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Chemical reagents can streamline drug discovery by validating targets and pathways
Thermo Scientific chemical probes are selective small-molecule modulators of a protein’s function, designed to allow researchers to ask mechanistic and phenotypic questions about their molecular target in cell-based or animal research studies.
Chemical probes represent an important component in both academic and pharmaceutical drug discovery research and development. These compounds help reduce the technical and biological risks of pursuing a pathway or target before incurring the time and expense of drug development and clinical trials. Chemical probes are essential in the validation of new molecular targets for a therapeutic indication.
Chemical probes in the drug discovery process
Choose your chemical probes
Each Thermo Scientific chemical probe has a known mechanism of action (MoA)—a key criterion for chemical probe quality. Each is verified for molecular structure and chemical purity to meet accepted standards. Our portfolio spans a broad range of target areas and applications.
Select your chemical probes from these links, or search for them using the search tools below.
To learn more about chemical probes and when and why you’d want to use them, read on below
What are chemical probes and how are they useful in drug discovery?
Chemical probes are small-molecule compounds known to modulate a particular protein target in a particular way. They can then be used in drug discovery and development to investigate the effects of modulating that target or pathway. Using a probe can preview whether a drug aimed at the same target could be effective before you embark on the long and costly process of development and clinical trials.
- This usage of chemical probes, while consistent with recent drug discovery terminology, should not be confused with probes used in genomics research—DNA or RNA sequences labeled with fluorescent or radioactive tags that can be used to search for their complementary sequences in a sample genome.
Chemical probes can be used to help establish the relationship between a molecular target and the broader biological consequences of modulating that target in cells or organisms. They can also help you discover new biology relating to that target, to clarify the relationship between the target and a phenotype, and to validate that a particular target is a suitable intervention point to impact the progression or outcome of a disease. Chemical probes offer a biological rather than a clinical validation of the target.
The Target 2035 initiative, an open-science alliance of international biomedical scientists, has set an aspirational goal of fostering the development of chemical probes for the entire human proteome using open science by 2035.
How are chemical probes different from drugs?
Probes that are shown to be effective can sometimes be used or developed into drugs. However, most probes are not designed or selected to exhibit drug-like properties ultimately, safety and effectiveness in a clinical setting that would make them good drugs.
Drugs may sometimes be used as probes, but caution is advised when doing so. The MoA of a drug may involve multiple proteins and pathways or it may be undefined or unknown. In contrast, the purpose of a probe is to validate a single MoA.
Comparison of small molecule drugs and chemical probes
| Drugs | Probes |
|---|---|
| Must be safe and effective | Ask a specific biological questio |
| May have undefined mechanism of action (MoA) | Defined MoA required |
| May affect multiple targets | High selectivity for target protein required |
| IP restrictions; limited availability | Both physical compound and activity data are freely available |
| Must have human bioavailability | Drug-like properties such as bioavailability are not required |
| High standards for physicochemical properties (molecular weight, lipophilicity, etc.) |
Value is markedly enhanced by use of structurally related inactive and structurally unrelated active compounds |
| High standards for pharmaceutic properties (stability, reasonable and economic synthesis, defined crystallization form, etc.) |
|
Table adapted from Arrowsmith CH, Audia JE, Austin C, et al. The promise and peril of chemical probes. |
|
Why use chemical probes?
By improving our understanding of targets and pathways, chemical probes can have a major impact in enabling and accelerating the discovery and development of new pharmaceuticals. For example, JQ1 and I-BET, BET inhibitor probes first published in 2010, have been linked to acute myeloid leukemia (AML) and multiple myeloma (MM) and have already led to more than 30 clinical trials.1
Pursuing drug development without first using chemical probes can be consequential and costly. For example, the compound iniparib was developed as an early poly(ADP-ribose) polymerase (PARP) inhibitor, especially for BRCA-mediated tumors. When iniparib failed in Phase 3 clinical trials, it cast doubt on whether PARP inhibition was effective at all and the whole field was endangered. Later, iniparib’s effects against PARP activity were disproven and it was found to modify cysteine-containing proteins nonspecifically. In contrast, validated PARP inhibitors such as olaparib and veliparib have demonstrated dramatic anti-tumor activity in BRCA-mediated models and patients.2 3
Olaparib and its Maybridge collection precursor molecule. Olaparib (right, trade name Lynparza), FDA-approved in 2014 for treatment of for BRCA-mutant ovarian cancer, was developed from a compound from our Maybridge Screening Collection (left), one of several such drugs that have received regulatory approval. Lynparza is now also a first-line maintenance treatment for BRCA-mutated metastatic pancreatic cancer, reducing the risk of disease progression or death in some patients.
