Viruses are a diverse biological group capable of infecting several hosts such as bacteria, plants, and animals, including humans. Viral infections constitute a threat to the human population as they ...may cause high mortality rates, decrease food production, and generate large economical losses. Viruses co-evolve with their hosts and this constant evolution must be clarified to better predict possible viral outbreaks, and to develop improved diagnostic methods and therapeutical approaches. In this review, we summarize several viral databases that store key information retrieved from a variety of omics approaches. Furthermore, we explore the use of such databases to predict Virus-Host interactions through artificial intelligence algorithms, focusing on the latest methodologies to characterize biological networks.
Diclofenac is a worldwide consumed drug included in the watch list of substances to be monitored according to the European Union Water Framework Directive (Directive 2013/39/EU). Aerobic granular ...sludge sequencing batch reactors (AGS-SBR) are increasingly used for wastewater treatment but there is scant information on the fate and effect of micropollutants to nutrient removal processes. An AGS-SBR fed with synthetic wastewater containing diclofenac was bioaugmented with a diclofenac degrading bacterial strain and performance and microbial community dynamics was analysed. Chemical oxygen demand, phosphate and ammonia removal were not affected by the micropollutant at 0.03 mM (9.54 mg L
-1
). The AGS was able to retain the degrading strain, which was detected in the sludge throughout after augmentation. Nevertheless, besides some adsorption to the biomass, diclofenac was not degraded by the augmented sludge given the short operating cycles and even if batch degradation assays confirmed that the bioaugmented AGS was able to biodegrade the compound. The exposure to the pharmaceutical affected the microbial community of the sludge, separating the two first phases of reactor operation (acclimatization and granulation) from subsequent phases. The AGS was able to keep the bioaugmented strain and to maintain the main functions of nutrient removal even through the long exposure to the pharmaceutical, but combined strategies are needed to reduce the spread of micropollutants in the environment.
Cancer has become one of the main leading causes of morbidity and mortality worldwide. One of the critical drawbacks of current cancer therapeutics has been the lack of the target-selectivity, as ...these drugs should have an effect exclusively on cancer cells while not perturbing healthy ones. In addition, their mechanism of action should be sufficiently fast to avoid the invasion of neighbouring healthy tissues by cancer cells. The use of conventional chemotherapeutic agents and other traditional therapies, such as surgery and radiotherapy, leads to off-target interactions with serious side effects. In this respect, recently developed target-selective Antibody-Drug Conjugates (ADCs) are more effective than traditional therapies, presumably due to their modular structures that combine many chemical properties simultaneously. In particular, ADCs are made up of three different units: a highly selective Monoclonal antibody (Mab) which is developed against a tumour-associated antigen, the payload (cytotoxic agent), and the linker. The latter should be stable in circulation while allowing the release of the cytotoxic agent in target cells. The modular nature of these drugs provides a platform to manipulate and improve selectivity and the toxicity of these molecules independently from each other. This in turn leads to generation of second- and third-generation ADCs, which have been more effective than the previous ones in terms of either selectivity or toxicity or both. Development of ADCs with improved efficacy requires knowledge at the atomic level regarding the structure and dynamics of the molecule. As such, we reviewed all the most recent computational methods used to attain all-atom description of the structure, energetics and dynamics of these systems. In particular, this includes homology modelling, molecular docking and refinement, atomistic and coarse-grained molecular dynamics simulations, principal component and cross-correlation analysis. The full characterization of the structure-activity relationship devoted to ADCs is critical for antibody-drug conjugate research and development.
•Enantioselective degradation of fluoxetine by L. portucalensis F11 was evaluated.•Strain F11 was able to biodegrade 2μM of FLX as sole carbon source in 30d.•Degradation of 2μM of FLX by F11 resulted ...in stoichiometric fluoride release.•The supplementation with acetate resulted in increased biodegradation rate constants.•Preferential degradation of the (R)-enantiomer over the corresponding (S)-enantiomer.
