Activity artifacts in drug discovery and different facets of compound promiscuity

Compounds with apparent activity in a variety of assays might disable target proteins or produce false assay signals in the absence of specific interactions. In some instances, such effects are easy to detect, in others they are not. Observed promiscuity of compounds might be due to such non-specific assay artifacts. By contrast, promiscuity might also result from specific interactions with multiple targets. In the latter case, promiscuous compounds can be attractive candidates for certain therapeutic applications. However, compounds with artificial activity readouts are often not recognized and are further progressed, which presents a substantial problem for drug discovery. In this context, the concept of PAINS (pan-assay interference compounds) should be seriously considered, which makes it possible to eliminate flawed compounds from the discovery pipeline, even if their activities appear to be sound at a first glance.

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Prospect into therapeutic potentials of Moringa oleifera phytocompounds against cancer upsurge: de novo synthesis of test compounds, molecular docking, and ADMET studies

Bulletin of the National Research Centre ◽

10.1186/s42269-021-00554-6 ◽

2021 ◽

Vol 45 (1) ◽

Author(s):

P. M. Aja ◽

P. C. Agu ◽

E. M. Ezeh ◽

J. N. Awoke ◽

H. A. Ogwoni ◽

...

Keyword(s):

Molecular Docking ◽

Drug Discovery ◽

Cancer Chemotherapy ◽

Moringa Oleifera ◽

De Novo ◽

Gas Chromatography Mass Spectrometry ◽

Molecular Docking Study ◽

Cancer Proliferation ◽

Target Proteins ◽

Potential Inhibitors

Abstract Background Cancer chemotherapy is difficult because current medications for the treatment of cancer have been linked to a slew of side effects; as a result, researchers are tasked with developing greener cancer chemotherapies. Moringa oleifera has been reported with several bioactive compounds which confirm its application for various ailments by traditional practitioners. In this study, we aim to prospect the therapeutic potentials of M. oleifera phytocompounds against cancer proliferation as a step towards drug discovery using a computational approach. Target proteins: dihydrofolate reductase (DHFR) and B-Cell Lymphoid-2 (BCL-2), were retrieved from the RCSB PDB web server. Sixteen and five phytocompounds previously reported in M. oleifera leaves (ML) and seeds (MS), respectively, by gas chromatography–mass spectrometry were synthesized and used in the molecular docking study. For accurate prediction of binding sites of the target proteins; standard inhibitors, Methotrexate (MTX) for DHFR, and Venetoclax (VTC) for BCL-2, were docked together with the test compounds. We further predicted the ADMET profile of the potential inhibitors for an insight into their chance of success as candidates in drug discovery. Results Results for the binding affinities, docking poses, and the interactions showed that ML2, ML4-6, ML8-15, and MS1-5 are potential inhibitors of DHFR and BCL-2, respectively. In the ADMET profile, ML2 and ML4 showed the best drug-likeness by non-violation of Lipski Rule of Five. ML4-6, ML8, ML11, ML14-15, and MS1, MS3-5 exhibit high GI absorption; ML2, ML4-6, ML8, MS1, and MS5 are blood–brain barrier permeants. ML2, ML4, ML9, ML13, and MS2 do not interfere with any of the CYP450 isoforms. The toxicity profile showed that all the potential inhibitors are non-carcinogenic and non-hERG I (human ether-a-go-go related gene I) inhibitors. ML4, ML11, and MS4 are hepatotoxic and ML7, ML10, and MS4 are hERG II inhibitors. A plethora of insights on the toxic endpoints and lethal concentration values showed that ML5, ML13, and MS2 are comparatively less lethal than other potential inhibitors. Conclusion This study has demonstrated that M. oleifera phytocompounds are potential inhibitors of the disease proteins involved in cancer proliferation, thus, an invaluable step toward the discovery of cancer chemotherapy with lesser limitations.

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The Discovery Channel: microfluidics and microengineered systems in drug screening

Integrative Biology ◽

10.1039/c5ib90004b ◽

2015 ◽

Vol 7 (3) ◽

pp. 285-288 ◽

Cited By ~ 5

Author(s):

Christopher Moraes

Keyword(s):

Drug Discovery ◽

Engineering Design ◽

High Throughput ◽

Drug Screening ◽

High Throughput Screening ◽

Recent Literature ◽

Analytical Strategies ◽

Discovery Pipeline

We highlight exciting findings and promising approaches in the recent literature in which researchers integrate advanced micro-engineering, design, and analytical strategies to improve the relevance and utility of high-throughput screening in the drug discovery pipeline.

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De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits

10.1101/636563 ◽

2019 ◽

Cited By ~ 1

Author(s):

Simon Ng ◽

Yu-Chi Juang ◽

Arun Chandramohan ◽

Hung Yi Kristal Kaan ◽

Ahmad Sadruddin ◽

...

