scholarly journals Evaluation of Gene Expression and Phenotypic Profiling Data as Quantitative Descriptors for Predicting Drug Targets and Mechanisms of Action

2019 ◽  
Author(s):  
Maris Lapins ◽  
Ola Spjuth
Keyword(s):  
Gene Expression ◽  
Drug Discovery ◽  
Drug Targets ◽  
Chemical Structure ◽  
Predictive Accuracy ◽  
Mechanisms Of Action ◽  
In Vitro Assays ◽  
Using Data ◽  
Drug Leads

AbstractProfiling drug leads by means of in silico and in vitro assays as well as omics is widely used in drug discovery for safety and efficacy predictions. In this study, we evaluate the performance of machine learning models trained on data from gene expression and phenotypic profiling assays, with models trained on chemical structure descriptors, for prediction of various drug mechanisms of action and target proteins. Models for several hundred mechanisms of actions and targets were trained using data on 1484 compounds characterized in both gene expression using L1000 profiles, and phenotypic profiling with cell painting assay. The results indicate that the accuracy of the three profiling technologies varies for different endpoints, and indicate a clear potential synergistic effect if these methods are combined. We also study the effect of predictive accuracy of data from different cell lines for L1000 profiles, showing that the choice of cell line has a non-negligible effect on the predictive accuracy. The results strengthen the idea of integrated approaches for predicting drug targets and mechanisms of action in preclinical drug discovery.

scholarly journals Integrating Cell Morphology with Gene Expression and Chemical Structure to Aid Mitochondrial Toxicity Detection

2022 ◽  
Author(s):  
Srijit Seal ◽  
Jordi Carreras-Puigvert ◽  
Maria-Anna Trapotsi ◽  
Hongbin Yang ◽  
Ola Spjuth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Discovery ◽  
Chemical Structure ◽  
Structural Information ◽  
Chemical Space ◽  
Model Performance ◽  
In Vitro Assays ◽  
Mitochondrial Toxicity ◽  
Mitochondrial Membrane Depolarization

Mitochondrial toxicity is an important safety endpoint in drug discovery. Models based solely on chemical structure for predicting mitochondrial toxicity are currently limited in accuracy and applicability domain to the chemical space of the training compounds. In this work, we aimed to utilize both -omics and chemical data to push beyond the state-of-the-art. We combined Cell Painting and Gene Expression data with chemical structural information from Morgan fingerprints for 382 chemical perturbants tested in the Tox21 mitochondrial membrane depolarization assay. We observed that mitochondrial toxicants significantly differ from non-toxic compounds in morphological space and identified compound clusters having similar mechanisms of mitochondrial toxicity, thereby indicating that morphological space provides biological insights related to mechanisms of action of this endpoint. We further showed that models combining Cell Painting, Gene Expression features and Morgan fingerprints improved model performance on an external test set of 236 compounds by 60% (in terms of F1 score) and improved extrapolation to new chemical space. The performance of our combined models was comparable with dedicated in vitro assays for mitochondrial toxicity; and they were able to detect mitochondrial toxicity where Tox21 assays outcomes were inconclusive because of cytotoxicity. Our results suggest that combining chemical descriptors with different levels of biological readouts enhances the detection of mitochondrial toxicants, with practical implications for use in drug discovery.

Comparison of Vibrio and Firefly Luciferases as Reporter Gene Systems for Use in Bacteria and Plants

1996 ◽  
Vol 23 (1) ◽  
pp. 75 ◽  
Author(s):  
SR Mudge ◽  
WR Lewis-Henderson ◽  
RG Birch
Keyword(s):  
Gene Expression ◽  
Reporter Gene ◽  
Ccd Camera ◽  
Reporter Gene Expression ◽  
In Vitro Assays ◽  
E Coli ◽  
Cell Extracts ◽  
Cooled Ccd

