Tuberculosis (TB) is a chronic infectious and contagious disease with high epidemiological rates. The rise of multi- and extensively drug-resistant strains as well as the side effects and the long term treatment become urgent the development of novel therapy options. The enzyme thymidine monophosphate kinase of Mycobacterium tuberculosis (TMPKmt) is essential to DNA synthesis and cell replication. Moreover, this enzyme has unique structural characteristics among TMPKs family, emerging as a potential target to rational design of novel anti-TB agents. The present work had as objective the application of Computer Aided Drug-Design (CADD) strategies, using a set of 109 thymidine analogues inhibitors of TMPKmt selected from the literature, aiming to elucidate the structural features relevant to the biological activity of this set of compounds and generate models able to predict the activity of untested compounds. Methodologies of 2D-QSAR (HQSAR), 3-D-QSAR (CoMFA and CoMSIA), QM/MM docking and bioisosteric fragment replacement were performed for proposing new TMPKmt inhibitors. The final models of HQSAR, CoMFA and CoMSIA exhibit good internal and external consistency, presenting good correlation ability and prediction of biological activity. The HQSAR contribution maps and the contour maps of CoMFA and CoMSIA provided important information about structural features related to affinity, such as the favorable presence of hydrophobic and less bulky substituents on thymine ring and more bulky, electronegative, hydrophilic and hydrogen acceptors on sulfone of naphtosultam ring. Gathering the information provided, it was planned nine new compounds as potential TMPKmt inhibitors, which showed optimized affinity and physicochemical properties.

Since the beginning of the Covid-19 pandemic, research groups have used in silico studies to screen potentially inhibitors for SARS-CoV-2 virus, where spike protein is the main target examines. Among these is the molecular docking, relevant in the virtual screening of structurally specific drugs, because it mimics the behavior of small molecules. Due to the urgency to find effective and safe therapies for Covid-19, strategies such as drug repositioning were widely used. With mutations leading to new variants, some selected drugs showed less affinity for their targets. The objective of this work was to perform blind docking between the drugs rendesivir, baricitinib, molnupiravir and dexamethasone with the protein Spike of the gamma, delta and omicron (BA.1) variants to obtain the best conformation of the ligands, the affinity values, as well as examine the intermolecular interactions of the complex. For this purpose, the three-dimensional structures of the drugs were optimized and the protein structures were prepared. The molecular docking proved to be adequate, with RMSD value equal to 1.2061 Å. The complexes with lower Gibbs free energies were: remdesivir - S omicron (-7.5 kcal/mol), baricitinib - S omicron (-7.0 kcal/mol), molnupiravir - S gamma (-6.6 kcal/mol) and dexamethasone - S gamma (-7.9 kcal/mol). All ligands anchored in the N-terminal region of the protein. The formation of complexes was spontaneous, and the rendesivir and baricitinib had higher affinity for the protein S variant omiron (BA.1), while the molnupiravir and dexamethasone had higher affinity for the protein S variant gamma. The most recurrent intermolecular interactions were hydrogen bonds as well as hydrophobic interactions, being relevant to the molecular recognition process of the drugs. For more conclusive studies one can approach molecular dynamics strategies.

The receptor protein PfATP6 has been identified as the common target of artemisinin and curcumin. The work was initiated to assess the antimalarial activity of six curcumin derivatives based on their binding affinities and correlating the in silico docking outcome with in vitro antimalarial screening results. A ligand library of thirty two Knoevenagel condensates of curcumin were designed and docked against PfATP6 protein and six compounds with the best binding scores were synthesized and screened for their antimalarial activity against the sensitive 3D7 strain of Plasmodium falciparum. ADME/Tox, pharmacokinetic and pharmacodynamic profiles of the designed compounds were analyzed and reported. 4-FB was found to have similar binding energy to the standard artemisinin (-6.75 and -6.73 respectively) while 4-MB, 3-HB, 2-HB, B, 4-NB displayed better binding energy than curcumin (-5.95, -5.89, -5.68, -5.35, -5.29 and -5.25 respectively). At a dose of 50 µg/mL all the six compounds showed 100% schizont inhibition while at 5µg/ml, five showed more than 75% inhibition and better results than curcumin. 4-FB showed the best activity with 97.8% schizonticidal activity. The in vitro results superimpose the results obtained from the in silico study thereby encouraging development of promising curcumin leads in the battle against malaria.

