of the title compounds with essential amino acids on the IN active site

Chelation motifs affecting metal-dependent viral enzymes: N′-acylhydrazone ligands as dual target inhibitors of HIV-1 Integrase and Reverse Transcriptase Ribonuclease H domain

Human immunodeficiency virus type 1 (HIV-1) infection, still represent a serious global health emergency. The chronic toxicity derived from the current anti-retroviral therapy limits the prolonged use of several antiretroviral agents, continuously requiring the discovery of new antiviral agents with innovative strategies of action. In particular, the development of single molecules targeting two proteins (dual inhibitors) is one of the current main goals in drug discovery. In this contest, metal-chelating molecules have been extensively explored as potential inhibitors of viral metal-dependent enzymes, resulting in some important classes of antiviral agents. Inhibition of HIV Integrase (IN) is, in this sense, paradigmatic. HIV-1 IN and Reverse Transcriptase-associated Ribonuclease H (RNase H) active sites show structural homologies, with the presence of two Mg(II) cofactors, hence it seems possible to inhibit both enzymes by means of chelating ligands with analogous structural features. Here we present a series of N′-acylhydrazone ligands with groups able to chelate the Mg(II) hard Lewis acid ions in the active sites of both the enzymes, resulting in dual inhibitors with micromolar and even nanomolar activities. The most interesting identified N′-acylhydrazone analog, compound 18, shows dual RNase H-IN inhibition and it is also able to inhibit viral replication in cell-based antiviral assays in the low micromolar range. Computational modeling studies were also conducted to explore the binding attitudes of some model ligands within the active site of both the enzymes

Development of a Raltegravir-based Photoaffinity-Labeled Probe for Human Immunodeficiency Virus-1 Integrase Capture

Photoaffinity labeling (PAL) is one of the upcoming and powerful tools in the field of molecular recognition. It includes the determination of dynamic parameters, such as the identification and localization of the target protein and the site of drug binding. In this study, a photoaffinity-labeled probe for full-length human immunodeficiency virus-1 integrase (HIV-1 IN) capture was designed and synthesized, following the structure of the FDA-approved drug Raltegravir. This photoprobe was found to retain the HIV IN inhibitory potential in comparison with its parent molecule and demonstrates the ability to label the HIV-1 IN protein. Putative photoprobe/inhibitor binding sites near the catalytic site were then identified after protein digestion coupled to mass and molecular modeling analyses

Peptidomimetics as protein arginine deiminase 4 (PAD4) inhibitors.

The protein arginine deiminase 4 (PAD4) is a calcium-dependent enzyme, which catalyses the irreversible conversion of peptidyl-arginines into peptidyl-citrullines and plays an important role in several diseases such as in the rheumatoid arthritis, multiple sclerosis, Alzheimer's disease, Creutzfeldt-Jacob's disease and cancer. In this study, we report the inhibition profiles and computational docking toward the PAD4 enzyme of a series of 1,2,3-triazole peptidomimetic-based derivatives incorporating the β-phenylalanine and guanidine scaffolds. Several effective, low micromolar PAD4 inhibitors are reported in this study