Hetero-bifunctional PROteolysis TArgeting Chimeras (PROTACs) represent a new emerging class of small molecules designed to induce polyubiquitylation and proteasomal-dependent degradation of a target ...protein. Despite the increasing number of publications about the synthesis, biological evaluation, and mechanism of action of PROTACs, the characterization of the pharmacokinetic properties of this class of compounds is still minimal. Here, we report a study on the metabolism of a series of 40 PROTACs in cryopreserved human hepatocytes at multiple time points. Our results indicated that the metabolism of PROTACs could not be predicted from that of their constituent ligands. Their linkers’ chemical nature and length resulted in playing a major role in the PROTACs’ liability. A subset of compounds was also tested for metabolism by human cytochrome P450 3A4 (CYP3A4) and human aldehyde oxidase (hAOX) for more in-depth data interpretation, and both enzymes resulted in active PROTAC metabolism.
The high chemical diversity of lipids allows them to perform multiple biological functions ranging from serving as structural building blocks of biological membranes to regulation of metabolism and ...signal transduction. In addition to the native lipidome, lipid species derived from enzymatic and non-enzymatic modifications (the epilipidome) make the overall picture even more complex, as their functions are still largely unknown. Oxidized lipids represent the fraction of epilipidome which has attracted high scientific attention due to their apparent involvement in the onset and development of numerous human disorders. Development of high-throughput analytical methods such as liquid chromatography coupled on-line to mass spectrometry provides the possibility to address epilipidome diversity in complex biological samples. However, the main bottleneck of redox lipidomics, the branch of lipidomics dealing with the characterization of oxidized lipids, remains the lack of optimal computational tools for robust, accurate and specific identification of already discovered and yet unknown modified lipids. Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics. Different levels of confidence for software assisted identification of redox lipidome are defined and necessary steps toward optimal computational solutions are proposed.
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•Oxidized lipids represent an important fraction of epilipidome.•Redox lipidomics provides large LC-MS/MS datasets.•High-throughput accurate identification solutions for modified lipids are limited.•Identification of modified lipids requires MS, LC, and tandem MS data.•New software tools combining speed and specificity of identifications are required.
Humans and mammalian species are unable to synthesize significant amounts of polyunsaturated fatty acids (PUFA), which therefore must be introduced with the diet. In birds, lipogenesis takes place ...primarily in the liver, whereas adipose tissue serves as the storage site for triacylglycerols (TG, composed by 80-85% esterified fatty acids). However, both the nature (unsaturation level, n-3, or n-6 series) and the allocation (such as constituents of complexed lipids) of PUFA are very important to evaluate their function in lipid metabolism. The objective of the present investigation was to study the liver lipid metabolism, with particular attention to non-esterified fatty acids (NEFA), TG, phospholipids (PL), FADS2 gene expression, and Δ6-desaturase activity of three chicken genotypes, Leghorn (Leg), Ross 308 (Ross), and their crossbreed (LxR), by LC/MS analysis. The concentration of single fatty acids in muscle was quantified by GC-FID. The results showed that the Ross has a lipid metabolism related mainly to storage and structural roles, exhibiting higher levels of TG, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) that are largely unsaturated. Meanwhile Leg showed a relevant amount of n-3 NEFA characterized by a higher phosphatidylserine (PS) unsaturation level, FADS2 gene expression and enzyme activity. The LxR seem to have a moderate trend: n-6 and n-3 NEFA showed intermediate values compared with that of the Ross and Leg and the TG trend was similar to that of the Ross, while PE and PC were largely unsaturated (mainly 6 and 7 UNS most of the metabolic energy for storage fatty acids in their tissues (TG) whereas, the Leg birds were characterized by different lipid metabolism showing in their liver a higher content of n-3 NEFA and higher unsaturation level in PS. Furthers details are needed to better attribute the lipid energy to the different metabolic portion.
Over the last decade, technological advances have improved the sensitivity and selectivity of LC/MS analyzers, providing very efficient tools for lipidomics research. In particular, the nine lipid ...classes that constitute 99 % of the human serum lipidome (sterols, cholesteryl esters, phosphocholines, phosphoethanolamines, sphingomyelins, triacylglycerols, fatty acids, lysophosphocholines, and diacylglycerols) can be easily detected. However, until today there has not been a unique technique for sample preparation that provides a satisfactory recovery for all of these nine classes together. In this work, we have developed and validated a new one-phase extraction (OPE) method that overcomes this limitation. This method was also compared with the gold standard lipid extraction methods such as Folch, Bligh & Dyer, and recently developed methods with methanol and methyl-tert-butyl ether. Results demonstrate that the mixture of methanol/chloroform/MTBE (MMC) provides a recovery very close to 100 % for all nine lipid classes of the human serum investigated. For this extraction method, 100 μL of human serum is incubated with 2 mL of the solvents mixture, then vortexed and centrifuged. For its simplicity of execution, rapidity, reproducibility, and the reduced volume of sample required, this method opens the door to the use of human serum lipid profiling for large-scale applications in scientific research and clinical trials.
We introduce a new chemical space for drugs and drug-like molecules, exclusively based on their in silico ADME behaviour. This ADME-Space is based on self-organizing map (SOM) applied to 26,000 ...molecules. Twenty accurate QSPR models, describing important ADME properties, were developed and, successively, used as new molecular descriptors not related to molecular structure. Applications include permeability, active transport, metabolism and bioavailability studies, but the method can be even used to discuss drug-drug interactions (DDIs) or it can be extended to additional ADME properties. Thus, the ADME-Space opens a new framework for the multi-parametric data analysis in drug discovery where all ADME behaviours of molecules are condensed in one map: it allows medicinal chemists to simultaneously monitor several ADME properties, to rapidly select optimal ADME profiles, retrieve warning on potential ADME problems and DDIs or select proper in vitro experiments.
