Sérgio F. Sousa

University of Porto | UP · Departamento de Biomedicina

The quorum sensing (QS) system is related to cell-to-cell communication as a function of population density, which regulates several physiological functions including biofilm formation and virulence gene expression. QS inhibitors have emerged as a promising strategy to tackle virulence and biofilm development. Among a wide variety of phytochemicals...

Background Non-B DNA conformations are molecular structures that do not follow the canonical DNA double helix. Mutagenetic instability in nuclear and mitochondrial DNA (mtDNA) genomes has been associated with simple non-B DNA conformations, as hairpins or more complex structures, as G-quadruplexes. One of these structures is Structure A, a cloverle...

Liposomal formulations were loaded with a new eugenol derivative with insecticidal activity. Molecular modelling has revealed that this compound can form a stable complex with insect odorant binding proteins and/or acetylcholinesterase. A compound-loaded nanoliposome formulation made of natural constituents (egg lecithin and cholesterol) has shown...

A recently synthesized new eugenol derivative, ethyl 4-(2-methoxy-4-(oxiran-2-ylmethyl)phenoxy)butanoate, with a high insecticidal activity against Sf9 (Spodoptera frugiperda) insect cells, was encapsulated in the liposomal formulations of egg-phosphatidylcholine/cholesterol (Egg-PC:Ch) 70:30 and 100% dioleoylphosphatidylglycerol (DOPG), aiming at...

Retroviral integration into cell chromatin requires the formation of integrase-viral DNA complexes, called intasomes, and their interaction with the target DNA wrapped around nucleosomes. To further study this mechanism we developed an alphaLISA approach using the prototype foamy virus (PFV) intasome and human nucleosome. This system allowed us to...

The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand–protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM...

The eugenol derivative, ethyl 4-(2-methoxy-4-(oxiran-2-ylmethyl)phenoxy)butanoate 1, with promising insecticidal capability was encapsulated in liposomal formulations of egg-phosphatidylcholine/cholesterol (Egg-PC:Ch) 70:30 and of 100% dioleoylphosphatidylglycerol (DOPG). Compound-loaded Egg-PC:Ch liposomes exhibit small hydrodynamic diameters (bel...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Disrupting this interaction would lead to early blockage of viral replication. To identify chemical tools to...

SARS-CoV-2 Mpro, also known as the main protease or 3C-like protease, is a key enzyme involved in the replication process of the virus that is causing the COVID-19 pandemic. It is also the most promising antiviral drug target targeting SARS-CoV-2 virus. In this work, the catalytic mechanism of Mpro was studied using the full model of the enzyme and...

The biological activity of Cd compounds has been investigated scarce since Cd has been recognized as a human carcinogen. However, the toxicity of cadmium is comparable to the toxicity of noble metals such as Pt and Pd. The paradigm of metal toxicity has been challenged suggesting that metal toxicity is not a constant property, yet it depends on man...

Increased levels of cathepsin B (CatB), a cysteine protease, have been associated with different types of tumors, including prostate cancer. Hence, the identification of novel targeting ligands homing CatB may be a promising approach for the development of CatB-targeted therapies. In this work, a methodology called systematic evolution of ligands b...

By understanding the mechanism of a stereoselective deacetylation reaction of an acetyloxybenzofuran intermediate to an unusal isoaurone product, the authors could assign the configuration of its glycolic acid precursor obtained from a highly stereoselective benzilic acid rearrangement. This puzzle was solved using state‐of‐the‐art DFT computationa...

The emergence of multi-drug resistant bacteria in the past decades has become one of the major public health issues of our time. One of the main mechanisms of resistance and persistence of bacteria is their ability to form biofilms. Quorum-sensing (QS) is one of the main mechanisms of biofilm formation. Interfering with the QS cascade constitutes a...

An atomistic description of Pdx2 catalytic mechanism is provided by QM/MM methodologies. Pdx2, the glutaminase subunit of pyridoxal 5’-phosphate (PLP) synthase, is characterized by a Cys-His-Glu catalytic triad used to deaminate glutamine to glutamate. While being absent in humans, Pdx2 is essential for the development and replication of the protoz...

Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium responsible for acute and chronic infections in planktonic state or in biofilms. The sessile structures are known to confer physical stability, increase virulence, and work as a protective armor against antimicrobial compounds. P. aeruginosa can control the expression of genes, popu...

The benzilic acid rearrangement (BAR) has been exploited with great effect over the last decades, used as the key step in many cases to afford complex target structures with interesting properties. Although the reaction is inherentely stereoselective in cyclic systems, the results achieved using acylic diketone systems can be less satisfactory. Thi...

