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Proteolysis-targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin-proteasome system. Despite the existence of several E3 ligase-related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC-ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com.

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.

Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression of this protein and development of drug resistance. We thus pursued an alternative strategy that led us to the discovery of TS-dimer destabilizers. These compounds bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. A structural, spectroscopic, and kinetic investigation has provided evidence and quantitative information on the effects of the interaction of these small molecules with hTS. Focusing on the best among them, E7, we have shown that it inhibits hTS in cancer cells and accelerates its proteasomal degradation, thus causing a decrease in the enzyme intracellular level. E7 also showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.

UDP-glucuronosyltransferase (UGT)1A4 and UGT2B10 are the human UGT isoforms most frequently involved in N-glucuronidation of drugs. UGT2B10 exhibits higher affinity than UGT1A4 for numerous substrates, making it potentially the more important enzyme for metabolism of these compounds in vivo. Clinically relevant UGT2B10 polymorphisms, including a null activity splice site mutation common in African populations, can lead to large exposure differences for UGT2B10 substrates that may limit their developability as marketed drugs. UGT phenotyping approaches using recombinantly expressed UGTs are limited by low enzyme activity and lack of validation of scaling to in vivo. In this study, we describe the use of an efficient experimental protocol for identification of UGT2B10-selective substrates (i.e., those with high fraction metabolized by UGT2B10), which exploits the activity difference between pooled human liver microsomes (HLM) and HLM from a phenotypically UGT2B10 poor metabolizer donor. Following characterization of the approach with eight known UGT2B10 substrates, we used ligand-based virtual screening and literature precedents to select 24 potential UGT2B10 substrates of 140 UGT-metabolized drugs for testing. Of these, dothiepin, cidoxepin, cyclobenzaprine, azatadine, cyproheptadine, bifonazole, and asenapine were indicated to be selective UGT2B10 substrates that have not previously been described. UGT phenotyping experiments and tests comparing conjugative and oxidative clearance were then used to confirm these findings. These approaches provide rapid and sensitive ways to evaluate whether a potential drug candidate cleared via glucuronidation will be sensitive to UGT2B10 polymorphisms in vivo. SIGNIFICANCE STATEMENT: The role of highly polymorphic UDP-glucuronosyltransferase (UGT)2B10 is likely to be underestimated currently for many compounds cleared via N-glucuronidation due to high test concentrations often used in vitro and low activity of UGT2B10 preparations. The methodology described in this study can be combined with the assessment of UGT versus oxidative in vitro metabolism to rapidly identify compounds likely to be sensitive to UGT2B10 polymorphism (high fraction metabolized by UGT2B10), enabling either chemical modification or polymorphism risk assessment before candidate selection.

Viral infections sustain their replication cycle promoting a pro-oxidant environment in the host cell. In this context, specific alterations of the levels and homeostatic function of the tripeptide glutathione have been reported to play a causal role in the pro-oxidant and cytopathic effects (CPE) of the virus. In this study, these aspects were investigated for the first time in SARS-CoV2-infected Vero E6 cells, a reliable and well-characterized in vitro model of this infection. SARS-CoV2 markedly decreased the levels of cellular thiols, essentially lowering the reduced form of glutathione (GSH). Such an important defect occurred early in the CPE process (in the first 24 hpi). Thiol analysis in N-acetyl-Cys (NAC)-treated cells and membrane transporter expression data demonstrated that both a lowered uptake of the GSH biosynthesis precursor Cys and an increased efflux of cellular thiols, could play a role in this context. Increased levels of oxidized glutathione (GSSG) and protein glutathionylation were also observed along with upregulation of the ER stress marker PERK. The antiviral drugs Remdesivir (Rem) and Nelfinavir (Nel) influenced these changes at different levels, essentially confirming the importance or blocking viral replication to prevent GSH depletion in the host cell. Accordingly, Nel, the most potent antiviral in our in vitro study, produced a timely activation of Nrf2 transcription factor and a GSH enhancing response that synergized with NAC to restore GSH levels in the infected cells. Despite poor in vitro antiviral potency and GSH enhancing function, Rem treatment was found to prevent the SARS-CoV2-induced glutathionylation of cellular proteins. In conclusion, SARS-CoV2 infection impairs the metabolism of cellular glutathione. NAC and the antiviral Nel can prevent such defect in vitro., Graphical abstract Schematic representation of the alterations that SARS-CoV2 infection generates in the metabolism and redox function of cellular glutathione.Image 1

Unfolded protein response (UPR) and endoplasmic reticulum (ER) stress are aspects of SARS‐CoV‐2‐host cell interaction with proposed role in the cytopathic and inflammatory pathogenesis of this viral infection. The role of the NF‐kB pathway in these cellular processes remains poorly characterized. When investigated in VERO‐E6 cells, SARS‐CoV‐2 infection was found to markedly stimulate NF‐kB protein expression and activity. NF‐kB activation occurs early in the infection process (6 hpi) and it is associated with increased MAPK signaling and expression of the UPR inducer IRE‐1α. These signal transduction processes characterize the cellular stress response to the virus promoting a pro‐inflammatory environment and caspase activation in the host cell. Inhibition of viral replication by the viral protease inhibitor Nelfinavir reverts all these molecular changes also stimulating c‐Jun expression, a key component of the JNK/AP‐1 pathway with important role in the IRE‐1α‐mediated transcriptional regulation of stress response genes with anti‐inflammatory and cytoprotection function. The present study demonstrates that UPR signaling and its interaction with cellular MAPKs and the NF‐kB activity are important aspects of SARS‐CoV‐2‐host cell interaction that deserve further investigation to identify more efficient therapies for this viral infection.

