AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Role of mtDNA-related mitoepigenetic phenomena in cancer

Abnormal mitochondrial function has long been associated with the development and the progression of cancer. Multiple defects in the mitochondrial genome have been reported for various cancers, however the often disregarded mitochondrial epigenetic landscape provides an additional source of deregulation that may contribute to carcinogenesis

Role of mtDNA-related mitoepigenetic phenomena in cancer

Abnormal mitochondrial function has long been associated with the development and the progression of cancer. Multiple defects in the mitochondrial genome have been reported for various cancers, however the often disregarded mitochondrial epigenetic landscape provides an additional source of deregulation that may contribute to carcinogenesis

Metabolic and Phenotypic Characterization of Human Skin Fibroblasts After Forcing Oxidative Capacity

Human skin fibroblasts present technical advantages for the study of mitochondrial-induced toxicity, because those cells can be isolated from patients by lowly invasive methods and present specific cumulative cellular damage and mutations of particular conditions. Several drugs lead to organ toxicity, with some of these drugs having been already withdrawn from the market. Frequently, drug-induced toxicity is attributed to mitochondrial liabilities. One of the approaches to identify drug-induced mitochondrial toxicity is using glucose-free/galactose/glutamine/pyruvate-containing cell culture media that force cells to be more dependent on oxidative phosphorylation for energy production. However, the effects of this modified culture medium itself on the mitochondrial phenotype of human skin fibroblasts have not been explored in detail. Our objective was to assess the mitochondrial biology of human skin fibroblasts under standard or modified culture conditions so that system can be validated and used in a more reliable way to disclose mitochondrial liabilities of drug candidates or intrinsic metabolic differences in fibroblasts. Our results showed that forcing mitochondrial remodeling in human skin fibroblasts increased oxygen consumption rate, ATP levels, and mitochondria-related transcripts and proteins. Moreover, the metabolic remodeling increased cytotoxicity of mitochondrial poisons. In general, no alterations in gene expression related with differentiation status were observed in human skin fibroblasts, with exception of increased paxilin gene expression. Not only the current work highlights the importance of using human skin primary cells to study drug-induced mitochondrial toxicity, it also reinforces the use of this tool to detect specific mitochondrial defects in skin fibroblasts from patients

Analysis of pro-apoptotic protein trafficking to and from mitochondria

Mitochondria play a key role in cell death and its regulation. The permeabilization of the outer mitochondrial membrane which is mainly controlled by proteins of the BCL-2 family, is a key event that can be directly induced by p53 and results in the release of pro-apoptotic factors to the cytosol, such as cytochrome c, second mitochondria derived activator of caspases/direct inhibitor-of-apoptosis (IAP) binding protein with low pI (SMAC/Diablo), Omi serine protease (Omi/HtrA2), apoptosis inducing factor (AIF), or endonuclease G (Endo-G). Hence, the determination of subcellular localization of these proteins is extremely important to predict cell fate and elucidate the specific mechanism of apoptosis. Here we describe the procedures that can be used to study the subcellular location of different pro-apoptotic proteins to be used in basic cell biology and toxicology studies

Analysis of pro-apoptotic protein trafficking to and from mitochondria

Mitochondria play a key role in cell death and its regulation. The permeabilization of the outer mitochondrial membrane which is mainly controlled by proteins of the BCL-2 family, is a key event that can be directly induced by p53 and results in the release of pro-apoptotic factors to the cytosol, such as cytochrome c, second mitochondria derived activator of caspases/direct inhibitor-of-apoptosis (IAP) binding protein with low pI (SMAC/Diablo), Omi serine protease (Omi/HtrA2), apoptosis inducing factor (AIF), or endonuclease G (Endo-G). Hence, the determination of subcellular localization of these proteins is extremely important to predict cell fate and elucidate the specific mechanism of apoptosis. Here we describe the procedures that can be used to study the subcellular location of different pro-apoptotic proteins to be used in basic cell biology and toxicology studies

Analysis of pro-apoptotic protein trafficking to and from mitochondria

Mitochondria play a key role in cell death and its regulation. The permeabilization of the outer mitochondrial membrane which is mainly controlled by proteins of the BCL-2 family, is a key event that can be directly induced by p53 and results in the release of pro-apoptotic factors to the cytosol, such as cytochrome c, second mitochondria derived activator of caspases/direct inhibitor-of-apoptosis (IAP) binding protein with low pI (SMAC/Diablo), Omi serine protease (Omi/HtrA2), apoptosis inducing factor (AIF), or endonuclease G (Endo-G). Hence, the determination of subcellular localization of these proteins is extremely important to predict cell fate and elucidate the specific mechanism of apoptosis. Here we describe the procedures that can be used to study the subcellular location of different pro-apoptotic proteins to be used in basic cell biology and toxicology studies