Luciferase genes from Vibrio harveyi (luxAB) and firefly (luc) were introduced into E. coli, Agrobacteriurn, Arabidopsis and tobacco. Transformed bacteria and plants were quantitatively assayed for luciferase activity using a range of in vitro and in vivo assay conditions. Both lux and luc proved efficient reporter genes in bacteria, although it is important to be aware that the sensitive assays may detect expression due to readthrough from distant promoters. LUX activity was undetectable by liquid nitrogen-cooled CCD camera assays on intact tissues of plants which showed strong luxAB expression by in vitro assays. The decanal substrate for the lux assay was toxic to many plant tissues, and caused chemiluminescence in untransformed Arabidopsis leaves. These are serious limitations to application of the lux system for sensitive, non-toxic assays of reporter gene expression in plants. In contrast, LUC activity was readily detectable in intact tissues of all plants with luc expression detectable by luminometer assays on cell extracts. Image intensities of luc-expressing leaves were commonly two to four orders of magnitude above controls under the CCD camera. Provided adequate penetration of the substrate luciferin is obtained, luc is suitable for applications requiring sensitive, non-toxic assays of reporter gene expression in plants.

scholarly journals MicroRNAs in Female Malignancies

2019 ◽  
Vol 18 ◽  
pp. 117693511982874 ◽  
Author(s):  
Themis Liolios ◽  
Stavroula Lila Kastora ◽  
Giorgia Colombo
Keyword(s):  
Gene Expression ◽  
Computational Analysis ◽  
Target Genes ◽  
Vulvar Cancer ◽  
Chemotherapeutic Agents ◽  
In Vitro Assays ◽  
Biological Processes ◽  
Potential Mechanism ◽  
Biological Functions

MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs that can play a fundamental regulatory role in the gene expression of various organisms. Current research suggests that miRNAs can assume pivotal roles in carcinogenesis. In this article, through bioinformatics mining and computational analysis, we determine a single miRNA commonly involved in the development of breast, cervical, endometrial, ovarian, and vulvar cancer, whereas we underline the existence of 7 more miRNAs common in all examined malignancies with the exception of vulvar cancer. Furthermore, we identify their target genes and encoded biological functions. We also analyze common biological processes on which all of the identified miRNAs act and we suggest a potential mechanism of action. In addition, we analyze exclusive miRNAs among the examined malignancies and bioinformatically explore their functionality. Collectively, our data can be employed in in vitro assays as a stepping stone in the identification of a universal machinery that is derailed in female malignancies, whereas exclusive miRNAs may be employed as putative targets for future chemotherapeutic agents or cancer-specific biomarkers.

Epigenetics—an emerging and highly promising source of new drug targets

MedChemComm ◽  
2012 ◽  
Vol 3 (2) ◽  
pp. 162-166 ◽  
Author(s):  
Nessa Carey
Keyword(s):  
Gene Expression ◽  
Drug Discovery ◽  
Drug Targets ◽  
Epigenetic Modifications ◽  
Regulatory Process ◽  
Human Diseases ◽  
Histone Proteins ◽  
New Drug ◽  
Promising Source

Epigenetic modifications to DNA and its associated histone proteins are major influences on gene expression. This regulatory process is disrupted in cancer and a range of chronic human diseases, and provides attractive new intervention points and targets for drug discovery.

Aroyl-Pyrrolyl-Hydroxy-Amides (APHAs), a Novel Family of Synthetic Histone Deacetylases Inhibitors, Are Potent Inducers of Human g-Globin Gene Expression.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1216-1216
Author(s):  
Antonello Mai ◽  
Silvio Massa ◽  
Antonella Di Noia ◽  
Katija Jelicic ◽  
Elena Alfani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sickle Cell ◽  
Sickle Cell Anemia ◽  
Histone Deacetylases ◽  
Globin Gene ◽  
Renilla Luciferase ◽  
In Vitro Assays ◽  
Luciferase Reporter ◽  
Globin Gene Expression