An analytical method for the quantification of thirty-three perfluoroalkyl and polyfluoroalkyl substances (PFASs) in animal liver was developed applying the isotopic dilution methodology with twenty-one labelled isotopologues of native compounds. The proposed protocol involved the determination of short and long aliphatic chain PFASs (C4C18) extracting liver with acetonitrile followed by two clean-up steps. The instrumental analysis was performed with liquid chromatography coupled to high-resolution mass spectrometry. The acquisition method combined full MS/dd-MS2, t-SIM/dd-MS2 and SIM experiments with variable resolution in order to maximize in one chromatographic run accuracy, sensitivity and selectivity. An eight-level validation study was performed evaluating linearity, trueness, precision, quantification and detection limits. Trueness was from 94 to 126% with intra-laboratory reproducibility lower than 20%. Limits of quantification were in the range 2-100 pg g-1, except for 2,3,3,3-tetrafluoro-2-(1,1,2,2,3,3,3-heptafluoropropoxy)-propanoic acid, HFPO-DA (500 pg g-1). The analysis of a certified reference material (IRMM-427) and participation in a proficiency test scheme (FAPAS - 0687) confirmed these satisfactory performances. Finally, the application of the developed procedure to detect PFASs in sixteen liver samples of farm animals revealed that chicken was the less contaminated species.

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.

Vitamin E metabolism is a complex and highly regulated process intimately associated with lipoprotein metabolism. Hepatic steps of this process markedly differ between alpha-tocopherol (α-TOH) and other forms of this vitamin, including the cytochrome P450-dependent transformation to a series of metabolites that are now utilized as both nutritional and functional indicators of the vitamin status and metabolism. In the last three decades a number of protein interactions and gene modulation effects that characterize these differences have identified. These aspects are described in this chapter along with the recently identified role of enzymatic and free radical-derived metabolites of this vitamin as bioactive lipids. Compelling in vitro and in vivo data demonstrate that long-chain metabolites of α-TOH are more potent than their precursor in modulating peroxidation reactions and lipid metabolism, inflammatory genes, cell cycle regulation, and antiatherogenic pathways. The majority of these studies took advantage of the recently developed lipidomics technology allowing unbiased identifications and quantification of the entire spectrum of physiological metabolite in biological fluids, cell culture samples, and tissues. Other achievements also included the recognition of new metabolites, the identity of which are currently under investigation. These studies on the functional metabolome of vitamin E have led to speculation that, similarly to other fat-soluble vitamins, vitamin E may provide some of its biological roles by behaving as a provitamin. If confirmed this would represent a real breakthrough in human nutrition and a major step forward in defining vitamin E essentiality and adequacy, and their assessment strategy as well.

Specific microRNAs (miRs), including the "angio-miR-126" and the "inflamma-miR-146a-5p," have been proposed as biomarkers and even therapeutic targets of obesity-associated metabolic diseases. Physical activity, a key measure of prevention for obesity and its complications, is reported to influence the expression of these miRs. In this study, we investigate whether a physical activity program proven to improve metabolic parameters in obese patients can correct the circulating levels of these miRs. Plasma miR-126 and miR-146a-5p were measured in a cohort of obese patients (n = 31, 16F + 15M) before and after the 3-month physical activity program of the CURIAMO trial (registration number for clinical trials: ACTRN12611000255987) and in 37 lean controls (24F + 13M). miR-146a-5p, but not miR-126, was significantly increased in obese patients as compared with lean controls and decreased in approximately two-thirds of the participants post-intervention with a response that positively correlated with pre-intervention levels of this miR. Waist circumference, the inflammatory cytokine IL-8 and lipid parameters, principally total cholesterol, showed the strongest correlation with both the baseline levels and post-intervention correction of miR-146a-5p. Post-hoc analysis of experimental data supports the use of miR-146a-5p as a biomarker and predictor of the clinical response to physical activity in obese patients. Furthermore, miR-146a-5p expression was confirmed to increase together with that of the inflammatory genes TLR4, NF-κB, IL-6, and TNF-α in LPS-stimulated human mononuclear leukocytes. In conclusion, the inflamma-miR-146a-5p can serve as a personalized predictor of clinical outcome in obese patients entering physical activity weight-reduction programs. © 2018 IUBMB Life, 70(10):1012-1022, 2018.

No abstract available. published

The discovery of vitamin E will have its 100th anniversary in 2022, but we still have more questions than answers regarding the biological functions and the essentiality of vitamin E for human health. Discovered as a factor essential for rat fertility and soon after characterized for its properties of fat-soluble antioxidant, vitamin E was identified to have signaling and gene regulation effects in the 1980s. In the same years the cytochrome P-450 dependent metabolism of vitamin E was characterized and a first series of studies on short-chain carboxyethyl metabolites in the 1990s paved the way to the hypothesis of a biological role for this metabolism alternative to vitamin E catabolism. In the last decade other physiological metabolites of vitamin E have been identified, such as α-tocopheryl phosphate and the long-chain metabolites formed by the ω-hydroxylase activity of cytochrome P-450. Recent findings are consistent with gene regulation and homeostatic roles of these metabolites in different experimental models, such as inflammatory, neuronal and hepatic cells, and in vivo in animal models of acute inflammation. Molecular mechanisms underlying these responses are under investigation in several laboratories and side-glances to research on other fat soluble vitamins may help to move faster in this direction. Other emerging aspects presented in this review paper include novel insights on the mechanisms of reduction of the cardiovascular risk, immunomodulation and antiallergic effects, neuroprotection properties in models of glutamate excitotoxicity and spino-cerebellar damage, hepatoprotection and prevention of liver toxicity by different causes and even therapeutic applications in non-alcoholic steatohepatitis. We here discuss these topics with the aim of stimulating the interest of the scientific community and further research activities that may help to celebrate this anniversary of vitamin E with an in-depth knowledge of its action as vitamin.

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.