The present study evaluates the antimicrobial susceptibility of persister cells of Bacillus cereus and Pseudomonas fluorescens after their regrowth in suspension and as biofilms. Two conventional (benzalkonium chloride—BAC and peracetic acid—PAA) and two emerging biocides (glycolic acid—GA and glyoxal—GO) were selected for this study. Persister cel...

Earth-abundant, cheap and non-toxic zinc-based coordination compounds are drawing research attention as promising candidates for various applications, such as photoluminescent materials and anticancer agents. In this paper we report six...

Fighting cancer is one of the major challenges of the 21st century. Among recently proposed treatments, molecular-targeted therapies are attracting particular attention. The potential targets of such therapies include a group of enzymes that possess the capability to catalyze at least two different reactions, so-called multifunctional enzymes. The...

Optimization of Classification Models for the Identification of Ligand-Target Inhibition Pairs in Biofilm Formation in P.aeruginosa

Epidermal growth factor receptor tyrosine kinase domain (EGFR-TK) has been one of the prominent targets for therapeutics of several human cancers, in particular non-small cell lung cancer. Although several small chemical compounds targeting EGFR-TK have been FDA-approved for treatment of such a cancer, the discovery of a new class of EGFR-TK inhibi...

The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia – the source of the nitrogen of pyridoxal 5’-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pa...

A series of β-amino alcohols were prepared by the reaction of eugenol epoxide with aliphatic and aromatic amine nucleophiles. The synthesized compounds were fully characterized and evaluated as potential insecticides through the assessment of their biological activity against Sf9 insect cells, compared with a commercial synthetic pesticide (chlorpy...

New compounds with potential insecticide activity were synthesized by structural modifications performed in the monoterpenoid phenolic moieties of carvacrol and thymol, resulting in a set of derivatives with the ether function containing the propyl, chloropropyl or hydroxypropyl chains, as well as a bicyclic ether with an unsaturated chain containi...

Plastics are highly durable and widely used materials. Current methodologies of plastic degradation, elimination, and recycling are flawed. In recent years, biodegradation (the usage of microorganisms for material recycling) has grown as a valid alternative to previously used methods. The evolution of bioengineering techniques and the discovery of...

With tuberculosis still being one of leading causes of death in the world and the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), researchers have been seeking to find further therapeutic strategies or more specific molecular targets. PknB is one of the 11 Ser/Thr protein kinases of Mtb and is responsible for phosphorylatio...

A non-negligible proportion of human pathogenic variants are known to be present as wild type in at least some non-human mammalian species. The standard explanation for this finding is that molecular mechanisms of compensatory epistasis can alleviate the mutations’ otherwise pathogenic effects. Examples of compensated variants have been described i...

The work, entitled “Development of a Classification Model for the Identification of Targets to Known P.aeruginosa Biofilm Formation Inhibitors”, constitutes an example of how machine learning algorithms can be employed to improve the drug design pipeline and fight biofilm infections more efficiently.

Lactoferrin (Lf), a bioactive milk protein, exhibits strong anticancer and antifungal activities. The search for Lf targets and mechanisms of action is of utmost importance to enhance its effective applications. A common feature among Lf-treated cancer and fungal cells is the inhibition of a proton pump called V-ATPase. Lf-driven V-ATPase inhibitio...

Non-B DNA conformations are molecules that do not follow the canonical double helix DNA structure[1]. This type of molecules, which can assume both simple (e.g. hairpins) and complex (e.g. G-quadruplexes) conformations, are highly related with mutagenetic instability in both nuclear and mitochondrial DNA (mtDNA)[2,3]. We have previously detected a...

Biofilms are aggregates of microorganisms anchored to a surface and embedded in a self-produced matrix of extracellular polymeric substances and have been associated with 80% of all bacterial infections in humans. Because bacteria in biofilms are less amenable to antibiotic treatment, biofilms have been associated with developing antibiotic resista...

Visualization can be a motivating way to teach students about molecules. Nowadays, the available experimental data and accurate computational results allow students to build realistic and accurate molecular models. These models include the representation of complex systems such as proteins, membranes, or nanotubes. However, the visualization of the...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Productive SARS-CoV-2 infection relies on viral entry into cells expressing angiotensin-converting enzyme 2 (ACE2). Indeed, viral entry into cells is mostly mediated by the early interaction be...

LegionellaDB is the first database on Legionella outbreaks; it is based on a metadata analysis of peer-reviewed manuscripts from PubMed and SCOPUS. LegionellaDB is dynamic and extensible, allowing users to search for specific outbreaks, suggest additional information to be included after curation, visualize statistical representations on specific o...

Biofilms play an important role in health, being associated with >80% of all microbial infections in the body and in the development of antibiotic resistance. Research in this field has continuously produced large volumes of data. Being able to handle all this information will be paramount for progress in this field. However, this places a heavy bu...

