Applications of network-based approaches in drug research

Recent research trends in computer-aided drug design have shown an increasing interest towards the implementation of advanced approaches able to deal with large amount of data. This demand arose from the awareness of the complexity of biological systems and from the availability of data provided by high-throughput technologies. As a consequence, drug research has embraced this paradigm shift exploiting approaches such as that based on networks. Indeed, the process of drug discovery can benefit from the implementation of network-based methods at different steps from target identification to drug repurposing. From this broad range of opportunities, this thesis is focused on three main topics: (i) chemical space networks (CSNs), which are designed to represent and characterize bioactive compound data sets; (ii) drug-target interactions (DTIs) prediction through a network-based algorithm that predicts missing links; (iii) COVID-19 drug research which was explored implementing COVIDrugNet, a network-based tool for COVID-19 related drugs. The main highlight emerged from this thesis is that network-based approaches can be considered useful methodologies to tackle different issues in drug research. In detail, CSNs are valuable coordinate-free, graphically accessible representations of structure-activity relationships of bioactive compounds data sets especially for medium-large libraries of molecules. DTIs prediction through the random walk with restart algorithm on heterogeneous networks can be a helpful method for target identification. COVIDrugNet is an example of the usefulness of network-based approaches for studying drugs related to a specific condition, i.e., COVID-19, and the same ‘systems-based’ approaches can be used for other diseases. To conclude, network-based tools are proving to be suitable in many applications in drug research and provide the opportunity to model and analyze diverse drug-related data sets, even large ones, also integrating different multi-domain information.

Low-molecular-weight gels: from the rational design to the application of versatile soft materials

Low-molecular-weight (LMW) gels are a versatile class of soft materials that gained increasing interest over the last few decades. They are made of a small percentage, often lower than 1.0 %, of organic molecules called gelators, dispersed in a liquid medium. Such molecules have a molecular weight usually lower than 1 kDa. The gelator molecules start to interact after the addition of a trigger, and form fibres, whose entanglement traps the solvent through capillary forces. A plethora of LMW gelators have been designed, including short peptides. Such gelators present several advantages: the synthesis is easy and can be easily scaled up; they are usually biocompatible and biodegradable; the gelation phenomenon can be rationalised by making small variation on the peptide scaffold; they find application in several fields. In this thesis, an overview of several peptide based LMW gels is presented. In each study, the gelation conditions were carefully studied, and the final materials were thoroughly investigated. First, the gelation ability of a fluorinated phenylalanine was assessed, to understand how the presence of a rigid moiety and the presence of fluorine may influence the gelation. In this context, a method for the dissolution of sensitive gelators was studied. Then, the control over the gel formation was studied both over time and space, taking advantage of either the pH-annealing of the gel or the reaction-diffusion of a hydrolysing reagent. Some gels were probed for various applications. Due to their ability of trapping water and organic solvents, we used gels for trapping pollutants dissolved in water, as well as a medium for the controlled release of either fragrances or bioactive compounds. Finally, the interaction of the gel matrix with a light-responsive molecule was assessed to understand wether the gel properties or the interaction of the additive with light were affected.

Wheat adaptation to climate change in the Mediterranean Basin: retracing the past to predict the future

Wheat productivity is alarmingly threatened by climate change in the Mediterranean Basin, where it is mainly cultivated as a rainfed crop and where the latest climatic projections foresee a rise in temperatures and a reduction in precipitation, with important yield losses expected, being drought the main abiotic stress hampering wheat productivity. Assessing and quantifying the alterations in wheat life cycle caused by climate change is thus a key goal, as well as understating the underlying mechanisms of drought resistance. The first part of this thesis is focused on these main topics. A precise quantification of climate change effects on wheat in this area was performed through a case study, coupling phenological, meteorological and grain quality data before and after climate change. Then, accurate and detailed literature search was performed, reviewing the main controversies regarding the reliability of various functional traits to be used as breeding tools for improving wheat drought stress resistance. The second part of this thesis is focused in identifying interesting genetic material to improve wheat drought stress resistance in the Mediterranean Basin, analyzing drought response on a panel of tetraploid wheat accessions in vitro and in vivo as well as in open field trials, chosen in the attempt to represent as much as possible the biodiversity of tetraploid wheat. The third part of this thesis highlights differences in technological, nutritional and nutraceutical quality between modern cultivars and landraces, focusing on lipids, primary metabolites and bioactive compounds. In fact, wheat adaptation to climate change does not only mean to guarantee satisfactory yields in adverse conditions. It also means to provide millions of consumers with a diet-base food crop, with an improved nutraceutical and nutritional quality. Therefore, investigation and selection process for abiotic stress resistance and for improved quality has to go hand in hand.