[Image: see text] The value of including protein flexibility in structure-based drug design (SBDD) is widely documented, and currently, molecular dynamics (MD) simulations represent a powerful tool to investigate protein dynamics. Yet, the inclusion of MD-derived information in pre-existing SBDD workflows is still far from trivial. We recently published an integrated MD-FLAP (Fingerprints for Ligands and Proteins) approach combining MD, clustering and Linear Discriminant Analysis (LDA) for enhancing accuracy, efficacy, and for protein conformational selection in virtual screening (VS) campaigns. Here we prospectively applied the MD-FLAP workflow to discover novel chemotypes inhibiting the Casein Kinase 1 delta (CSNK1D) enzyme. We first obtained a VS model able to separate active from inactive compounds, with a global AUC of 0.9 and a partial ROC enrichment at 0.5% of 0.18, and use it to mine the internal Pfizer screening database. Seven active molecules sharing a phenyl-indazole scaffold, not yet reported among CSNK1D inhibitors, were found. The most potent inhibitor showed an IC(50) of 134 nM.

Background . PI3Kδ is expressed in B-cells and has a central role in the B-cell receptor signaling in B-cell derived malignancies. Idelalisib was the first-in-class PI3Kδ inhibitors and several second-generation compounds are undergoing clinical investigation as single agents and in combinations. To identify modalities to overcome the resistance that develops to this class of agents, we have developed two idelalisib-resistant models derived from splenic marginal zone lymphoma (SMZL) cell lines. Materials and Methods. Cells were kept under idelalisib (IC90) until acquisition of resistance (RES) or with no drug (parental, PAR). Stable resistance was confirmed by MTT assay after 2-weeks of drug-free culture. Multi-drug resistance phenotype was ruled out. Cells underwent transcriptome and miRNA profiling by RNA-Seq, whole exome sequencing (WES), lipidomics profiling, pharmacological screening (348 compounds), and FACS analysis. Cytokines and growth factor secretion was performed by ELISA. Results. Two RES models were obtained from VL51 and Karpas1718 with 7-10 fold times higher IC50s than PAR counterparts. In both models, conditioned media from RES cells transferred the resistance in the PAR cells. While WES did not identify somatic mutations associated with resistance, RNA-Seq and lipidomics analyses showed that the two cell lines had developed resistance activating different modalities. The VL51 RES model showed an enrichment in BCR-TLR-NFkB (TLR4, CD19, SYK), IL6-STAT3 (IL6, CD44), chemokines (CXCL10, CXCR4, CXCR3) and PDGFR (PDGFRA, PRKCE) signatures, paired with increased p-AKT and p-BTK levels, decreased cardiolipins and sphingomyelins levels, and increased levels of specific triacylglycerols and glycerophosphocholines. In particular, there was an over-expression of surface expression of PDGFRA and secretion of IL6 in the medium. Silencing of both IL6and PDGFRA by siRNAs reverted the resistance, while the silencing of the individual genes had only a partial effect. These data were paired with the acquired sensitivity to the PDGFR inhibitor masitinib, identified in the pharmacologic screening. In the Karpas1718 model, we observed an increased p-AKT activity with an enrichment for B-cell activation signatures (RAG1, RAG2, TCL1A), proliferation (E2F2, MKI67), ERBB signaling (HBEGF, NRG2, ERRB4), increased levels of some triacylglycerols and repressed levels for specific glycerophosphocholines. HBEGF secretion was confirmed by ELISA. The addition of recombinant HBEGF to the medium induced resistance in the PAR cells. Combination with the pan ERBB inhibitor lapatinib was beneficial in the K1718 RES. Recombinant HBEGF also induced resistance to the BTK inhibitor ibrutinib in the PAR cells and in the mantle cell lymphoma SP-53 cell line. Specific members of the let-7 family of miRNAs were repressed in the RES lines derived from both cell lines, indicating the involvement of miRNA deregulation in the mechanism of resistance. Indeed, let-7 members are known to directly target IL6-STAT3 and cytokine signaling cascade, as well PI3K-AKT network. In solid tumors, let-7 members are also expressed at low levels in tumors with constitutive active ERBB signaling, in accordance with the activation of ERBB pathway and p-AKT we observed in our Karpas1718model. Experiments with a LIN28B inhibitor are now on-going. Finally, we validated the findings across a panel of 34 B-cell lymphoma cell lines, in which IL6, PDGFRA, HBEGF and LIN28 expression levels were negatively correlated with idelalisib sensitivity, while the latter was positively correlated with let-7 levels (P Conclusions. We developed two distinct models derived from MZL of secondary resistance to the PI3Kδ inhibitor idelalisib. We identified treatments that might overcome resistance to idelalisib and are worth of further investigations. The two models, driven by different biologic processes, will allow the evaluation of further alternative therapeutic approaches. Disclosures Stathis: PharmaMar: Other: Renumeration; ADC Therapeutics: Other: Institutional research funding; Abbvie: Other: Renumeration; Bayer: Other: Institutional research funding; Novartis: Other: Institutional research funding; MEI-Pharma: Other: Institutional research funding; Roche: Other: Institutional research funding; Pfizer: Other: Institutional research funding; Merck: Other: Institutional research funding. Stuessi:Gilead: Speakers Bureau. Zucca:Gilead: Honoraria, Other: travel grant. Rossi:Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Honoraria, Other: Scientific advisory board; Janseen: Honoraria, Other: Scientific advisory board; Roche: Honoraria, Other: Scientific advisory board; Astra Zeneca: Honoraria, Other: Scientific advisory board. Bertoni:Nordic Nanovector ASA: Research Funding; Acerta: Research Funding; Jazz Pharmaceuticals: Other: travel grants; ADC Therapeutics: Research Funding; Bayer AG: Research Funding; Cellestia: Research Funding; CTI Life Sciences: Research Funding; EMD Serono: Research Funding; Helsinn: Consultancy, Research Funding; ImmunoGen: Research Funding; Menarini Ricerche: Consultancy, Research Funding; NEOMED Therapeutics 1: Research Funding; Oncology Therapeutic Development: Research Funding; PIQUR Therapeutics AG: Other: travel grant, Research Funding; HTG: Other: Expert Statements ; Amgen: Other: travel grants; Astra Zeneca: Other: travel grants.

