A drug similarity network for understanding drug mechanism of action

2014 ◽  
Vol 12 (02) ◽  
pp. 1441007 ◽  
Author(s):  
Nermin Pinar Karabulut ◽  
Murodzhon Akhmedov ◽  
Murat Cokol
Keyword(s):  
Quality Assessment ◽  
Mechanism Of Action ◽  
Drug Targets ◽  
Gene Deletion ◽  
Similarity Network ◽  
Biologically Relevant ◽  
Drug Mechanism ◽  
Small Set ◽  
Drug Similarity ◽  
Shed Light

Chemogenomic experiments, where genetic and chemical perturbations are combined, provide data for discovering the relationships between genotype and phenotype. Traditionally, analysis of chemogenomic datasets has been done considering the sensitivity of the deletion strains to chemicals, and this has shed light on drug mechanism of action and detecting drug targets. Here, we computationally analyzed a large chemogenomic dataset, which combines more than 300 chemicals with virtually all gene deletion strains in the yeast S. cerevisiae. In addition to sensitivity relation between deletion strains and chemicals, we also considered the deletion strains that are resistant to chemicals. We found a small set of genes whose deletion makes the cell resistant to many chemicals. Curiously, these genes were enriched for functions related to RNA metabolism. Our approach allowed us to generate a network of drugs and genes that are connected with resistance or sensitivity relationships. As a quality assessment, we showed that the higher order motifs found in this network are consistent with biological expectations. Finally, we constructed a biologically relevant network projection pertaining to drug similarities, and analyzed this network projection in detail. We propose this drug similarity network as a useful tool for understanding drug mechanism of action.

scholarly journals To explore the pharmacological mechanism of action using digital twin

2022 ◽  
Vol 9 (2) ◽  
pp. 55-62
Author(s):  
Rahman et al. ◽  
Keyword(s):  
Mechanism Of Action ◽  
Drug Targets ◽  
Physical Structure ◽  
Physical Models ◽  
Laboratory Research ◽  
Animal Testing ◽  
Digital Twin ◽  
Pharmacological Mechanism ◽  
Drug Mechanism ◽  
Pharmaceutical Manufacturers

With the advent of medical technology and science, the number of animals used in research has increased. For decades, the use of animals in research and product testing has been a point of conflict. Experts and pharmaceutical manufacturers are harming animals worldwide during laboratory research. Animals have also played a significant role in the advancement of science; animal testing has enabled the discovery of various novel drugs. The misery, suffering, and deaths of animals are not worth the potential human benefits. As a result, animals must not be exploited in research to assess the drug mechanism of action (MOA). Apart from the ethical concern, animal testing has a few more downsides, including the requirement for skilled labor, lengthy processes, and cost. Because it is critical to investigate adverse effects and toxicities in the development of potentially viable drugs. Assessment of each target will consume the range of resources as well as disturb living nature. As the digital twin works in an autonomous virtual world without influencing the physical structure and biological system. Our proposed framework suggests that the digital twin is a great reliable model of the physical system that will be beneficial in assessing the possible MOA prior to time without harming animals. The study describes the creation of a digital twin to combine the information and knowledge obtained by studying the different drug targets and diseases. Mechanism of Action using Digital twin (MOA-DT) will enable the experts to use an innovative approach without physical testing to save animals, time, and resources. DT reflects and simulates the actual drug and its relationships with its target, however presenting a more accurate depiction of the drug, which leads to maximize efficacy and decrease the toxicity of a drug. In conclusion, it has been shown that drug discovery and development can be safe, effective, and economical in no time through the combination of the digital and physical models of a pharmaceutical as compared to experimental animals.

Pleiotropic drug-resistance attenuated genomic library improves elucidation of drug mechanisms

2015 ◽  
Vol 11 (11) ◽  
pp. 3129-3136 ◽  
Author(s):  
Namal V. C. Coorey ◽  
James H. Matthews ◽  
David S. Bellows ◽  
Paul H. Atkinson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Mechanism Of Action ◽  
Gene Deletion ◽  
Genomic Library ◽  
Deletion Mutants ◽  
Pleiotropic Drug Resistance ◽  
Genome Wide

Identifying Saccharomyces cerevisiae genome-wide gene deletion mutants that confer hypersensitivity to a xenobiotic aids the elucidation of its mechanism of action (MoA).

scholarly journals Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions

2018 ◽  
Vol 17 (6) ◽  
pp. 1144-1155 ◽  
Author(s):  
Amir Ata Saei ◽  
Pierre Sabatier ◽  
Ülkü Güler Tokat ◽  
Alexey Chernobrovkin ◽  
Mohammad Pirmoradian ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Anticancer Drugs ◽  
Drug Targets ◽  
Life And Death ◽  
Proteomic Data ◽  
Drug Mechanism ◽  
Cell Life ◽  
Comparable Performance ◽  
Hct 116 ◽  
Proteome Changes