Fluoxetine (FLX) is a chiral fluorinated pharmaceutical indicated mainly for the treatment of depression and is one of the most dispensed drugs in the world. There is clear evidence of environmental contamination with this drug and its active metabolite norfluoxetine (NFLX). In this study the enantioselective biodegradation of racemic FLX and of its enantiomers by Labrys portucalensis strain F11 was assessed. When 2μM of racemic FLX was supplemented as sole carbon source, complete removal of both enantiomers, with stoichiometric liberation of fluoride, was achieved in 30d. For racemic FLX concentration of 4 and 9μM, partial degradation of the enantiomers was obtained. In the presence of acetate as an additional carbon source, at 4, 9 and 21μM of racemic FLX and at 25μM of racemic FLX, (S)-FLX or (R)-FLX, complete degradation of the two enantiomers occurred. At higher concentrations of 45 and 89μM of racemic FLX, partial degradation was achieved. Preferential degradation of the (R)-enantiomer was observed in all experiments. To our knowledge, this is the first time that enantioselective biodegradation of FLX by a single bacterium is reported.
Microbial degradation is the most important process to remove organic pollutants in Waste Water Treatment Plants. Regarding chiral compounds this process is normally enantioselective and needs the ...suitable analytical methodology to follow the removal of both enantiomers in an accurate way. Thus, this paper describes the development and validation of an enantioselective High Performance Liquid Chromatography with Fluorescence Detection (HPLC-FD) method for simultaneous analysis of fluoxetine (FLX) and norfluoxetine (NFLX) in wastewater effluents. Briefly, this method preconcentrated a small volume of wastewater samples (50 mL) on 500 mg Oasis MCX cartridges and used HPLC-FD with a vancomycin-based chiral stationary phase under reversed mode for analyses. The optimized mobile phase was EtOH/aqueous ammonium acetate buffer (92.5/7.5, v/v) at pH 6.8. The effect of EtOH percentage, buffer concentration, pH, column oven temperature and flow rate on chromatographic parameters was systematically investigated. The developed method was validated within the wastewater effluent used in microcosms laboratory assays. Linearity (R(2)>0.99), selectivity and sensitivity were achieved in the range of 4.0-60 ng mL(-1) for enantiomers of FLX and 2.0-30 ng mL(-1) for enantiomers of NFLX. The limits of detection were between 0.8 and 2.0 ng mL(-1) and the limits of quantification were between 2.0 and 4.0 ng mL(-1) for both enantiomers of FLX and the enantiomers of its demethylated metabolite NFLX. The validated method was successfully applied and proved to be robust to follow the degradation of both enantiomers of FLX in wastewater samples, during 46 days.
•Enantioselective removal of fluoxetine by aerobic granular sludge was evaluated.•Sorption of fluoxetine to aerobic granules occurred.•Bacterial community gradually changed during operation of ...sequential batch reactor.•Main biological processes occurring within the granules were preserved.•Overall performance of the reactor was recovered after initial fluoxetine shock loads.
Fluoxetine (FLX) is a chiral fluorinated pharmaceutical mainly indicated for treatment of depression and is one of the most distributed drugs. There is a clear evidence of environmental contamination with this drug. Aerobic granular sludge sequencing batch reactors constitute a promising technology for wastewater treatment; however the removal of carbon and nutrients can be affected by micropollutants. In this study, the fate and effect of FLX on reactor performance and on microbial population were investigated. FLX adsorption/desorption to the aerobic granules was observed. FLX shock loads (≤4μM) did not show a significant effect on the COD removal. Ammonium removal efficiency decreased in the beginning of first shock load, but after 20 days, ammonia oxidizing bacteria became adapted. The nitrite concentration in the effluent was practically null indicating that nitrite oxidizing bacteria was not inhibited, whereas, nitrate was accumulated in the effluent, indicating that denitrification was affected. Phosphate removal was affected at the beginning showing a gradual adaptation, and the effluent concentration was <0.04mM after 70 days. A shift in microbial community occurred probably due to FLX exposure, which induced adaptation/restructuration of the microbial population. This contributed to the robustness of the reactor, which was able to adapt to the FLX load.