Lipidomics is going to leave its role of “Cinderella” of omics technologies. Innovative mass spectrometry and bioinformatics technology is bursting into the omics scene and this is leading lipid science to gain renewed attention and interest by the scientific community. New lipidomics challenges have already launched including that of extensive (high-throughput) exploration of oxidized lipids in biological matrices (that is “redox lipidomics”). Alpha-tocopherol, the main form of vitamin E in human tissues, is a H donor with exclusive pertinence to lipid peroxide substrates of cellular membranes and lipoprotein particles. The direct or enzyme-mediated interaction of this vitamin with lipid oxidation pathways generates specific metabolites and functional responses. This area of redox lipidomics is now gaining increasing interest for its role in PUFA oxidation and lipid signaling, and more in general in long-chain lipid metabolism under both physiological and pathological conditions. Targeted and untargeted lipidomics protocols of investigation are now available to characterize the functional lipidome of vitamin E that is discussed in this paper along with other emerging aspects of redox lipidomics.

In two consecutive randomized placebo-control trials, DHA has been used in combination with other micronutrient vitamins (choline (CHO), vitamin E as alpha-tocopherol and vitamin D) to treat obese nonalcoholic steatohepatitis (NASH) patients along with dietary restriction and physical activity. Regardless of micronutrient vitamins combination, the two DHA-based trials resulted in an improved liver echogenicity (primary end-point), NAFLD Activity Score (NAS) that included biopsy-derived fibrosis and steatosis indices, and metabolic parameters such as fasting blood glucose, LDL, triglycerides and AST. In these trials increased concentrations of plasma free DHA and, even more, a decreased AA/DHA ratio were the strongest predictors of the clinical outcome. A stable correction of DHA concentrations and metabolism may thus represent a major nutritional end-point and precious indicator in the clinical management of pediatric NASH. DHA therapy deserves further investigation as a first-lane intervention in these patients.

Combinatorially generated molecular repertoires have been largely used to identify novel bioactive compounds. Ever more sophisticated technological solutions have been proposed to simplify and speed up such process, expanding the chemical diversity space and increasing the prospect to select new molecular entities with specific and potent activities against targets of therapeutic relevance. In this context, random mixtures of oligomeric peptides were originally used and since 25 years they represent a continuous source of bioactive molecules with potencies ranging from the sub-nM to microM concentration. Synthetic peptide libraries are still employed as starting “synthetic broths” of structurally and chemically diversified molecular fragments from which lead compounds can be extracted and further modified. Thousands of studies have been reported describing the application of combinatorial mixtures of synthetic peptides with different complexity and engrafted on diverse structural scaffolds for the identification of new compounds which have been further developed and also tested in in vivo models of relevant diseases. We briefly review some of the most used methodologies for library preparation and screening and the most recent case studies appeared in the literature where compounds have reached at least in vivo testing in animal or similar models. Recent technological advancements in biotechnology, engineering and computer science have suggested new options to facilitate the discovery of new bioactive peptides. In this instance, we anticipate here a new approach for the design of simple but focused tripeptide libraries against druggable cavities of therapeutic targets and its complementation with existing approaches.

The structural comparison of protein binding sites is increasingly important in drug design; identifying structurally similar sites can be useful for techniques such as drug repurposing, and also in a polypharmacological approach to deliberately affect multiple targets in a disease pathway, or to explain unwanted off-target effects. Once similar sites are identified, identifying local differences can aid in the design of selectivity. Such an approach moves away from the classical “one target one drug” approach and toward a wider systems biology paradigm. Here, we report a semiautomated approach, called BioGPS, that is based on the software FLAP which combines GRID Molecular Interactions Fields (MIFs) and pharmacophoric fingerprints. BioGPS comprises the automatic preparation of protein structure data, identification of binding sites, and subsequent comparison by aligning the sites and directly comparing the MIFs. Chemometric approaches are included to reduce the complexity of the resulting data on large datasets, enabling focus on the most relevant information. Individual site similarities can be analyzed in terms of their Pharmacophoric Interaction Field (PIF) similarity, and importantly the differences in their PIFs can be extracted. Here we describe the BioGPS approach, and demonstrate its applicability to rationalize off-target effects (ERα and SERCA), to classify protein families and explain polypharmacology (ABL1 kinase and NQO2), and to rationalize selectivity between subfamilies (MAP kinases p38α/ERK2 and PPARδ/PPARγ). The examples shown demonstrate a significant validation of the method and illustrate the effectiveness of the approach. Proteins 2015; 83:517–532. © 2015 Wiley Periodicals, Inc.

β-Lactamases (BLs) able to hydrolyze β-lactam antibiotics and more importantly the last resort carbapenems, represent a major mechanism of resistance in Gram-negative bacteria showing multi-drug or extensively drug resistant phenotypes. The early detection of BLs responsible of resistant infections is challenging: approaches aiming at the identification of new BLs inhibitors (BLI) can thus serve as the basis for the development of highly needed diagnostic tools. Starting from benzo-[b]-thiophene-2-boronic acid (BZB), a nanomolar inhibitor of AmpC β-lactamase (K i = 27 nM), we have identified and characterized a set of BZB analogues able to inhibit clinically-relevant β-lactamases, including AmpC, Extended-Spectrum BLs (ESBL), KPC- and OXA-type carbapenemases and metallo-β-lactamases (MBL). A multiligand set of boronic acid (BA) β-lactamase inhibitors was obtained using covalent molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. Data confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of their inhibition profile. Interestingly, this work also allowed the identification of potent KPC-2 and NDM-1 inhibitors able to potentiate the activity of cefotaxime (CTX) and ceftazidime (CAZ) against resistant clinical isolates (MIC reduction, 32-fold). Our results open the way to the potential use of our set of compounds as a diagnostic tool for the sensitive detection of clinically-relevant β-lactamases., This work was supported by the OPTObacteria project within the 7FP (Grant agreement no: 286998; www.optobacteria.eu), and by the National Institute of Health (Grant no: GM63815). JB was supported by the Spanish Network for Research in Infectious Pathology (REIPI) RD12/0015/0012, funded by Ministerio de Economía y Competitividad, Instituto de Salud Carlos III, and co-financed by the European Development Regional Fund “A way to achieve Europe” ERDF.