Nitrilase 2 (Nit2) is a representative member of the nitrilase superfamily that catalyzes the hydrolysis of α‐ketosuccinamate into oxaloacetate. It has been associated with the metabolism of rapidly dividing cells like cancer cells. The catalytic mechanism of Nit2 employs a catalytic triad formed by Cys191, Glu81 and Lys150. The Cys191 and Glu81 pl...

Breast cancer diagnosis remains a challenge, mostly due to its heterogeneity. This reality translates in delayed treatments, increasing treatment aggressiveness and lower chances of overall survival. The conventional detection techniques, although becoming increasingly sophisticated each year, still lack the ability to provide reliable conclusions...

Novel pharmacological strategies for the treatment of diabetic patients are now focusing on inhibiting glycogenolysis steps. In this regard, glycogen phosphorylase (GP) is a validated target for the discovery of innovative antihyperglycemic molecules. Natural products, and in particular flavonoids, have been reported as potent inhibitors of GP at t...

In this article, quantum mechanical/molecular mechanical (QM/MM) methods were used to study the full catalytic mechanism of xanthine oxidase (XO). XO catalyzes the conversion of xanthine (XAN) to uric acid (URC), in the presence of a molybdenum cofactor (Moco). The mechanism occurs through four reaction steps. Initially, the proton from the hydroxy...

Sulfur oxides emitted by the burning of fossil fuels are a major environmental hazard. Strict legislation limits the sulfur content in fuels to ultra-low levels, only achieved through harsh chemical methods that produce massive amounts of CO2. Biodesulfurization represents a much environmentally friendly alternative, with the bacteria Rhodococcus e...

Enzymes are responsible for controlling many biological processes, catalyzing different reactions using substrates with diverse complexity, size and chemistry. How enzymes work and achieve their catalytic efficiency are some of the fundamental questions of life. Most studies have focused on specific enzymes to elucidate their reaction mechanisms an...

The Biofilms Structural Database (BSD) is a collection of structural, mutagenesis, kinetics, and inhibition data to understand the processes involved in biofilm formation. Presently, it includes curated information on 425 structures of proteins and enzymes involved in biofilm formation and development for 42 different bacteria. It is available at w...

Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐established alternative for the study of enzymatic reaction mechanisms. They enable the description of a small part of the enzyme, where reactions take place through QM, while the majority of the thousands of atoms that comprise these biomolecules are handled through MM. Whi...

Biofilms are a growing concern to human health, particularly due to the increased drug resistance associated with them. One way to inhibit biofilm formation is through interfering with the process of quorum sensing, a cell-to-cell communication mechanism in bacteria. Computational methods can be used to evaluate “in silico” a variety of aspects rel...

AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting point for many virtual screening campaigns, particularly in academia. Here, we evaluated the performance...

Herein we present the VMD Store, an open-source VMD plugin that simplifies the way how users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism to install and configure VMD ex...

Tryptophan Synthase (TSase) is an emergent therapeutic target in the treatment of tuberculosis. Interest in TSase as a drug target arose from the fact that this enzyme is not present in humans, while in bacteria, like M. tuberculosis , it catalyses the last two steps in the tryptophan biosynthetic pathway. Several inhibitors of TSase have recently...

Enzymes catalyze a plethora of chemical reactions in nature. These biocatalysts offer a variety of benefits that no other synthetic catalyst can offer: high turnover, regio- and stereoselectivity, and ability to work under mild conditions and to react in environmentally friendly manufacturing processes. However, enzymes are not normally optimally s...

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixati...

Human Fatty Acid Synthase (hFAS) is a multidomain enzyme responsible for the biosynthesis of saturated fatty acids, which are crucial for numerous biological processes. During the biosynthetic reaction, hFAS incorporates acetyl and malonyl moieties through the action of its malonyl‐acetyl transferase (MAT) domain. These precursor molecules are tran...

Membrane proteins are essential vessels for cell communication both with other cells and noncellular structures. They modulate environment responses and mediate a myriad of biological processes. Dimerization and multimerization processes have been shown to further increase the already high specificity of these processes. Due to their central role i...

Flavin monoxygenases (FMOs) are enzymes of increasing biotechnological (e.g., crude oil biodesulfurization) and pharmacological (e.g., drug metabolism) interest that perform the oxidation of soft nucleophiles and play key roles in the excretion of xenobiotics or in sulfur amino acid metabolism. DszC is a key FMO involved in sulfur oxidation of dibe...

Poly(ethylene) glycol (PEG) is the most used polymer in drug delivery due to its unique properties, such as reduced toxicity and high solubility. PEGylation is the process of attaching PEG chains to compounds. Its effect on drug delivery has motivated a lot of experimental and computational studies. To explain and complement experimental findings,...