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A ‘TripAdvisor-style’ website that helps scientists choose the best small-molecule tools for their experiments has been greatly expanded to include expert reviews of hundreds of chemical probes that can be used to increase the robustness of fundamental and applied research and help develop an arsenal of new cancer drugs.
First launched in 2015 to combat the widespread use of low-quality compounds, The Chemical Probes Portal is aimed at improving the quality and robustness of biomedical experimentation, including both fundamental ‘blue-sky’ research as well as more applied translational studies, including drug discovery.
A new research article, published in the special 2024 database issue of Nucleic Acids Research, summarises the major updates in the content and functionality of the Portal, which now provides information and free expert advice on more than 800 chemical probes. The Portal also features updated guidelines to support scientists in choosing the best small-molecule probes for their protein and using them appropriately.
A one-stop trusted resource
Chemical probes are powerful and versatile tools for determining the function in experimental systems of a particular protein of interest to a researcher. However, to be useful, they must be of high quality – as judged by their potency for the desired protein target and their molecular selectivity (for example, having as few effects as possible on ‘off-target’ proteins) together with evidence of modulating the protein of interest in intact cells.
Unfortunately, the vast amount of information on chemical probes is scattered across a huge number of research articles and other sources, making it challenging for researchers to access and distil the data they require. The Chemical Probes Portal is a trusted one-stop resource designed specially to help researchers make the decisions needed for their own work.
A unique feature of the Portal is that probes are reviewed by a large panel of international experts. Each probe is given a ‘TripAdvisor-style’ star rating, ranging from one to four stars (with four stars being the highest score), designed to help researchers assess the suitability of chemical probes for use in biological and biomedical research. Around 85% of probes reviewed on the Portal are rated as having three or four stars, meaning that they can be used with especially high confidence in biological experiments.
As well as the star ratings, the expert reviewers also provide a range of comments – for example on the concentrations at which the probes should be used, any experimental control compounds that should ideally be included alongside the probe (both inactive analogues and additional active tools, if available) along with any caveats that users should be aware of.
Finding new drug targets
The Portal, which is hosted by The Institute of Cancer Research, London and funded mainly by Wellcome, was set up by an international group of leading scientists, to address a major problem with the use of chemical probes in biomedical research.
Chemical probes play an important role by helping researchers to understand the normal function of specific proteins in healthy physiology of cells and model organisms. They are complementary to, and have some advantages over, orthogonal genetic technologies such as RNA interference and CRISPR – for example, providing more versatile control of concentration- and time-dependent perturbation of the desired target.
Importantly, these small-molecule research tools can help determine which proteins are involved in a disease, making them potentially suitable for therapeutic modulation. By inhibiting or modifying the activity of such specific proteins, chemical probes can show researchers whether targeting them could be effective in treating the disease.
Addressing a major problem in research
But despite considerable progress in recent years in the availability and application of these small molecules, researchers across the world are frequently still using poor-quality compounds even when newer, better compounds become available and are also not following consensus best practice in their use. This results in misleading research conclusions, wasted resources and even wrong decisions and delays in drug development.
Using the wrong molecule, for example, a broad kinase inhibitor such as staurosporine rather than a selective inhibitor of the protein of interest, makes it impossible to understand what is happening in the cell, as multiple targets are affected at the same time. And using a probe at too high a concentration and without suitable controls can increase the risk of non-specific effects.
When it was first launched almost a decade ago, the Portal had only a limited number of probes and covered a restricted range of protein families.
However, with dedicated funding and support from the global scientific community, the number and diversity of probes has increased. The latest update reports that the Portal now includes 803 expert-annotated chemical probes, representing a huge expansion over the original number in 2015 and an impressive increase of 47 per cent from the count of 547 reported in the previous published Portal update just two years ago.
Expanding the Portal
Most of the chemical probes on the Portal act as inhibitors, but the team behind the initiative are expanding and broadening the database to include more diverse probes with different modes of action. As a result, there are now 122 classical agonists/antagonists, 28 covalent binders and 51 degraders included.
The expansion of the number and diversity of chemical probes is accompanied by a 34 per cent increase in the coverage of human protein targets, rising to 570 from 425 in 2022. The range of target families and disease applications of the probes has also increased, including those acting on protein targets relevant to neurological diseases such as Alzheimer's and Parkinson's, as well as diabetes.
This broader disease coverage is crucial for researchers working in areas outside oncology, which has traditionally been relatively well-served, as compared to the comparatively fewer high-quality chemical probes that are available to researchers working on certain other disorders, especially neurodegenerative diseases. This is an area of future focus for the Portal, although chemical probes for cancer research will continue to be important.
Introducing ‘The Unsuitables’
In addition to chemical probes that justify a star rating, the Portal also highlights 258 compounds now known as ‘The Unsuitables’. These are compounds which are not appropriate for use as chemical probes to investigate the function of any one particular protein in cells or organisms.
Once known as ‘Historical Compounds’, these are small molecules that are not fit to be used as high-quality chemical probes. Although many of these compounds may once have been useful as pathfinders, they are no longer suitable for this purpose because other, higher-quality chemical probes are now recommended instead. Others have long been recognised as promiscuously active and should never have been used as chemical probes.
To further enhance the Portal, user-friendly connectivity with other useful resources such as canSAR is being automated. A very important, independent, public translational resource in its own right, canSAR also supplies valuable up-to-date technical information on chemical probes to the Portal’s expert reviewers and users. It was created by Professor Bissan AL-Lazikani, formerly Head of Data Science at the ICR, now at MD Anderson Cancer Centre in Houston, Texas where canSAR is hosted – who is also a member of the Portal leadership team.
canSAR combines data from various sources and uses AI to create new insights. A recent sister paper to the Portal publication, also published in the 2024 database issue of Nucleic Acids Research, describes how canSAR has added more data and updated its algorithms. These updates include enhanced tools for finding drug targets, including incorporation of AlphaFold 2 models, and a new system for organising chemical data.
Looking to the future, The Chemical Probes Portal will work with the Target 2035 initiative to support acceleration toward the challenge of developing a chemical probe for every human protein. In addition, the Portal will continue to run its highly successful Hackathon events to help introduce chemical probes to early career researchers, while also getting batches of reviews of chemical probes completed under the supervision of experienced experts.
Professor Paul Workman, Harrap Professor of Pharmacology and Therapeutics at The Institute of Cancer Research, London, who is also Executive Director of the Chemical Probes Portal and senior author of the Nucleic Acids Research Portal update paper, said:
"Chemical probes are super important for studying protein functions and developing new treatments for diseases. However, if poorly selected or misused in experiments, they can lead to incorrect or misleading results. Yet researchers face a formidable challenge in finding the information they need to select and use the best chemical probe for their work.
“The Chemical Probes Portal is a free resource designed to help the biomedical research community by offering expert advice on the best tools for a given protein of interest and on their optimal usage in experiments. High-quality chemical probes are recommended by experts based on well-established criteria such as high potency and selectivity towards the target protein, broad target profiling showing the minimal possible off-target effects, and evidence supporting modulation of the protein’s function in living cells.
“We are excited that our latest updates to the content and functionality of the Portal will further enhance the selection and use of the best tools for experimental research, thereby helping the research community to improve the quality and reliability of basic and translational biomedical research, including drug discovery.”