Toward wellbeing: investigation of traditional, classical and innovative approaches to improve population and environmental health

As the word population continues to grow and global resources are limited, the WHO definition of health is difficult to achieve for a large part of the population. Humanity is facing the need to improve both environmental and human wellbeing. This can be done through careful planning and management of natural resources, ensuring food safety and reducing and converting wastes. This work aims to contribute to the improvement of population and environmental health exploring different research fields: urban park ecosystem services, food chemical risk assessment and agri-food by-product valorization. To highlight the importance of urban parks and their ecosystem services, an ethnobotanical study was carried out in the Ausa urban park in Rimini, using a citizen science approach. The results showed that Ausa Park is an important focal point for plant gatherers in Rimini, as it allows for plant foraging and contributes to preserve the knowledge of the use of plants. Two food safety studies were carried out, looking at the exposure of Poles to bisphenol A through the consumption of soft drinks and to cadmium through the consumption of chocolate bars. The results, compared with EFSA’s scientific opinion, show that the exposure of the Polish population to BPA is of health concern, while cadmium is not. In the agri-food by-product valorization, a green extraction method was optimized to recover valuable phenolic compounds from red-fleshed apple pomace; moreover, the possibility of recovering pectin from the residue was evaluated. Furthermore, valuable compounds in four different types of wheat milling by-products, considered as an alternative source of bioactive compounds with potential human health benefits, were investigated. In conclusion, this work produced usable data in urban green area management and planning, in food chemical risk assessment and in business production decisions, thus contributing to improving environmental and people wellbeing.

Bioactive and volatile organic compounds in Southern Brazilian blackberry (Rubus Fruticosus) fruit cv. Tupy

Blackberry (Rubus fruticosus, cultivar Tupy), an expanding fruit crop in southern Brazil, is greatly appreciated for its flavor and bioactive potential with limited characterization of its metabolite content. The purpose of this study was to characterize the bioactive and volatile organic compound (VOC) content of mature blackberry fruit of cultivar Tupy. Gallic acid, (-)-epicatechin, ferulic acid, and quercetin were the main phenolic compounds found in mature fruit. Among the VOCs identified in 'Tupy' blackberry were important flavor components characteristic of fruit berries, including hydrocarbons, alcohols, aldehydes, ketones, esters, and terpenoids. Some of the VOCs had not been previously found in blackberry, while others have been associated with typical blackberry flavor.

Synthesis of new bioactive β-lactam compounds

New biologically active β-lactams were designed and synthesized, developing novel antibiotics and enzymatic inhibitors directed toward specific targets. Within a work directed to the synthesis of mimetics for RGD (Arg-Gly-Asp) sequence able to interact with αvβ3 and α5β1-type integrins, new activators were developed and their Structure-Activity Relationships (SAR) analysis deepened, enhancing their activity range towards the α4β1 isoform. Moreover, to synthesize novel compounds active both against bacterial infections and pulmonary conditions of cystic fibrosis patients, new β-lactam candidates were studied. Among the abundant library of β-lactams prepared, mainly with antioxidant and antibacterial double activities, it was identified a single lead to be pharmacologically tested in vivo. Its synthesis was optimized up to the gram-scale, and pretreatment method and HPLC-MS/MS analytical protocol for sub-nanomolar quantifications were developed. Furthermore, replacement of acetoxy group in 4-acetoxy-azetidinone derivatives was studied with different nucleophiles and in aqueous media. A phosphate group was introduced and the reactivity exploited using different hydroxyapatites, obtaining biomaterials with multiple biological activities. Following the same kind of reactivity, a small series of molecules with a β-lactam and retinoic hybrid structure was synthesized as epigenetic regulators. Interacting with HDACs, two compounds were respectively identified as an inhibitor of cell proliferation and a differentiating agent on steam cells. Additionally, in collaboration with Professor L. De Cola at ISIS, University of Strasbourg, some new photochemically active β-lactam Pt (II) complexes were designed and synthesized to be used as bioprobes or theranostics. Finally, it was set up and optimized the preparation of new chiral proline-derived α-aminonitriles through an enantioselective Strecker reaction, and it was developed a chemo-enzymatic oxidative method for converting alcohols to aldehydes or acid in a selective manner, and amines to relative aldehydes, amides or imines. Moreover, enzymes and other green chemistry methodologies were used to prepare Active Pharmaceutical Ingredients (APIs).