A series of stigmasterol and ergosterol derivatives, characterized by the presence of oxygenated functions at C-22 and/or C-23 positions, were designed as potential liver X receptor (LXR) agonists. The absolute configuration of the newly created chiral centers was definitively assigned for all the corresponding compounds. Among the 16 synthesized compounds, 21, 27, and 28 were found to be selective LXRα agonists, whereas 20, 22, and 25 showed good selectivity for the LXRβ isoform. In particular, 25 showed the same degree of potency as 22R-HC (3) at LXRβ, while it was virtually inactive at LXRα (EC50 = 14.51 μM). Interestingly, 13, 19, 20, and 25 showed to be LXR target gene-selective modulators, by strongly inducing the expression of ABCA1, while poorly or not activating the lipogenic genes SREBP1 and SCD1 or FASN, respectively.

This pilot study was performed to study the main metabolic reactions of four synthetic cannabinoids: JWH-015, JWH-098, JWH-251, and JWH-307 in order to setup a screening method for the detection of main metabolites in biological fluids. In silico prediction of main metabolic reactions was performed using MetaSite(™) software. To evaluate the agreement between software prediction and experimental reactions, we performed in vitro experiments on the same JWHs using rat liver slices. The obtained samples were analyzed by liquid chromatography-quadrupole time-of-flight and the identification of metabolites was executed using Mass-MetaSite(™) software that automatically assigned the metabolite structures to the peaks detected based on their accurate masses and fragmentation. A comparison between the experimental findings and the in silico metabolism prediction using MetaSite(™) software showed a good accordance between experimental and in silico data. Thus, the use of in silico metabolism prediction might represent a useful tool for the forensic and clinical toxicologist to identify possible main biomarkers for synthetic cannabinoids in biological fluids, especially urine, following their administration.

Despite intensive research the physiological role and molecular mechanisms of action of the lipophilic antioxidant α-tocopherol (α-TOH) are still poorly understood. Hepatic α-TOH catabolism results in intermediate formation of the long-chain metabolites (α-LCMs) α-13'-hydroxy- and α-13'-carboxychromanol (α-13'-OH and α-13'-COOH). We propose that α-LCMs have biological functions that need further exploration. Here we report that α-13'-COOH, as detected by LC/MS Q-TOF, occurs in human serum, providing evidence for its systemic bioavailability. Using semisynthetically derived α-LCMs we performed flow cytometric analyses and found that α-LCMs decrease oxidized LDL (oxLDL) uptake (α-13'-OH, 24±6%, α-13'-COOH, 20±5% vs control) and oxLDL-induced lipid accumulation in human macrophages in vitro (α-13'-OH, 26±4%, α-13'-COOH, 21±9% vs oxLDL), probably owing to α-LCM-mediated reduction in phagocytosis of oxLDL (α-13'-OH, 16±6%, α-13'-COOH, 41±3% vs oxLDL). At the same time, α-LCMs induced expression of CD36, the major scavenger receptor for oxLDL, in human macrophages by about 4.5-fold. Blocking experiments provided evidence that α-LCMs influence oxLDL uptake independent of CD36. A key finding of our study is that bioactivity of the α-LCMs occurs at lower concentrations and with mechanisms distinct from those of their metabolic precursor α-TOH. Our findings shed new light on the mechanistic aspects of α-TOH function in macrophages, which seem to be complicated by circulating α-LCMs. We speculate that α-LCMs represent a new class of regulatory metabolites. Further studies are required to elucidate their physiological role and contribution to cardiovascular disease.

Alternariol (AOH) is a mycotoxin produced by Alternaria species. In vitro studies suggest the genotoxic, mutagenic, and endocrine disruptor effects of AOH, and an increased incidence of esophageal cancer has been reported related to higher AOH exposure. Human serum albumin (HSA) is the most abundant plasma protein in the circulation, it is able to affect toxicokinetic properties of numerous xenobiotics. HSA forms stable complexes with several mycotoxins, however, the interaction of AOH with albumin has not been examined. In this study, the complex formation of AOH with HSA was tested, employing fluorescence spectroscopy, ultrafiltration, and molecular modeling. Each spectroscopic measurement shows the formation of stable AOH-HSA complexes (K = 4 &times, 105 L/mol). Investigations with site markers (in spectroscopic and ultrafiltration models) as well as modeling studies suggest that AOH occupies Sudlow&rsquo, s site I as a high-affinity binding site in HSA. The binding affinity of AOH towards bovine, porcine, and rat albumins was also tested, suggesting that AOH binds to rat albumin with considerably higher affinity than other albumins tested. Our results demonstrate the strong interaction of AOH with serum albumins, suggesting the potential in vivo importance of these interactions.

Drug discovery is a highly complex and costly process, and in recent years, the pharmaceutical industry has shifted from traditional to genomics- and proteomics-based drug research strategies. The identification of druggable target sites, promising hits, and high quality leads are crucial steps in the early stages of drug discovery projects. Pharmacokinetic (PK) and drug metabolism profiling to optimize bioavailability, clearance, and toxicity are increasingly important areas to prevent costly failures in preclinical and clinical studies. The integration of a wide variety of technologies and expertise in multidisciplinary research teams combining synergistic effects between experimental and computational approaches on the selection and optimization of bioactive compounds to pass these hurdles is now commonplace, although there remain challenging areas. Molecular interaction fields (MIFs) are widely used in a range of applications to support the discovery teams, characterizing molecules according to their favorable interaction sites and therefore enabling predictions to be made about how molecules might interact. The utility of MIF-based in silico approaches in drug design is extremely broad, including approaches to support experimental design in hit-finding, lead-optimization, physicochemical property prediction and PK modeling, drug metabolism prediction, and toxicity. C � 2013 John Wiley & Sons, Ltd.