Dimethylaminopyridine derivatives of lupane triterpenoids cause mitochondrial disruption and induce the permeability transition

Triterpenoids are a large class of naturally occurring compounds, and some potentially interesting as anticancer agents have been found to target mitochondria. The objective of the present work was to investigate the mechanisms of mitochondrial toxicity induced by novel dimethylaminopyridine (DMAP) derivatives of pentacyclic triterpenes, which were previously shown to inhibit the growth of melanoma cells in vitro. MCF-7, Hs 578T and BJ cell lines, as well as isolated hepatic mitochondria, were used to investigate direct mitochondrial effects. On isolated mitochondrial hepatic fractions, respiratory parameters, mitochondrial transmembrane electric potential, induction of the mitochondrial permeability transition (MPT) pore and ion transport-dependent osmotic swelling were measured. Our results indicate that the DMAP triterpenoid derivatives lead to fragmentation and depolarization of the mitochondrial network in situ, and to inhibition of uncoupled respiration, induction of the permeability transition pore and depolarization of isolated hepatic mitochondria. The results show that mitochondrial toxicity is an important component of the biological interaction of DMAP derivatives, which can explain the effects observed in cancer cells.This work was supported by projects Pest-C/SAU/LA0001/2013– 2014 and PTDC/QUI-QUI/101409/2008 funded by Fundação para a Ciência e a Tecnologia (FCT), Portugal, and cofinanced by: ‘COMPETE- Programa Operacional Factores de Competitividade’, QREN and European Union (FEDER-Fundo Europeu de Desenvolvimento Regional). T.C.-O. was supported by the FCT postdoctoral fellowship SFRH/BPD/34711/2007, T.L.S. supported by the FCT postdoctoral fellowship SFRH/BPD/75959/2011, both co-financed by POPHPrograma Operacional Potencial Humano, QREN and European Union

Mitochondrially targeted effects of berberine [Natural Yellow 18, 5,6-dihydro-9,10-dimethoxybenzo(g)-1,3-benzodioxolo(5,6-a) quinolizinium] on K1735-M2 mouse melanoma cells: comparison with direct effects on isolated mitochondrial fractions

Berberine [Natural Yellow 18, 5,6-dihydro-9,10-dimethoxybenzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium] is an alkaloid present in plant extracts and has a history of use in traditional Chinese and Native American medicine. Because of its ability to arrest the cell cycle and cause apoptosis of several malignant cell lines, it has received attention as a potential anticancer therapeutic agent. Previous studies suggest that mitochondria may be an important target of berberine, but relatively little is known about the extent or molecular mechanisms of berberine-mitochondrial interactions. The objective of the present work was to investigate the interaction of berberine with mitochondria, both in situ and in isolated mitochondrial fractions. The data show that berberine is selectively accumulated by mitochondria, which is accompanied by arrest of cell proliferation, mitochondrial fragmentation and depolarization, oxidative stress, and a decrease in ATP levels. Electron microscopy of berberine-treated cells shows a reduction in mitochondria-like structures, accompanied by a decrease in mitochondrial DNA copy number. Isolated mitochondrial fractions treated with berberine had slower mitochondrial respiration, especially when complex I substrates were used, and increased complex I-dependent oxidative stress. It is also demonstrated for the first time that berberine stimulates the mitochondrial permeability transition. Direct effects on ATPase activity were not detected. The present work demonstrates a number of previously unknown alterations of mitochondrial physiology induced by berberine, a potential chemotherapeutic agent, although it also suggests that high doses of berberine should not be used without a proper toxicology assessmen

Intermediary metabolism: An intricate network at the crossroads of cell fate and function

Intermediary metabolism is traditionally viewed as the large, highly integrated network of reactions that provides cells with metabolic energy, reducing power and biosynthetic intermediates. The elucidation of its major pathways and molecular mechanisms of energy transduction occupied some of the brightest scientific minds for almost two centuries. When these goals were achieved, a sense that intermediary metabolism was mostly a solved problem pervaded the broader biochemical community, and the field lost its vitality. However, intermediary metabolism has recently been re-energized by several paradigm-shifting discoveries that challenged its perception as a self-contained system and re-positioned it at the crossroads of all aspects of cell function, from cell growth, proliferation and death to epigenetics and immunity. Emphasis is now increasingly placed on the involvement of metabolic dysfunction in human disease. In this review, we will navigate from the dawn of intermediary metabolism research to present day work on this ever-expanding field.Associação de Apoio ao Centro de Investigação em Meio Ambiente, Genética e Oncobiologia (ACIMAGO, grant 16/12). L.M.R.F. is the Jeffrey G. Klein Family Diabetes Fellow at the University of California, San Francisco. A.M.L. was supported by an NIH T32 Training Grant (CA009302-40).D31F-2F85-32BE | Margarida Conceição Moreira Sobralinfo:eu-repo/semantics/publishedVersio