Polyfunctional N,O,O,N-type ligands such as the oxalyl dihydrazide (ODH) may induce formation of mono-, di-, and polynuclear complexes with natural monoterpene ketones, involving ligand bridging and Oxo-bridging. In this context, a novel chiral dihydrazone is designed through hemi-synthesis process by reacting oxalyldihydrazide (ODH) with (s)-carvone, the major compound of caraway's seeds essential oil. The C = N imine bi-condensation is performed without prior isolation of the natural (s)-carvone and the resulting (s)-carvone dihydrazone (s-CHD) is structurally characterized by Single-crystal X-ray diffraction, 2D-NMR spectroscopy and chiral LCMS analysis to confirm the formation of a single pure enantiomer. In-vitro cell-based assays were conducted on normal fibroblast (L929) using a presBlue (PB) fluorescence quantification method of cell-viability and by sulforhodamine B calorimetric cytotoxicity assays to determine the anti-proliferative effect on four human tumoral lines (NCI-H460, Hela, HepG2 and MCF-7) and normal PLP2. Anti-inflammatory assays were determined through NO production by Maurine LPS-stimulated macrophages (RAW 264.7). The (s)-CHD has no effect on normal cells viability (>88%) and PLP2 (GI50= 326 ug/mL), while a moderate (∼55%) to significant (∼63%) antigrowth potential was recorded against HepG2, Hela and MCF-7 tumor cell lines, where RAW 264.7 was feebly sensitive. A molecular docking was performed using Autodock vina software on the protein kinase CK2 and Epidermal Growth factor Kinase proteins EGFK and the dock scores allowed to identify significant binding affinities (lower ΔG and Ki values) and potential hydrophilic/hydrophobic interactions with (s)-CHD comparing to the clinical ellipticine as potential ligands. Molecular docking suggests that (s)-CHD possesses high affinity towards the kinase domain receptors CK2 and EGFR, being able to bind to the ATP region.

A doença de Alzheimer (AD) é uma doença neurodegenerativa progressiva e é considerada a forma mais comum de demência na população idosa. Atualmente, apesar dos esforços da comunidade científica ainda não existe cura para a AD. Existem, no entanto, fármacos disponíveis no mercado capazes de melhorar os sintomas da doença. Estes fármacos têm como base a inibição do enzima acetilcolinesterase (AChE), que catalisa a hidrólise do neurotransmissor acetilcolina. No entanto esta abordagem é reconhecida como insuficiente e a procura de novos agentes terapêuticos é uma tarefa importante. Como a AD é uma doença multi-etiológica, o objetivo deste trabalho foi o desenvolvimento de novos compostos inibidores de AChE que também tivessem a capacidade de atuar noutros alvos ou processos caraterísticos da doença, como a diminuição do stress oxidativo no cérebro. Isto poderá ser realizado através da conjugação de grupos funcionais com diferentes propriedades na mesma entidade molecular. Assim, como estratégia para o desenvolvimento de novos compostos com potencial ação anti-AD optou-se pelo seu design com base na seleção de uma unidade básica com potente atividade inibitória do AChE, a tacrina, e na sua funcionalização com grupos com diferentes propriedades biológicas. Especificamente, fez-se a sua conjugação com derivados do ácido cinâmico, variando a substituição aromática e a extensão da dupla ligação conjugada, assim como o comprimento das cadeias de ligação entre aqueles grupos funcionais. Um conjunto de compostos selecionados (14) foi depois sintetizado e testado quanto à sua atividade inibitória do AChE e antioxidante. Neste conjunto destacam-se os compostos conjugados 9b e 8b, cujas capacidades inibitórias de AChE e antioxidante são superiores às dos fragmentos moleculares individuais (tacrina e cinamato). O incremento na inibição do AChE pode ser racionalizado pela interação bimodal com os dois centros catalíticos do enzima. Muito embora os estudos de interação com a β-amilóide não estavam inseridos no âmbito desta tese, estes incluem-se numa perspetiva futura, assim como a introdução de novos substituintes de modo a melhorar as propriedades antioxidantes e de interação com a β-amilóide.