Repurposing and repositioning drugs has become a frequently pursued and successful strategy in the current era, as new chemical entities are increasingly difficult to find and get approved. Herein we report an integrated BioGPS/FLAPdock pipeline for rapid and effective off-target identification and drug repurposing. Our method is based on the structural and chemical properties of protein binding sites, that is, the ligand image, encoded in the GRID molecular interaction fields (MIFs). Protein similarity is disclosed through the BioGPS algorithm by measuring the pockets' overlap according to which pockets are clustered. Co-crystallized and known ligands can be cross-docked among similar targets, selected for subsequent in vitro binding experiments, and possibly improved for inhibitory potency. We used human thymidylate synthase (TS) as a test case and searched the entire RCSB Protein Data Bank (PDB) for similar target pockets. We chose casein kinase IIα as a control and tested a series of its inhibitors against the TS template. Ellagic acid and apigenin were identified as TS inhibitors, and various flavonoids were selected and synthesized in a second-round selection. The compounds were demonstrated to be active in the low-micromolar range.

Bosentan, the first-in-class drug used in treatment of pulmonary arterial hypertension, is principally metabolized by the cytochromes P450, and it is responsible for cytochromes induction and drug-drug interaction events with moderate to severe consequences. A strategy to reduce drug-drug interactions consists of increasing the metabolic stability of the perpetrator, and fluorinated analogues are often designed to block the major sites of metabolism. In this paper bosentan analogues were synthesized, and their metabolism and biological activity were evaluated. All synthesized compounds showed an improved metabolic stability towards CYP2C9, with one maintaining a moderate antagonist effect towards the ETA receptor.

L-aspartate oxidase (LASPO) is a flavoenzyme catalyzing the first step in the de novo biosynthesis of NAD+. The enzyme oxidizes L-aspartate both under aerobic and anaerobic conditions using oxygen as well as fumarate as electron acceptor. In accordance with its catalytic activities, LASPO displays strong primary and tertiary structure similarity with the flavin containing subunit of the proteins belonging to the succinate dehydrogenase/fumarate reductase family. The similarity extends to the active site residues, with LASPO differing from the other enzymes of the family only for the presence of a conserved glutamate (E121), which is substituted by apolar amino acids in the other enzymes. Three complementary approaches have been used to define the role of E121 in LASPO: characterization of mutants (E121A, E121Q, E121D and E121K), investigation of the catalytic activities of WT and mutants towards substrates and substrate analogues and molecular docking studies. All mutants retain fumarate reductase activity. On the contrary, all mutants lack L-aspartate oxidase activity, although retaining the ability to bind L-aspartate (except for E121K). These results and investigations on the oxidase activity towards substrate analogues suggest that the roles of E121 in catalysis include orienting L-aspartate in a productive binding mode and favouring proton abstraction from C2 by an active site base. Molecular docking studies of the substrate (L-aspartate), inhibitor (D-aspartate) and product (imino aspartate) in the active site of LASPO confirm that (a) the substrate/product energetically favoured orientation in the active site supports the conclusions reported above, (b) E121 interacts favourably with the charged amino group of the substrate and (c) different ligands might assume different orientations in the active site of the enzyme.

A statistical method to predict protein pK(a) has been developed by using the 3D structure of a protein and a database of 434 experimental protein pK(a) values. Each pK(a) in the database is associated with a fingerprint that describes the chemical environment around an ionizable residue. A computational tool, MoKaBio, has been developed to identify automatically ionizable residues in a protein, generate fingerprints that describe the chemical environment around such residues, and predict pK(a) from the experimental pK(a) values in the database by using a similarity metric. The method, which retrieved the pK(a) of 429 of the 434 ionizable sites in the database correctly, was crossvalidated by leave-one-out and yielded root mean square error (RMSE) = 0.95, a result that is superior to that obtained by using the Null Model (RMSE 1.07) and other well-established protein pK(a) prediction tools. This novel approach is suitable to rationalize protein pK(a) by comparing the region around the ionizable site with similar regions whose ionizable site pK(a) is known. The pK(a) of residues that have a unique environment not represented in the training set cannot be predicted accurately, however, the method offers the advantage of being trainable to increase its predictive power.

A multiclass method for screening and confirmatory analysis of antimicrobial residues in muscle has been developed and validated, according to Commission Decision 2002/657/EC. Sixty-two antibiotics belonging to ten different drug families (amphenicols, beta-lactams, diamino-pyrimidine, lincosamides, macrolides, pleuromutilins, quinolones, rifamycins, sulfonamides and tetracyclines) have been included in the method. After the addition of an aqueous solution of EDTA, the minced muscle was extracted with acetonitrile/water mixture and, later, with pure acetonitrile. The extract was evaporated and redissolved in ammonium acetate buffer prior to LC injection. Instrumental determination was performed by liquid chromatography coupled to hybrid high resolution mass analyser (LC-HRMS/MS) operating in positive electrospray ionization mode. Chromatographic separation was optimized on a Poroshell 120 EC-C18 column (100 × 3.0 mm, 2.7 μm) with gradient using methanol and water containing 0.1% of formic acid as mobile phases. The method was validated in bovine muscle in the range 3.3-150 μg kg(-1) for all antibiotics; for some compounds with MRL higher than 100 μg kg(-1), the validation interval has been extended until 1500 μg kg(-1). The studied performance characteristics were selectivity, linearity, precision, trueness (recovery), decision limits, detection capabilities, detection and quantification limits. Satisfactory quantitative performances were obtained for all the analytes. Ruggedness tests demonstrated the applicability to swine and poultry muscle, too. Finally the wide participation in proficiency tests allowed to investigate in deep the method performances.

The limited clinical efficacy of many cancer therapeutics has initiated intense research efforts toward the discovery of novel chemical entities in this field. In this study, 31 hit candidates were selected from nearly 800,000 database compounds in a ligand-based virtual screening campaign. In turn, three of these hits were found to have (sub)micromolar potencies in proliferation assays with the Jurkat acute lymphatic leukemic cell line. In this assay, the three hits were found to exhibit higher potency than clinically tested cell-death inducers (GDC-0152, AT-406, and birinapant). Importantly, antiproliferative activity toward non-cancer peripheral blood mononuclear cells (PBMCs) was found to be marginal. Further biological characterization demonstrated the cell-death-inducing properties of these compounds. Biological testing of hit congeners excluded a nonspecific, toxic effect of the novel structures. Altogether, these findings may have profound relevance for the development of clinical candidates in tumor therapy.