Abstract Post-natal pharmacological reactivation of HbF, by restoring the unbalanced α/non-α globin chain production in red cells of patients affected by β-thalassemia or sickle cell anemia, represents a potential cure for these diseases. Many classes of compounds have been identified capable to induce Hb F synthesis in vitro by acting at different levels of the globin gene expression regulatory machinery. One of these classes is represented by inhibitors of a family of enzymes, the histone deacetylases (HDACs), involved in chromatin remodelling and gene transcription regulation. HDACs act in multi-protein complexes that remove acetyl groups from lysine residues on several proteins, including histones and are divided into three distinct structural classes, depending on whether their catalytic activity is zinc (class I/II)- or NAD+ (class III)-dependent. The effects of the HDACs inhibitors identified so far on HbF synthesis is, however, modest and often associated with high toxicity. Therefore, the potential of their clinical use is unclear. We have recently described a new family of synthetic HDACs inhibitors, the Aroyl-pyrrolyl-hydroxy-amides (APHAs), that induce differentiation, growth arrest and/or apoptosis of transformed cell in culture [Mai A et al, J Med Chem2004;47:1098]. In this study, we investigate the capability of 10 different APHA compounds to induce Hb F in two in vitro assays. One assay is based on the ability of APHA compounds to activate either the human Aγ-driven Firefly (Aγ-F) or the β-promoter drives Renilla Luciferase (β-R) reporter in GM979 cells stably transfected with a Dual Luciferase Reporter construct. The second assay is represented by the induction of γ-globin expression (by quantitative RT-PCR) in primary adult erythroblasts obtained in HEMA cultures of mononuclear cells from normal donors. The majority of the compounds tested did not significantly increased the Aγ−F (Aγ−F+β−R) reporter ratio in GM979 cells. However, the compound MC1575 increased by 3-fold (from 0.09 to 0.30) the reporter ratio in GM979 cells at a concentration of 20 μM, with modest effects of the proliferation activity of GM979 cells over the three days of the assay. When MC1575 was added at a concentration of 2–10 μM in cultures of primary adult erythroblasts induced to differentiate in serum-free media for 4 days, it induced a three fold increase of the γ/(γ+β) globin ratio (from 0.04 to 0.12), with no apparent cellular toxicity. Among the HDAC inhibitors tested in this study, MC1575 was not the most potent inhibitor of total enzyme activity. However, it was the compound that most selectively inhibited the activity of the maize homologue of mammalian class IIa HDAC enzymes [Mai et al, J Med Chem2003;46:4826]. These results are consistent with the hypothesis that each class of histone deacetylases might have a specific biological function and indicate that those of class IIa might represent the enzymes most specifically involved in globin gene regulation. We suggest that, by targeting the chemical inhibitors toward the catalytic domain of this class of enzymes, it should be possible to identify more specific, more potent and less toxic compounds for pharmacological treatment of β-thalassemia or sickle cell anemia.

Cadherin 13 overexpression as an important factor related to the absence of tumor fluorescence in 5-aminolevulinic acid–guided resection of glioma

2013 ◽  
Vol 119 (5) ◽  
pp. 1331-1339 ◽  
Author(s):  
Tomonari Suzuki ◽  
Satoru Wada ◽  
Hidetaka Eguchi ◽  
Jun-ichi Adachi ◽  
Kazuhiko Mishima ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Analysis ◽  
Aminolevulinic Acid ◽  
Glioma Cells ◽  
Mechanisms Of Action ◽  
Negative Regulators ◽  
Resection Rate ◽  
Fluorescent Signal ◽  
U251 Cells