Keyword(s):

Drug Discovery ◽

False Positive ◽

A549 Cells ◽

Titration Calorimetry ◽

Stapled Peptide ◽

Exchange Mass Spectrometry ◽

Membrane Rupture ◽

Macrocyclic Peptide ◽

Assay Interference

AbstractDiscovery of false-positive target binding, due to assay interference or aggregation, presents a significant problem for drug discovery programs. These issues may often be unrealized and could lead researchers astray if not subject to independent verification of reproducibility and/or on-target mechanism of action. Although well-documented for small molecules, this issue has not been widely explored for peptide modality. As a case study, we demonstrate that two purported KRas inhibitors, stapled peptide SAH-SOS1A and macrocyclic peptide cyclorasin 9A5, exemplify false-positive molecules – both in terms of their sub-micromolar KRas binding affinities and their on-target cellular activities. We observed that the apparent binding of fluorescein-labeled SAH-SOS1A given by a fluorescence polarization assay is sensitive to detergent. False-positive readouts can arise from peptide adsorption to the surface of microplates. Hence, we used surface plasmon resonance and isothermal titration calorimetry to unambiguously show that both SAH-SOS1A and cyclorasin 9A5 are non-binders for KRas. Thermal shift assay and hydrogen-deuterium exchange mass spectrometry further demonstrate that both peptides destabilize KRas and induce unfolding of the protein. Furthermore, both peptides caused significant release of intracellular lactate dehydrogenase, suggesting that membrane rupture rather than on-target activity is accountable for their reported cytotoxicity. Finally, both peptides exhibited off-target activities by inhibiting the proliferation of U-2 OS and A549 cells, despite their independency of the KRas signaling pathway. Our findings demonstrate the critical need to employ orthogonal binding assays and cellular counter-screens to de-risk false-positive molecules. More rigorous workflows should lead to improved data and help obviate inadvertent scientific conclusions.Significance statementFalse positive molecule hits occur frequently in high-throughput screens and can contaminate the scientific literature. This has become an increasingly serious issue in small molecule drug discovery and chemical probe development and it is not surprising that peptides may be similarly prone to assay interference. Using KRas as a target and two known macrocyclic peptide inhibitors as a case study, we clearly show that reporter-free biophysical assays and cellular counter-screens offer the solution to detect and de-risk the potential of false-positive compounds. We further discuss the advantages, limitations and overall strategic importance of such methods.

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Drug-Discovery Pipeline for Novel Inhibitors of the Androgen Receptor

Methods in Molecular Biology - The Nuclear Receptor Superfamily ◽

10.1007/978-1-4939-3724-0_4 ◽

2016 ◽

pp. 31-54 ◽

Cited By ~ 3

Author(s):

Kush Dalal ◽

Ravi Munuganti ◽

Hélène Morin ◽

Nada Lallous ◽

Paul S. Rennie ◽

...

Keyword(s):

Androgen Receptor ◽

Drug Discovery ◽

Discovery Pipeline

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Modern Paradigm Towards Potential Target Identification for Antiviral (SARS-nCoV-2) and Anticancer Lipopeptides: A Pharmacophore-Based Approach

Avicenna Journal of Medical Biotechnology ◽

10.18502/ajmb.v14i1.8172 ◽

2022 ◽

Author(s):

Manisha Yadav ◽

J. Satya Eswari

Keyword(s):

Drug Discovery ◽

Target Identification ◽

Target Prediction ◽

Cost Effective ◽

Time Saving ◽

Web Based ◽

Target Proteins ◽

Lead Compounds ◽

Potential Target ◽

Biopharmaceutical Properties

Background: Lipopeptides are potential microbial metabolites that are abandoned with broad spectrum biopharmaceutical properties ranging from antimicrobial, antiviral and anticancer, etc. Clinical studies are not much explored beyond the experimental methods to understand drug mechanisms on target proteins at the molecular level for large molecules. Due to the less available studies on potential target proteins of lipopeptide based drugs, their potential inhibitory role for more obvious treatment on disease have not been explored in the direction of lead optimization. However, Computational approaches need to be utilized to explore drug discovery aspects on lipopeptide based drugs, which are time saving and cost-effective techniques. Methods: Here a ligand-based drug discovery approach is coupled with reverse pharmacophore-mapping for the prediction of potential targets for antiviral (SARS-nCoV-2) and anticancer lipopeptides. Web-based servers PharmMapper and Swiss Target Prediction are used for the identification of target proteins for lipopeptides surfactin and iturin produced by Bacillus subtilis. Results: The studies have given the insight to treat the diseases with next-generation large molecule therapeutics. Results also indicate the affinity for Angiotensin-Converting Enzymes (ACE) and proteases as the potential viral targets for these categories of peptide therapeutics. A target protein for the Human Papilloma Virus (HPV) has also been mapped. Conclusion: The work will further help in exploring computer-aided drug designing of novel compounds with greater efficiency where the structure of the target proteins and lead compounds are known.

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