Chemotherapeutics cause the detachment and death of adherent cancer cells. When studying the proteome changes to determine the protein target and mechanism of action of anticancer drugs, the still-attached cells are normally used, whereas the detached cells are usually ignored. To test the hypothesis that proteomes of detached cells contain valuable information, we separately analyzed the proteomes of detached and attached HCT-116, A375, and RKO cells treated for 48 h with 5-fluorouracil, methotrexate and paclitaxel. Individually, the proteomic data on attached and detached cells had comparable performance in target and drug mechanism deconvolution, whereas the combined data significantly improved the target ranking for paclitaxel. Comparative analysis of attached versus detached proteomes provided further insight into cell life and death decision making. Six proteins consistently up- or downregulated in the detached versus attached cells regardless of the drug and cell type were discovered; their role in cell death/survival was tested by silencing them with siRNA. Knocking down USP11, CTTN, ACAA2, and EIF4H had anti-proliferative effects, affecting UHRF1 additionally sensitized the cells to the anticancer drugs, while knocking down RNF-40 increased cell survival against the treatments. Therefore, adding detached cells to the expression proteomics analysis of drug-treated cells can significantly increase the analytical value of the approach. The data have been deposited to the ProteomeXchange with identifier PXD007686.

scholarly journals Synthetic small-molecule RNA ligands: future prospects as therapeutic agents

MedChemComm ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 1242-1255 ◽  
Author(s):  
A. Di Giorgio ◽  
M. Duca
Keyword(s):  
Small Molecule ◽  
Drug Targets ◽  
Therapeutic Agents ◽  
Future Prospects ◽  
Biologically Relevant ◽  
Biological Targets ◽  
Rna Ligands ◽  
Innovative Drugs ◽  
Synthetic Small Molecule

RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in many pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified.

scholarly journals Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

2019 ◽  
Vol 36 (5) ◽  
pp. 1607-1613 ◽  
Author(s):  
Joseph C Boyd ◽  
Alice Pinheiro ◽  
Elaine Del Nery ◽  
Fabien Reyal ◽  
Thomas Walter
Keyword(s):  
Drug Discovery ◽  
Single Cell ◽  
Cell Line ◽  
Cell Lines ◽  
Mechanism Of Action ◽  
Molecular Subtype ◽  
Supplementary Information ◽  
Breast Cancer Cell Lines ◽  
Molecular Heterogeneity ◽  
Drug Mechanism

Abstract Motivation High-content screening is an important tool in drug discovery and characterization. Often, high-content drug screens are performed on one single-cell line. Yet, a single-cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterize drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process. Results The contribution of this article is 2-fold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimization of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multi-task autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease. Availability and implementation https://github.com/jcboyd/multi-cell-line or https://zenodo.org/record/2677923. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Aryl-4,5-dihydro-1H-pyrazole-1-carboxamide Derivatives Bearing a Sulfonamide Moiety Show Single-digit Nanomolar-to-Subnanomolar Inhibition Constants against the Tumor-associated Human Carbonic Anhydrases IX and XII

2020 ◽  
Vol 21 (7) ◽  
pp. 2621
Author(s):  
Priya Hargunani ◽  
Nikhil Tadge ◽  
Mariangela Ceruso ◽  
Janis Leitans ◽  
Andris Kazaks ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Inhibitory Activity ◽  
Phenyl Ring ◽  
Drug Targets ◽  
Binding Mode ◽  
Docking Studies ◽  
Carbonic Anhydrases ◽  
Single Digit ◽  
Ca Ix ◽  
Shed Light

A series of new 3-phenyl-5-aryl-N-(4-sulfamoylphenyl)-4,5-dihydro-1H-pyrazole-1-carboxamide derivatives was designed here, synthesized, and studied for carbonic anhydrase (CAs, EC 4.2.1.1) inhibitory activity against the human (h) isozymes I, II, and VII (cytosolic, off-target isoforms), and IX and XII (anticancer drug targets). Generally, CA I was not effectively inhibited, whereas effective inhibitors were identified against both CAs II (KIs in the range of 5.2–233 nM) and VII (KIs in the range of 2.3–350 nM). Nonetheless, CAs IX and XII were the most susceptible isoforms to this class of inhibitors. In particular, compounds bearing an unsubstituted phenyl ring at the pyrazoline 3 position showed 1.3–1.5 nM KIs against CA IX. In contrast, a subset of derivatives having a 4-halo-phenyl at the same position of the aromatic scaffold even reached subnanomolar KIs against CA XII (0.62–0.99 nM). Docking studies with CA IX and XII were used to shed light on the derivative binding mode driving the preferential inhibition of the tumor-associated CAs. The identified potent and selective CA IX/XII inhibitors are of interest as leads for the development of new anticancer strategies.

scholarly journals Candidate Effector Proteins of the Rust Pathogen Melampsora larici-populina Target Diverse Plant Cell Compartments