To date, the main limitations for LC-MS-based untargeted lipidomics reside in the lack of adequate computational and cheminformatics tools that are able to support the analysis of several thousands ...of species from biological samples, enabling data mining and automating lipid identification and external prediction processes. To address these issues, we developed Lipostar, novel vendor-neutral high-throughput software that effectively supports both targeted and untargeted LC-MS lipidomics, implementing data acquisition, user-friendly multivariate analysis (to be used for model generation and new sample predictions), and advanced lipid identification protocols that can work with or without the support of preformed lipid databases. Moreover, Lipostar integrates the lipidomic processes with a full metabolite identification (MetID) procedure, essential in drug safety applications and in translational studies. Case studies demonstrating a number of Lipostar features are also presented.
Flavonoids are plant bioactives that are recognized as hormone-like polyphenols because of their similarity to the endogenous sex steroids 17β-estradiol and testosterone, and to their estrogen- and ...androgen-like activity. Most efforts to verify flavonoid binding to nuclear receptors (NRs) and explain their action have been focused on ERα, while less attention has been paid to other nuclear and non-nuclear membrane androgen and estrogen receptors. Here, we investigate six flavonoids (apigenin, genistein, luteolin, naringenin, quercetin, and resveratrol) that are widely present in fruits and vegetables, and often used as replacement therapy in menopause. We performed comparative computational docking simulations to predict their capability of binding nuclear receptors ERα, ERβ, ERRβ, ERRγ, androgen receptor (AR), and its variant AR
and membrane receptors for androgens, i.e., ZIP9, GPRC6A, OXER1, TRPM8, and estrogens, i.e., G Protein-Coupled Estrogen Receptor (GPER). In agreement with data reported in literature, our results suggest that these flavonoids show a relevant degree of complementarity with both estrogen and androgen NR binding sites, likely triggering genomic-mediated effects. It is noteworthy that reliable protein-ligand complexes and estimated interaction energies were also obtained for some suggested estrogen and androgen membrane receptors, indicating that flavonoids could also exert non-genomic actions. Further investigations are needed to clarify flavonoid multiple genomic and non-genomic effects. Caution in their administration could be necessary, until the safe assumption of these natural molecules that are largely present in food is assured.
The aim of this study was to establish the persistence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on inanimate surfaces such as plastic, stainless steel, and glass during UV-C ...irradiation which is a physical means commonly utilized in sanitization procedures. The viral inactivation rate, virus half-life, and percentage of titer reduction after UV-C irradiation were assessed. Infectivity was maintained on plastic and glass until 120 h and on stainless steel until 72 h. The virus half-life was 5.3, 4.4, and 4.2 h on plastic, stainless steel, and glass, respectively. In all cases, titer decay was >99% after drop drying. UV-C irradiation efficiently reduced virus titer (99.99%), with doses ranging from 10.25 to 23.71 mJ/cm
. Plastic and stainless steel needed higher doses to achieve target reduction. The total inactivation of SARS-CoV-2 on glass was obtained with the lower dose applied. SARS-CoV-2 survival can be long lasting on inanimate surfaces. It is worth recommending efficient disinfection protocols as a measure of prevention of viral spread. UV-C can provide rapid, efficient and sustainable sanitization procedures of different materials and surfaces. The dosages and mode of irradiation are important parameters to consider in their implementation as an important means to fight the SARS-CoV-2 pandemic.
Lipids are a structurally diverse class of biomolecules which can undergo a variety of chemical modifications. Among them, lipid (per)oxidation attracts most of the attention due to its significance ...in the regulation of inflammation, cell proliferation and death programs. Despite their apparent regulatory significance, the molecular repertoire of oxidized lipids remains largely elusive as accurate annotation of lipid modifications is complicated by their low abundance and often unknown, biological context-dependent structural diversity. Here, we provide a workflow based on the combination of bioinformatics and LC-MS/MS technologies to support identification and relative quantification of oxidized complex lipids in a modification type- and position-specific manner. The developed methodology is used to identify epilipidomics signatures of lean and obese individuals with and without type 2 diabetes. The characteristic signature of lipid modifications in lean individuals, dominated by the presence of modified octadecanoid acyl chains in phospho- and neutral lipids, is drastically shifted towards lipid peroxidation-driven accumulation of oxidized eicosanoids, suggesting significant alteration of endocrine signalling by oxidized lipids in metabolic disorders.
Mass Spectrometry Imaging (MSI) is an established and powerful MS technique that enables molecular mapping of tissues and cells finding widespread applications in academic, medical, and ...pharmaceutical industries. As both the applications and MSI technology have undergone rapid growth and improvement, the challenges associated both with analyzing large datasets and identifying the many detected molecular species have become apparent. The lack of readily available and comprehensive software covering all necessary data analysis steps has further compounded this challenge. To address this issue we developed LipostarMSI, comprehensive and vendor-neutral software for targeted and untargeted MSI data analysis. Through user-friendly implementation of image visualization and co-registration, univariate and multivariate image and spectral analysis, and for the first time, advanced lipid, metabolite, and drug metabolite (MetID) automated identification, LipostarMSI effectively streamlines biochemical interpretation of the data. Here, we introduce LipostarMSI and case studies demonstrating the versatility and many capabilities of the software.
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