Object Gliomas contain aggressive malignant cancer, and resection rate remains an important factor in treatment. Currently, fluorescence-guided resection using orally administered 5-aminolevulinic acid (5-ALA) has proved to be beneficial in improving the prognosis of patients with gliomas. 5-ALA is metabolized to protoporphyrin IX (PpIX) that accumulates selectively in the tumor and exhibits strong fluorescence upon excitation, but glioma cells do not always respond to 5-ALA, which can result in incomplete or excessive resection. Several possible mechanisms for this phenomenon have been suggested, but they remain poorly understood. To clarify the probable mechanisms underlying the variable induction of fluorescence and to improve fluorescence-guided surgery, the authors searched for key negative regulators of fluorescent signal induced by 5-ALA. Methods A comprehensive gene expression analysis was performed using microarrays in 11 pairs of tumor specimens, fluorescence-positive and fluorescence-negative tumors, and screened genes overexpressed specifically in fluorescence-negative tumors as the possible candidates for key negative regulators of 5-ALA–induced fluorescence. The most possible candidate was selected through annotation analysis in combination with a comparison of expression levels, and the relevance of expression of the selected gene to 5-ALA–induced fluorescence in tumor tissues was confirmed in the quantified expression levels. The biological significance of an identified gene in PpIX accumulation and 5-ALA–induced fluorescence was evaluated by in vitro PpIX fluorescence intensity analysis and in vitro PpIX fluorescence molecular imaging in 4 human glioblastoma cell lines (A1207, NMCG1, U251, and U373). Knockdown analyses using a specific small interfering RNA in U251 cells was also performed to determine the mechanisms of action and genes working as partners in the 5-ALA metabolic pathway. Results The authors chose 251 probes that showed remarkably high expression only in fluorescent-negative tumors (median intensity of expression signal > 1.0), and eventually the cadherin 13 gene (CDH13) was selected as the most possible determinant of 5-ALA–induced fluorescent signal in gliomas. The mean expression level of CDH13 in the fluorescence-negative gliomas was statistically higher than that in positive ones (p = 0.027), and knockdown of CDH13 expression enhanced the fluorescence image and increased the amount of PpIX 13-fold over controls (p < 0.001) in U251 glioma cells treated with 5-ALA. Comprehensive gene expression analysis of the CDH13-knockdown U251 cells demonstrated another two genes possibly involved in the PpIX biosynthesis: ATP-binding cassette transporter (ABCG2) significantly decreased in the CDH13 knockdown, while oligopeptide transporter 1 (PEPT1) increased. Conclusions The cadherin 13 gene might play a role in the PpIX accumulation pathway and act as a negative regulator of 5-ALA–induced fluorescence in glioma cells. Although further studies to clarify the mechanisms of action in the 5-ALA metabolic pathway would be indispensable, the results of this study might lead to a novel fluorescent marker able to overcome the obstacles of existing fluorescence-guided resection and improve the limited resection rate.

scholarly journals Increased SERPINA3 Level Is Associated with Ulcerative Colitis

Diagnostics ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2371
Author(s):  
Jingwei Zhang ◽  
Wei Wang ◽  
Shenglong Zhu ◽  
Yongquan Chen
Keyword(s):  
Gene Expression ◽  
Ulcerative Colitis ◽  
Drug Targets ◽  
Mrna Level ◽  
Inflammatory Factors ◽  
Potential Drug ◽  
New Genes ◽  
Potential Biomarker ◽  
Pubmed Database

Ulcerative colitis (UC) is a recurrent, chronic intestinal disease that is currently incurable. Its pathogenesis remains to be further understood. Therefore, seeking new biomarkers and potential drug targets is urgent for the effective treatment of UC. In this study, the gene expression profile GSE38713 was obtained from the GEO (Gene Expression Omnibus) database. Data normalisation and screening of the differentially expressed genes (DEGs) were conducted using R software, and gene ontology (GO) enrichment was performed using Metascape online tools. The PubMed database was used to screen new genes that have not been reported, and SERPINA3 was selected. The correlation between SERPINA3 and other inflammatory factors was analysed by Spearman correlation analysis. Finally, colitis model mice and an in-vitro model were established to validate the function of the SERPINA3 gene. SERPINA3 gene expression was markedly increased in UC patient samples, colitis models and in-vitro models and showed an association with other inflammatory factors. ROC analysis indicated that SERPINA3 could represent a potential biomarker of active UC. Additionally, silencing SERPINA3 in an in-vitro intestinal epithelial inflammatory model significantly decreased the mRNA level of inflammatory factors. This study provides supportive evidence that SERPINA3 may act as a key biomarker and potential drug target in UC treatment.