2015 ◽  
Vol 28 (6) ◽  
pp. 689-700 ◽  
Author(s):  
Benjamin Petre ◽  
Diane G. O. Saunders ◽  
Jan Sklenar ◽  
Cécile Lorrain ◽  
Joe Win ◽  
...  
Keyword(s):  
Rust Fungus ◽  
Effector Proteins ◽  
Host Cells ◽  
Plant Proteins ◽  
In Planta ◽  
Biologically Relevant ◽  
Heterologous System ◽  
Biotrophic Pathogens ◽  
Small Set ◽  
Clone And Express

Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalog of secreted proteins, some of which have been considered candidate effectors. Unraveling how these proteins function in host cells is a key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localization and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria, and discrete cellular bodies. We also used coimmunoprecipitation (coIP) and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and TOPLESS-related protein 4 from poplar by in planta coIP. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.

scholarly journals Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System

mSphere ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Kyunghun Min ◽  
Yuichi Ichikawa ◽  
Carol A. Woolford ◽  
Aaron P. Mitchell
Keyword(s):  
Drug Resistance ◽  
Candida Albicans ◽  
Genetic Analysis ◽  
Genome Editing ◽  
Drug Targets ◽  
Gene Deletion ◽  
Genetic Manipulation ◽  
Content Type ◽  
Biological Features ◽  
Link Type

ABSTRACT The fungus Candida albicans is a major pathogen. Genetic analysis of this organism has revealed determinants of pathogenicity, drug resistance, and other unique biological features, as well as the identities of prospective drug targets. The creation of targeted mutations has been greatly accelerated recently through the implementation of CRISPR genome-editing technology by Vyas et al. [Sci Adv 1(3):e1500248, 2015, http://dx.doi.org/10.1126/sciadv.1500248 ]. In this study, we find that CRISPR elements can be expressed from genes that are present only transiently, and we develop a transient CRISPR system that further accelerates C. albicans genetic manipulation. Clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-Cas9) systems are used for a wide array of genome-editing applications in organisms ranging from fungi to plants and animals. Recently, a CRISPR-Cas9 system has been developed for the diploid fungal pathogen Candida albicans; the system accelerates genetic manipulation dramatically [V. K. Vyas, M. I. Barrasa, and G. R. Fink, Sci Adv 1(3):e1500248, 2015, http://dx.doi.org/10.1126/sciadv.1500248 ]. We show here that the CRISPR-Cas9 genetic elements can function transiently, without stable integration into the genome, to enable the introduction of a gene deletion construct. We describe a transient CRISPR-Cas9 system for efficient gene deletion in C. albicans. Our observations suggest that there are two mechanisms that lead to homozygous deletions: (i) independent recombination of transforming DNA into each allele and (ii) recombination of transforming DNA into one allele, followed by gene conversion of the second allele. Our approach will streamline gene function analysis in C. albicans, and our results indicate that DNA can function transiently after transformation of this organism. IMPORTANCE The fungus Candida albicans is a major pathogen. Genetic analysis of this organism has revealed determinants of pathogenicity, drug resistance, and other unique biological features, as well as the identities of prospective drug targets. The creation of targeted mutations has been greatly accelerated recently through the implementation of CRISPR genome-editing technology by Vyas et al. [Sci Adv 1(3):e1500248, 2015, http://dx.doi.org/10.1126/sciadv.1500248 ]. In this study, we find that CRISPR elements can be expressed from genes that are present only transiently, and we develop a transient CRISPR system that further accelerates C. albicans genetic manipulation.

scholarly journals Reviewing Chandipura: A Vesiculovirus in Human Epidemics

2007 ◽  
Vol 27 (4-5) ◽  
pp. 275-298 ◽  
Author(s):  
Soumen Basak ◽  
Arindam Mondal ◽  
Smarajit Polley ◽  
Subhradip Mukhopadhyay ◽  
Dhrubajyoti Chattopadhyay
Keyword(s):  
Life Cycle ◽  
Vesicular Stomatitis Virus ◽  
Drug Targets ◽  
Viral Rna ◽  
Virus Life Cycle ◽  
Chandipura Virus ◽  
Comprehensive Picture ◽  
Vesicular Stomatitis ◽  
Potential Drug Targets ◽  
Shed Light

Chandipura virus, a member of the rhabdoviridae family and vesiculovirus genera, has recently emerged as human pathogen that is associated with a number of outbreaks in different parts of India. Although, the virus closely resembles with the prototype vesiculovirus, Vesicular Stomatitis Virus, it could be readily distinguished by its ability to infect humans. Studies on Chandipura virus while shed light into distinct stages of viral infection; it may also allow us to identify potential drug targets for antiviral therapy. In this review, we have summarized our current understanding of Chandipura virus life cycle at the molecular detail with particular interest in viral RNA metabolisms, namely transcription, replication and packaging of viral RNA into nucleocapsid structure. Contemporary research on otherwise extensively studied family member Vesicular Stomatitis Virus has also been addressed to present a more comprehensive picture of vesiculovirus life cycle. Finally, we reveal examples of protein economy in Chandipura virus life-cycle whereby each viral protein has evolved complexity to perform multiple tasks.

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