The human skin is constantly exposed to external factors that affect its integrity, UV radiation being one of the main stress factors. The repeated exposure to this radiation leads to increased production of Reactive Oxygen Species (ROS) which activate a series of processes involved in photoaging. Excessive UV exposure also exacerbates melanin production leading to a variety of pigmentation disorders. Xanthones are reported to exhibit properties that prevent deleterious effects of UV exposure and high levels of ROS in the organism, so in this work a wide library of xanthones with different patterns of substitution was synthesized and tested for their inhibitory activity against the skin enzymes tyrosinase, elastase, collagenase and hyaluronidase, many of which were evaluated for the first time. Most of the compounds were tyrosinase inhibitors, with the best one (xanthone 27) presenting an IC50 of 1.9 µM, which is approximately 6 times lower than the IC50 of the positive control kojic acid. Concerning the other enzymes, only one compound presented IC50 lower than 150 µM in elastase inhibition (xanthone 14 = 91.8 µM) and none in collagenase and hyaluronidase inhibition. A QSAR model for tyrosinase inhibitory activity was built using six molecular descriptors, with a partial negative surface area descriptor and the relative number of oxygen atoms being positively contributing to the tyrosinase inhibitory activity. Docking using AutoDock Vina shows that all the tested compounds have more affinity to mushroom tyrosinase than kojic acid. Docking results implied that the tyrosinase inhibitory mechanisms of xanthonic derivatives are attributed to an allosteric interaction. Taken together, these data suggest that xanthones might be useful scaffolds for the development of new and promising candidates for the treatment of pigmentation-related disorders and for skin whitening cosmetic products.

The emergence and consumption of New Psychoactive Substances, NPS, has been growing considerably worldwide, and is therefore a concern for the various international entities responsible for monitoring and regulating the problem of drugs abuse. The classification as NPS includes all compounds, newly synthesized or recently available on the market, as well as those used improperly, with psychotropic properties, either pure or in mixtures, which are not controlled by the United Nations Conventions on Narcotic Drugs and Psychotropic Substances. These substances are created to mimic the effects of drugs already existing and controlled under these conventions, and may pose a threat to public health.Due to the significant increase in the commercialization and consumption of NPS, the investigation of this phenomenon, as well as the rapid identification and characterization of this type of compounds, is an increasingly pressing need.In this sense, the work presented here aims to contribute to the development of new tools and methodologies to efficiently characterize unknown NPS based on their chemical profile and comparison with already regulated NPS.The combination of two unsupervised machine learning methods, Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA), allowed the determination of the most relevant molecular descriptors for the discrimination between families of NSP and also the formation of groups with common structural characteristics.The most relevant interaction patterns of these groups were explored using Molecular Dynamics and Docking simulation. Selecting as model group the family of synthetic cannabinoids, it was possible to verify that compounds belonging to the same group present similar structural profiles and behavior both in the presence of a model membrane and in the interaction with the cannabinoid receptor type 1.The results obtained allow establishing an effective classification methodology for unregulated NPS without the need for experimental studies.