scholarly journals Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs

2020 ◽  
Vol 21 (5) ◽  
pp. 1791 ◽  
Author(s):  
Darcy C. Engelhart ◽  
Jeffry C. Granados ◽  
Da Shi ◽  
Milton H. Saier Jr. ◽  
Michael E. Baker ◽  
...  
Keyword(s):  
Cyclic Nucleotides ◽  
Signaling Molecules ◽  
In Vitro Assays ◽  
Specific Substrate ◽  
In Vivo Models ◽  
Using Data ◽  
Carnitine Derivatives ◽  
Metabolite Network

The SLC22 family of OATs, OCTs, and OCTNs is emerging as a central hub of endogenous physiology. Despite often being referred to as “drug” transporters, they facilitate the movement of metabolites and key signaling molecules. An in-depth reanalysis supports a reassignment of these proteins into eight functional subgroups, with four new subgroups arising from the previously defined OAT subclade: OATS1 (SLC22A6, SLC22A8, and SLC22A20), OATS2 (SLC22A7), OATS3 (SLC22A11, SLC22A12, and Slc22a22), and OATS4 (SLC22A9, SLC22A10, SLC22A24, and SLC22A25). We propose merging the OCTN (SLC22A4, SLC22A5, and Slc22a21) and OCT-related (SLC22A15 and SLC22A16) subclades into the OCTN/OCTN-related subgroup. Using data from GWAS, in vivo models, and in vitro assays, we developed an SLC22 transporter-metabolite network and similar subgroup networks, which suggest how multiple SLC22 transporters with mono-, oligo-, and multi-specific substrate specificity interact to regulate metabolites. Subgroup associations include: OATS1 with signaling molecules, uremic toxins, and odorants, OATS2 with cyclic nucleotides, OATS3 with uric acid, OATS4 with conjugated sex hormones, particularly etiocholanolone glucuronide, OCT with neurotransmitters, and OCTN/OCTN-related with ergothioneine and carnitine derivatives. Our data suggest that the SLC22 family can work among itself, as well as with other ADME genes, to optimize levels of numerous metabolites and signaling molecules, involved in organ crosstalk and inter-organismal communication, as proposed by the remote sensing and signaling theory.

Innovative Methodology in the Discovery of Novel Drug Targets in the Free-Living Amoebae

2018 ◽  
Vol 20 (1) ◽  
pp. 60-69 ◽  
Author(s):  
Abdul Mannan Baig
Keyword(s):  
Drug Targets ◽  
Mortality Rates ◽  
In Vitro Assays ◽  
Cancer Drug ◽  
Cns Infection ◽  
Free Living ◽  
Drug Target Discovery ◽  
Novel Drug ◽  
Novel Drug Targets

Despite advances in drug discovery and modifications in the chemotherapeutic regimens, human infections caused by free-living amoebae (FLA) have high mortality rates (~95%). The FLA that cause fatal human cerebral infections include Naegleria fowleri, Balamuthia mandrillaris and Acanthamoeba spp. Novel drug-target discovery remains the only viable option to tackle these central nervous system (CNS) infection in order to lower the mortality rates caused by the FLA. Of these FLA, N. fowleri causes primary amoebic meningoencephalitis (PAM), while the A. castellanii and B. Mandrillaris are known to cause granulomatous amoebic encephalitis (GAE). The infections caused by the FLA have been treated with drugs like Rifampin, Fluconazole, Amphotericin-B and Miltefosine. Miltefosine is an anti-leishmanial agent and an experimental anti-cancer drug. With only rare incidences of success, these drugs have remained unsuccessful to lower the mortality rates of the cerebral infection caused by FLA. Recently, with the help of bioinformatic computational tools and the discovered genomic data of the FLA, discovery of newer drug targets has become possible. These cellular targets are proteins that are either unique to the FLA or shared between the humans and these unicellular eukaryotes. The latter group of proteins has shown to be targets of some FDA approved drugs prescribed in non-infectious diseases. This review out-lines the bioinformatics methodologies that can be used in the discovery of such novel drug-targets, their chronicle by in-vitro assays done in the past and the translational value of such target discoveries in human diseases caused by FLA.

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