Isolation and analysis of bioactive isoflavonoids and chalcone from a new type of Brazilian propolis

Activity-directed fractionation and purification processes were employed to identify isoflavonoids with antioxidant and antimicrobial activities from Brazilian red propolis. Crude propolis was extracted with ethanol (80%. v/v) and fractioned by liquid-liquid extraction technique using hexane and chloroform. Since chloroform fraction showed strong antioxidant and antimicrobial activities it was purified and isolated using various chromatographic techniques. Comparing our spectral data (UV, NMR, and mass spectrometry) with values found in the literature, we identified two bioactive isoflavonoids (vestitol and neovestitol), together with one chalcone (isoliquiritigenin). Vestitol presented higher antioxidant activity against beta-carotene consumption than neovestitol. The antimicrobial activity of these three compounds against Staphylococcus aureus, Streptococcus mutans, and Actinomyces naeslundii was evaluated and we concluded that isoliquiritigenin was the most active one with lower MIC, ranging from 15.6 to 62.5 mu g/mL. Our results showed that Brazilian red propolis has biologically active isoflavonoids that may be used as a mild antioxidant and antimicrobial for food preservation. (C) 2010 Elsevier B.V. All rights reserved.

Volatile organic compounds produced by Saccharomyces cerevisiae inhibit the in vitro development of Guignardia citricarpa, the causal agent of citrus black spot

Due to the low chemical control effectiveness of citrus black spot, caused by the fungus Guignardia citricarpa at postharvest, and to the search for alternative control methods, this study aimed to evaluate the in vitro effect of volatile organic compounds (VOCs), produced by yeast Saccharomyces cerevisiae, on G. citricarpa. It was observed that the yeast strains evaluated acted as antagonists by VOC production, whose maximum inhibitory capacity was as high as 87.2%. The presence of fermentable carbon sources in the medium was essential for the bioactive VOC production by the yeast. The analysis of VOCs produced in PDA medium by SPME-GC-MS indicated the presence of high quantities of alcohols as well as esters. An artificial VOC mixture prepared on the basis of the composition of the VOCs mimicked the inhibitory effects of the natural VOCs released by S. cerevisiae. Thus, the VOCs produced by the yeast or the artificial mixtures can be a promising control method for citrus black spot or others postharvest diseases.

Endophytic fungi found in association with Smallanthus sonchifolius (Asteraceae) as resourceful producers of cytotoxic bioactive natural products

Smallanthus sonchifolius is a traditional Andean plant which has been cultured mainly in Brazil, Japan and New Zealand due to its medicinal properties. A study of the endophytic fungi associated to the plant was carried out in order to characterize new cytotoxic agents. Thirty two fungal strains were isolated and submitted to cultivation and extraction producing 186 extracts. Of these, 12% displayed moderate to high cytotoxic activities and were considered promising anticancer compound sources. The ethyl acetate fractions of Nigrospora sphaerica and Phoma betae liquid fermentations contained the synergistic compounds 8-hydroxy-6-methoxy-3-methylisocoumarin and (22E,24R)-ergosta-4,6,8(14),22-tetraen-3-one which are potential compounds for drug discovery. Another isolated compound, pimara-7,15-dien-3-beta-ol diterpene is being characterized for the first time through a detailed spectroscopic analysis including GC/MS, homo- and hetero-nuclear correlated NMR experiments (HMQC, HMBC, COSY and NOEdiff) along with its optical rotation.