In continuing our efforts to identify small molecules able to disrupt the interaction of the polymerase acidic protein–basic protein 1 (PA–PB1) subunits of influenza virus (Flu) RNA-dependent RNA polymerase, this paper is devoted to the optimization of a dihydrotriazolopyrimidine derivative, previously identified through structure-based drug discovery. The structure modifications performed around the bicyclic core led to the identification of compounds endowed with both the ability to disrupt PA–PB1 subunits interaction and anti-Flu activity with no cytotoxicity. Very interesting results were obtained with the hybrid molecules 36 and 37, designed by merging some peculiar structural features known to impart PA–PB1 interaction inhibition, with compound 36 that emerged as the most potent PA–PB1 interaction inhibitor (IC50 = 1.1 μM) among all the small molecules reported so far. Calculations showed a very favored H-bonding between the 2-amidic carbonyl of 36 and Q408, which seems to justify its potent ability to interfere with the interaction of the polymerase subunits.

Serine racemase, the enzyme responsible for D-serine synthesis in the central nervous system, has been identified as a potential therapeutic target to treat N-methyl-D-aspartate receptors-related pathologies. The search for specific inhibitors of the enzyme has revealed that serine racemase is a difficult target, with the best inhibitor currently identified, 2,2-dichloromalonate, showing a K-i of 19 mu M. In order to expand the chemical space of hit compounds, we have performed an in silico structure-based screening campaign on a filtered ZINC library applying the FLAP software. The identified hits were docked with GOLD and re-scored with HINT, and the most promising molecules experimentally evaluated on recombinant human serine racemase. Two inhibitors, with chemical structures totally unrelated to inhibitors described so far showed K-i values of about 1.5 mM.

We report here a general method for the prediction of hERG potassium channel blockers using computational models generated from correlation analyses of a large dataset and pharmacophore-based GRIND descriptors. These 3D-QSAR models are compared favorably with other traditional and chemometric based HQSAR methods.

In the framework of our interest in racemic thiazinooxadiazol-3-ones we determined the absolute configuration and the biological activity as L-type calcium channel blockers of two compounds that differ in the length of the acetal chain, which could affect the pharmacological profile. We observed an interesting inversion of the stereoselectivity, with the activity residing on the R-form for a short chain compound (n = 1) and on the S-form for a long chain one (n = 12). The length of the linear acetal chain appears to be able to invert the stereoselectivity of such a class of compounds, and in silico simulations suggested that this different behaviour might be explained by different hydrophilic and hydrophobic interactions with the binding site.

The original GRID/PCA technique was adapted for the development of a tool potentially useful for the plan of a research strategy in rational enzyme design. The use of the MOVE directive of GRID made it possible to partially take into account protein flexibility, and the multivariate analysis was used as an instrument for focusing only on relevant information related to the differences in enzyme substrate selectivities. The comparison of two different penicillin G acylases, from Escherichia coli and from Providentia rettgeri, was used as a case study; these enzymes are very similar and their reported selectivities differ only for a couple of mutations around the active site. The "flexible" GRID/PCA method was able to correctly predict the observed selectivity differences caused not only by mutations of residues of the active site but also by long range effects on substrate selectivity due to sequence mutations on residues not directly involved in substrate recognition.

Structural patterns for antitumor drugs, evidenced by means of a molecular interaction field (MIF) approach using grid independent descriptors (GRIND), resembled closely those of a previous independent pharmacological classification based on their antitumor mechanism of action. For topoisomerase II inhibitors, antimitotic agents and DNA antimetabolites, systematic structural patterns were evidenced by MIF and the structural features of "outliers" in these classes corresponded to peculiar pharmacological mechanisms of action supported by literature evidences. Alkylating agents and DNA/RNA antimetabolites, interacting with a large variety of targets by different molecular mechanisms, did not exhibit clustering in the structure-based MIF approach. Moreover MIFS were able to point out similarities between drugs which, in spite of apparent dramatic differences in chemical structure, exhibit the same pharmacological behaviour.

The aim of the present study is to develop a method for predicting the site at which molecules will be metabolized by CYP 2C9 (cytochrome P450 2C9) using a previously reported protein homology model of the enzyme. Such a method would be of great help in designing new compounds with a better pharmacokinetic profile, or in designing prodrugs where the compound needs to be metabolized in order to become active. The methodology is based on a comparison between alignment-independent descriptors derived from GRID Molecular Interaction Fields for the CYP 2C9 active site, and a distance-based representation of the substrate. The predicted site of metabolism is reported as a ranking list of all the hydrogen atoms of each substrate molecule. Eighty-seven CYP 2C9-catalyzed oxidative reactions reported in the literature have been analyzed. In more than 90% of these cases, the hydrogen atom ranked at the first, second, or third position was the experimentally reported site of oxidation.

Cocaine is one of the most widely abused drugs in the industrial world. Substantial evidence has accumulated that the dopamine transporter (DAT) is a key target for cocaine regarding its reinforcing effects. This work describes the application of chemometric methods to a data set of 54 N(1)-benzhydryl-oxy-alkyl-N(4)-phenyl-alk(en)yl-piperazines (GBR compounds) and chemically related mepyramines as putative candidates in cocaine abuse therapy. The aim of the study is to gain insight into the structural requirements that determine the affinity of the data set molecules to the DAT and the serotonin transporter (SERT) as well as their inhibitory potency on dopamine uptake. The compounds in the dataset are described using the recently developed GRID independent descriptors (GRIND), which allow one to obtain fast three-dimensional quantitative structure-activity relationship models without the need of aligning and superimposing the structures; the results are interpreted in a convenient pharmacophoric-like fashion. In the first part of the work, the selectivity of the database molecules for DAT binding vs dopamine reuptake inhibition is investigated. In the second part, the selectivity of the compounds for DAT binding vs SERT binding is studied. In both cases, significant models are obtained, which define the structural features responsible for the respective selectivity profiles. Moreover, the information has potential interest for the design of new derivatives with improved selectivity.