Cada vez mais, a área da robótica se tem dedicado ao desenvolvimento de robôs móveis destinados a prestar serviços a humanos. Desta forma, são muitas as situações em que um robô móvel necessita de realizar uma acoplagem mecânica, fazendo-o através de um processo de docagem. O objetivo deste trabalho é o desenvolvimento de um sensor de docagem de baixo custo e complexidade com aplicação em robôs holonómicos, uma vez que a maior parte das soluções encontradas não cumpriam esses parâmetros. Assim, a implementação final do sistema é composta por três LEDs de infravermelhos instalados na estação.de docagem, e por uma câmara Pixart associada a um computador de placa única Arduino, colocados no robô. O robô consegue calcular a sua posição relativamente à estação de docagem com precisão de aproximadamente 1 centímetro a 1 metro de distância através da imagem observada. Com base nessa informação, toma decisões quanto ao seu movimento. O algoritmo de movimento foi desenvolvido com a robustez em mente, para que o computador central do robô tenha o mínimo de intervenção no processo. Infelizmente, não foi possível testar eficazmente o algoritmo de docagem, uma vez que todas as formas para o fazer apresentaram grandes obstáculos à sua implementação. No entanto, a minha expetativa e da equipa com quem trabalhei é de que, resolvidos os problemas com os simuladores e/ou com a plataforma robótica, seja possível testar do ponto de vista prático o algoritmo desenvolvido e confirmar o seu potencial.

Polyfunctional N,O,O,N-type ligands such as the oxalyl dihydrazide (ODH) may induce formation of mono- , di-, and polynuclear complexes with natural monoterpene ketones, involving ligand bridging and Oxo- bridging. In this context, a novel chiral dihydrazone is designed through hemi-synthesis process by re- acting oxalyldihydrazide (ODH) with ( s )-carvone, the major compound of caraway’s seeds essential oil. The C = N imine bi-condensation is performed without prior isolation of the natural ( s )-carvone and the resulting ( s )-carvone dihydrazone (s-CHD) is structurally characterized by Single-crystal X-ray diffrac- tion, 2D-NMR spectroscopy and chiral LCMS analysis to confirm the formation of a single pure enan- tiomer. In -vitro cell-based assays were conducted on normal fibroblast (L929) using a presBlue (PB) flu- orescence quantification method of cell-viability and by sulforhodamine B calorimetric cytotoxicity as- says to determine the anti-proliferative effect on four human tumoral lines (NCI-H460, Hela, HepG2 and MCF-7) and normal PLP2. Anti-inflammatory assays were determined through NO production by Maurine LPS-stimulated macrophages (RAW 264.7). The ( s )-CHD has no effect on normal cells viability ( > 88%) and PLP2 (GI50 = 326 ug/mL), while a moderate ( ∼55%) to significant ( ∼63%) antigrowth potential was recorded against HepG2, Hela and MCF-7 tumor cell lines, where RAW 264.7 was feebly sensitive. A molecular docking was performed using Autodock vina software on the protein kinase CK2 and Epi- dermal Growth factor Kinase proteins EGFK and the dock scores allowed to identify significant bind- ing affinities (lower G and Ki values) and potential hydrophilic/hydrophobic interactions with ( s )-CHD comparing to the clinical ellipticine as potential ligands. Molecular docking suggests that ( s )-CHD pos- sesses high affinity towards the kinase domain receptors CK2 and EGFR, being able to bind to the ATP region.

Aim and Methods: Although the antimicrobial activity of extracts from several mushroom species have been reported, studies with the individual compounds present in that extracts are scarce. Herein, the antimicrobial activity of different phenolic compounds identified and quantified in mushroom species from all over the world was evaluated. Furthermore, a structure activity relationship (SAR) analysis and molecular docking studies were performed, in order to provide insights in the mechanism of action of potential antimicrobial drugs for resistant microorganisms. Results: 2,4-Dihydroxybenzoic and protocatechuic acids were the phenolic compounds with higher activity against the majority of Gram negative and Gram positive bacteria. Furthermore, phenolic compounds inhibited more MRSA than methicillin sensible Staphylococcus aureus. MRSA was inhibited by 2,4-dihydroxybenzoic, vanillic, syringic (MICs=0.5 mg/mL) and p-coumaric (MIC= 1 mg/mL) acids, while these compounds at the same concentrations had no inhibitory effects against methicillin sensible Staphylococcus aureus. Conclusions: The presence of carboxylic acid (COOH), two hydroxyl (OH) groups in para and ortho positions of the benzene ring, as also a methoxyl (OCH3) group in the meta position seems to be important for anti-MRSA activity. Significance and Impact of the Study: Phenolic compounds could be used as antimicrobial agents, namely against some microorganisms resistant to commercial antibiotics.