G-Protein coupled receptors (GPCRs) are involved in a myriad of pathways key for human physiology through the formation of complexes with intracellular partners such as G-proteins and arrestins ...(Arrs). However, the structural and dynamical determinants of these complexes are still largely unknown. Herein, we developed a computational big-data pipeline that enables the structural characterization of GPCR complexes with no available structure. This pipeline was used to study a well-known group of catecholamine receptors, the human dopamine receptor (DXR) family and its complexes, producing novel insights into the physiological properties of these important drug targets. A detailed description of the protein interfaces of all members of the DXR family (D1R, D2R, D3R, D4R, and D5R) and the corresponding protein interfaces of their binding partners (Arrs: Arr2 and Arr3; G-proteins: Gi1, Gi2, Gi3, Go, Gob, Gq, Gslo, Gssh, Gt2, and Gz) was generated. To produce reliable structures of the DXR family in complex with either G-proteins or Arrs, we performed homology modeling using as templates the structures of the β2-adrenergic receptor (β2AR) bound to Gs, the rhodopsin bound to Gi, and the recently acquired neurotensin receptor-1 (NTSR1) and muscarinic 2 receptor (M2R) bound to arrestin (Arr). Among others, the work demonstrated that the three partner groups, Arrs and Gs- and Gi-proteins, are all structurally and dynamically distinct. Additionally, it was revealed the involvement of different structural motifs in G-protein selective coupling between D1- and D2-like receptors. Having constructed and analyzed 50 models involving DXR, this work represents an unprecedented large-scale analysis of GPCR-intracellular partner interface determinants. All data is available at www.moreiralab.com/resources/dxr.
Alanine-scanning mutagenesis of protein−protein interfacial residues is a very important process for rational drug design. In this study, we have used the improved MM-PBSA approach that combining ...molecular mechanics and continuum solvent permits one to calculate the free energy differences through alanine mutation. To identify the binding determinants of the complex formed between the IgG1 (immunoglobulin-binding protein G) and protein G, we have extended the experimental alanine scanning mutagenesis study to both proteins of this complex and, therefore, to all interfacial residues of this binding complex. As a result, we present new residues that can be characterized as warm spots and, therefore, are important for complex formation. We have further increased the understanding of the functionality of this improved computational alanine-scanning mutagenesis approach testing its sensitivity to a protein−protein complex with an interface made up of residues mainly polar. In this study, we also have improved the method for the detection of an important amino acid residue that frequently constitutes a hot spot tryptophan.
This paper describes an exciting big data analysis compiled in a freely available database, which can be applied to characterize the coupling of different G-Protein coupled receptors (GPCRs) families ...with their intracellular partners. Opioid receptor (OR) family was used as case study in order to gain further insights into the physiological properties of these important drug targets, known to be associated with the opioid crisis, a huge socio-economic issue directly related to drug abuse. An extensive characterization of all members of the ORs family (
μ
(MOR),
δ
(DOR),
κ
(KOR), nociceptin (NOP)) and their corresponding binding partners (ARRs: Arr2, Arr3; G-protein: G
i1
, G
i2
, G
i3
, G
o
, G
ob
, G
z
, G
q
, G
11
, G
14
, G
15
, G
12
, G
ssh
, G
slo
) was carried out. A multi-step approach including models’ construction (multiple sequence alignment, homology modeling), complex assembling (protein complex refinement with HADDOCK and complex equilibration), and protein-protein interface characterization (including both structural and dynamics analysis) were performed. Our database can be easily applied to several GPCR sub-families, to determine the key structural and dynamical determinants involved in GPCR coupling selectivity.
G protein-coupled receptors (GPCRs) are ubiquitously expressed transmembrane proteins associated with a wide range of diseases such as Alzheimer's, Parkinson, schizophrenia, and also implicated in in ...several abnormal heart conditions. As such, this family of receptors is regarded as excellent drug targets. However, due to the high number of intracellular signaling partners, these receptors have a complex interaction networks and it becomes challenging to modulate their function. Experimentally determined structures give detailed information on the salient structural properties of these signaling complexes but they are far away from providing mechanistic insights into the underlying process. This chapter presents some of the computational tools, namely molecular dynamics, molecular docking, and molecular modeling and related analyses methods that have been used to complement experimental findings.
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