In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia., Author summary Traditionally, the fact that most drugs are promiscuous binders has been a major concern in pharmacology, due to the occurrence of undesired off-target clinical events. In the recent years, however, the realization that many diseases are the result of complex biological processes has encouraged rethinking of drug promiscuity as a promising feature, since it is sometimes necessary to interfere with multiple receptors in order to overcome the robustness of disease-related networks. One way to identify groups of proteins that could be targeted simultaneously is to look for similar binding sites. We have massively done so for all human proteins with a known high-resolution three-dimensional structure, unveiling a vast space of ‘polypharmacology’ opportunities. Of these, we know, a great majority is not of therapeutic interest. To pinpoint promising multi-target combinations, we advocate for the use of computational tools that are able to rapidly simulate the effect of drug-target interactions on biological networks.

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.

FMO enzymes (FMOs) play a key role in the processes of detoxification and/or bioactivation of specific pharmaceuticals and xenobiotics bearing nucleophilic centers. The N-oxide and S-oxide metabolites produced by FMOs are often active metabolites. The FMOs are more active than cytochromes in the brain and work in tandem with CYP3A4 in the liver. FMOs might reduce the risk of phospholipidosis of CAD-like drugs, although some FMOs metabolites seem to be neurotoxic and hepatotoxic. However, in silico methods for FMO metabolism prediction are not yet available. This paper reports, for the first time, a substrate-specificity and catalytic-activity model for FMO3, the most relevant isoform of the FMOs in humans. The application of this model to a series of compounds with unknown FMO metabolism is also reported. The model has also been very useful to design compounds with optimal clearance and in finding erroneous literature data, particularly cases in which substances have been reported to be FMO3 substrates when, in reality, the experimentally validated in silico model correctly predicts that they are not.

Cystalysin from Treponema denticola is a pyridoxal 5'-phosphate dependent lyase that catalyzes the formation of pyruvate, ammonia, and sulfide from cysteine. It is a virulence factor in adult periodontitis because its reaction contributes to hemolysis, which sustains the pathogen. Therefore, it was proposed as a potential antimicrobial target. To identify specific inhibitors by structure-based in silico methods, we first validated the crystal structure of cystalysin as a reliable starting point for the design of ligands. By using single-crystal absorption microspectrophotometry, we found that the enzyme in the crystalline state, with respect to that in solution, exhibits: 1) the same absorption spectra for the catalytic intermediates, 2) a close pKa value for the residue controlling the keto enamine ionization, and 3) similar reactivity with glycine, L-serine, L-methionine, and the nonspecific irreversible inhibitor aminoethoxyvinylglycine. Next, we screened in silico a library of 9357 compounds with the Fingerprints for Ligands and Proteins (FLAP) software, by using the three-dimensional structure of cystalysin as a template. From the library, 17 compounds were selected and experimentally evaluated by enzyme assays and spectroscopic methods. Two compounds were found to competitively inhibit recombinant T. denticola cystalysin, with inhibition constant (Ki ) values of 25 and 37 μM. One of them exhibited a minimum inhibitory concentration (MIC) value of 64 μg mL(-1) on Moraxella catarrhalis ATCC 23246, which proves its ability to cross bacterial membranes.

A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space). The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of ‘‘pre-organized environment’’ able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS ‘‘roadmap’’.

Fifty-nine xanthones (= 9H-xanthen-9-ones) of natural or synthetic origin were investigated for their inhibitory activity toward monoamine-oxidase A (MAO-A) and MAO-B. The compounds demonstrated reversible. time-independent activities, with selectivity toward MAO-A. The most active inhibitor had an IC50 of 40 nM. Electron absorption spectroscopy revealed the formation of a 1:1 charge-transfer complex between lumiflavine and xanthones. 3D-QSAR Studies according to the CoMFA/GOLPE procedure provided information on the relationship between steric and electrostatic fields and MAO-A inhibition. The ALMOND procedure yielded additional topographical information on structural factors favoring activity

Calculated molecular properties from 3D molecular fields of interaction energies have become a valuable approach to correlate 3D molecular structures with physicochemical and pharmacodynamic properties. In contrast, their use in correlations with pharmacokinetic properties is still poorly explored and exploited. 3D molecular fields can be obtained from ab initio, semiempirical or molecular mechanics levels of calculation. The newly developed procedure called VolSurf is able to compress the relevant information present in 3D maps into a few descriptors characterised by the simplicity of their use and interpretation. These descriptors can be quantitatively compared and used to build multivariate models correlating 3D molecular structures with biological responses. The VolSurf procedure is applied here to generate descriptors and models of structure-permeation relationships. The VolSurf procedure, which was originally designed to handle a medium amount of data, can easily be applied to problems of large size such as bioisostere databases, CombyChem databases and related approaches. (C) 2000 Elsevier Science B.V. All rights reserved

Partial least squares regression (PLS1 and PLS2) and GOLPE variable selection procedures were used for the treatment of differential pulse polarographic and UV spectrophotometric data obtained from the analysis of the therapeutic combination of metronidazole and pefloxacin. The analytical method used for the determination was set up using experimental design strategies (Doehlert's design, full factorial design, fractional face center cube design, etc.) and by involving the simultaneous optimization of several responses (desirability function). Method validation was also performed, determining accuracy, precision, linearity and range, detection and quantification limits and robustness. The quantitative prediction abilities in determining metronidazole and pefloxacin plasma levels of the PLS1 and PLS2 models were tested on spiked plasma samples and good results were obtained (metronidazole, 97.5%, RSD = 4.8%, n = 3; pefloxacin, 100.6%, RSD = 3.6%, n = 3). The use of multivariate calibration was particularly useful for spectrophotometric quantification because of the highly overlapping spectra of the binary mixture.

The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.