Bioactive Chemical Constituents and Comparative Antimicrobial Activity of Callus Culture and Adult Plant Extracts from Alternanthera tenella

Crude extracts of a callus culture (two culture media) and adult plants (two collections) from Alternanthera tenella Colla (Amaranthaceae) were evaluated for their antibacterial and antifungal activity, in order to investigate the maintenance of antimicrobial activity of the extracts obtained from plants in vivo and in vitro. The antibacterial and antifungal activity was determined against thirty strains of microorganisms including Gram-positive and Gram-negative bacteria, yeasts and dermatophytes. Ethanolic and hexanic extracts of adult plants collected during the same period of the years 1997 and 2002 [Ribeirao Preto (SP), collections 1 and 2] and obtained from plant cell callus culture in two different hormonal media (AtT43 and AtT11) inhibited the growth of bacteria, yeasts and dermatophytes with inhibition halos between 6 and 20 mm. For the crude extracts of adult plants bioassay-guided fractionation, purification, and isolation were performed by chromatographic methods, and the structures of the isolated compounds were established by analysis of chemical and spectral evidences (UV, IR, NMR and ES-MS). Steroids, saponins and flavonoids (aglycones and C-glycosides) were isolated. The minimum inhibitory concentration (MIC) of the isolated compounds varied from 50 to 500 mu g/mL.

Bioactive meroditerpenes from Cystoseira abies-marina, collected from the coast of S. Miguel island

3rd Portuguese Meeting on Medicinal Chemistry and 1st Portuguese-Spanish-Brazilian Meeting on Medicinal Chemistry, Aveiro, 28-30 Novembro 2012.

Study of membrane emulsification process as a pre-step for the microencapsulation of lipid compounds by spray drying

Dissertation presented to Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa for obtaining the master degree in Membrane Engineering

In vivo antioxidant activity of phenolic compounds: facts and gaps

Background: Numerous diseases have been related with free radicals overproduction and oxidative stress. Botanical preparations possess a multitude of bioactive properties, including antioxidant potential, which has been mainly related with the presence of phenolic compounds. However, the mechanisms of action of these phytochemicals, in vivo effects, bioavailability and bio-efficacy still need research. Scope and Approach: The present report aims to provide a critical review on the aspects related with the in vivo antioxidant activity of phenolic extracts and compounds from plant origin. Key findings: Biological functions beyond the human metabolism were discussed, comparing in vivo vs. in vitro studies, as also focusing the conditioning factors for phenolic compounds bioavailability and bio-efficacy. Furthermore, an upcoming perspective about the use of phytochemicals as life expectancy promoters and anti-aging factors in human individuals was provided. Conclusions: Overall, and despite all of those advances, the study of the biological potential of numerous natural matrices still remains a hot topic among the scientific community. In fact, the available knowledge about the responsible phytochemicals for the biological potential, their mechanisms of action, the establishment of therapeutic and prophylactic doses, and even the occurrence of biochemical inter-relations, is considerable scarce.

Bioactivity of phenolic acids: Metabolites versus parent compounds: A review

Phenolic acids are present in our diet in different foods. In particular, mushrooms are a good source of these molecules. Due to their bioactive properties, phenolic acids are extensively studied and there is evidence of their role in disease prevention. Nevertheless, in vivo, these compounds are metabolized and circulate in the organism as glucuronated, sulfated and methylated metabolites, displaying higher or lower bioactivity. To clarify the importance of the metabolism of phenolic acids, the knowledge about the bioactivity of the metabolites is extremely important. In this review, chemical features, biosynthesis and bioavailability of phenolic acids are discussed as well as the chemical and enzymatic synthesis of their metabolites. Finally, the metabolites bioactive properties are compared with that of the corresponding parental compounds.

Chemical characterization and bioactive properties of Prunus avium L.: The widely studied fruits and the unexplored stems

The aim of this study was to characterize sweet cherry regarding nutritional composition of the fruits, and individual phytochemicals and bioactive properties of fruits and stems. The chromatographic profiles in sugars, organic acids, fatty acids, tocopherols and phenolic compounds were established. All the preparations (extracts, infusions and decoctions) obtained using stems revealed higher antioxidant potential than the fruits extract, which is certainly related with its higher phenolic compounds (phenolic acids and flavonoids) concentration. The fruits extract was the only one showing antitumor potential, revealing selectivity against HCT-15 (colon carcinoma) (GI50~74 μg/mL). This could be related with anthocyanins that were only found in fruits and not in stems. None of the preparations have shown hepatotoxicity against normal primary cells. Overall, this study reports innovative results regarding chemical and bioactive properties of sweet cherry stems, and confirmed the nutritional and antioxidant characteristics of their fruits.