Free Tool Simplifies Cancer Research

Every cell contains a vast number of proteins, each of which has a specific function, for example as a receptor for another molecule or an enzyme that catalyses chemical reactions. Disorders of such mechanisms can seriously affect a cell and cause diseases such as cancer, in which the sick cell functions in a fundamentally different way to a healthy cell. It is therefore very common for a drug to have a protein as its target, one that the substance either inhibits or stimulates the production or uptake of. At the same time, there are a great many approved drugs with a tried and tested effect on certain diseases but without a known protein target. For such substances, it is said that the mechanism of action is either wholly or partly unknown.

Scientists are therefore interested in developing a relatively straightforward method able to identify which proteins are affected by a certain drug. Some such methods are already available, but all have their shortcomings. Researchers at Karolinska Institutet have now made use of these methods to create a new tool that gives more reliable and precise results.

The researchers developed their method by experimenting on lung cancer cells treated with 56 different kinds of drug. For each of the drugs they first worked out the dose that kills half of the cells after 48 hours (LC50) and then used this dose for all the drugs. Once half of the cells had died, they examined each cell's proteome (i.e. which proteins are present and their abundances) to ascertain which proteins the drugs targeted. In further experiments, they tested the drugs on other cells from breast and intestinal tumours, and drew conclusions about the extent to which the drugs are specific or general in their targeting of cancer cells.

The results of these experiments are described in the searchable database that the researchers have now created (see link below), while the method itself is detailed in the article published in Nature Communications. The idea is for other researchers to be able to perform similar experiments with other drugs using the same model, and to thus expand the database with more target proteins for more substances.

"We find that the cells are killed in different ways by different drugs," says Roman Zubarev, professor of medical proteomics at Karolinska Institutet. "Not so long ago we used to think that cells could only die in three ways - necrosis, apoptosis or autophagy - but now we've observed at least thirteen different ways in which cells can die. This method can help to speed up certain parts of the process of new drug development or improve our understanding of existing drugs."

Amir Ata Saei, Christian Michel Beusch, Alexey Chernobrovkin, Pierre Sabatier, Bo Zhang, Ülkü Güler Tokat, Eleni Stergiou, Massimiliano Gaetani, Ákos Végvári, Roman A Zubarev.
ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery.
Nat Commun 10, 5715, 2019. doi: 10.1038/s41467-019-13582-8.

Most Popular Now

New AI Tool Predicts Protein-Protein Int…

Scientists from Cleveland Clinic and Cornell University have designed a publicly-available software and web database to break down barriers to identifying key protein-protein interactions to treat with medication. The computational tool...

AI for Real-Rime, Patient-Focused Insigh…

A picture may be worth a thousand words, but still... they both have a lot of work to do to catch up to BiomedGPT. Covered recently in the prestigious journal Nature...

New Research Shows Promise and Limitatio…

Published in JAMA Network Open, a collaborative team of researchers from the University of Minnesota Medical School, Stanford University, Beth Israel Deaconess Medical Center and the University of Virginia studied...

G-Cloud 14 Makes it Easier for NHS to Bu…

NHS organisations will be able to save valuable time and resource in the procurement of technologies that can make a significant difference to patient experience, in the latest iteration of...

Start-Ups will Once Again Have a Starrin…

11 - 14 November 2024, Düsseldorf, Germany. The finalists in the 16th Healthcare Innovation World Cup and the 13th MEDICA START-UP COMPETITION have advanced from around 550 candidates based in 62...

Hampshire Emergency Departments Digitise…

Emergency departments in three hospitals across Hampshire Hospitals NHS Foundation Trust have deployed Alcidion's Miya Emergency, digitising paper processes, saving clinical teams time, automating tasks, and providing trust-wide visibility of...

MEDICA HEALTH IT FORUM: Success in Maste…

11 - 14 November 2024, Düsseldorf, Germany. How can innovations help to master the great challenges and demands with which healthcare is confronted across international borders? This central question will be...

A "Chemical ChatGPT" for New M…

Researchers from the University of Bonn have trained an AI process to predict potential active ingredients with special properties. Therefore, they derived a chemical language model - a kind of...

Siemens Healthineers co-leads EU Project…

Siemens Healthineers is joining forces with more than 20 industry and public partners, including seven leading stroke hospitals, to improve stroke management for patients all over Europe. With a total...

MEDICA and COMPAMED 2024: Shining a Ligh…

11 - 14 November 2024, Düsseldorf, Germany. Christian Grosser, Director Health & Medical Technologies, is looking forward to events getting under way: "From next Monday to Thursday, we will once again...

In 10 Seconds, an AI Model Detects Cance…

Researchers have developed an AI powered model that - in 10 seconds - can determine during surgery if any part of a cancerous brain tumor that could be removed remains...

Does AI Improve Doctors' Diagnoses?

With hospitals already deploying artificial intelligence to improve patient care, a new study has found that using Chat GPT Plus does not significantly improve the accuracy of doctors' diagnoses when...