Lin et al (2019) investigated ten cancer drugs and targets in various stages of testing by using CRISPR-Cas9 mutagenesis to knock out the genes responsible for the proteins they supposedly targeted. In all ten cases, the cells continued to proliferate, demonstrating that the targeted proteins were not essential for cancer cell proliferation.
Moreover, all ten drugs retained their effectiveness, indicating that their cancer cell killing was due to off-target effects! The authors suggest that validating drug candidates’ MoA pre-clinically could help to reduce the 97% failure rate of cancer drugs in clinical trials.4
When would I use a chemical probe?
In a typical drug discovery workflow, chemical probes are often used after using high-throughput (HTS) or fragment screening to identify compounds that affect a target in a certain way ( hits ), and after using medicinal chemistry methods to develop promising hits into lead candidates. The probes are used to assess the action and pathways used by lead compounds, reducing risk before incurring the time and expense of clinical trials.
Many authors suggest using chemical probes to complement genetic methods (such as removing, suppressing, or editing a gene) to study protein targets.1 Chemical methods can be quicker and more focused than genetic methods, taking advantage of a wide range of cell and animal models, and thus are often used to validate a target before genetic manipulation or clinical trials.
How can I evaluate the quality of a chemical probe?
There is reasonable consensus on desirable properties for a high-quality chemical probe.5
- Biological properties include a known MoA, high in vitro potency, high selectivity, and demonstrated on-target effects in cells.
- Physicochemical properties include stability, solubility, membrane permeability, and a characterized, reproducible structure .
- Pan-assay interference (PAINS) properties to avoid include covalent reactivity, redox activity, and colloidal aggregation.
Some authors have defined quantitative metrics for these properties, such as in vitro potency of <100 nM at the target protein,1 but others suggest that such metrics should be tempered by what is available for any given target.6
You can obtain this data on specific probes through a variety of public resources.6 Leading the category of expert-curated resources, the Chemical Probes Portal was set up in 2015 to provide benchmark data and unbiased expert reviews and advice. It also includes a helpful list of historical compounds that were used to study targets in the past and in many cases are still offered by vendors today but are not selective or potent enough to qualify as valid probes.
Chemical Probes Portal search results for the PI3 kinase PIK3CA. Two probes receive strong reviews: alpelisib (BYL 719), which is highly selective for PIK3CA, and pictilisib (GDC-0941), which also inhibits other PI3K isoforms. Either may be used successfully depending on the biological context of interest. A third, newer probe, NVP-CRL 457, is still under review. Note that LY294002, the preferred chemical inhibitor to study PI3 kinases in the 1990s (and still widely used in publications), is listed as a historical compound that is inferior to those listed due to its broad inhibition of kinases and other targets.6
In the category of computational resources, ProbeMiner serves as a source for objective, quantitative, data-driven probe assessment. These two databases can be viewed as complementary to each other.
All Thermo Scientific chemical probes have a known MoA a key criterion for chemical probe quality and many achieve high ratings in the probe databases. However, some don’t yet have enough confirmatory data to rank highly.
Featured chemical probe webinar
Chemical Probes: Choosing and using small-molecule tools to investigate protein targets
21st July 2021, 9:00 am CDT
Join us as Drs. Susanne Müller-Knapp and Albert Antolin provide an overview of chemical probes, advice on their use, and a demonstration of the Chemical Probes Portal- currently the only expert curated online resource for information and recommendations about the use of chemical probes in biomedical research
Susanne Müller
Susanne Müller-Knapp, PhD
Director of Operations, Chemical Probes Portal Chief Operating Officer, SGC Frankfurt
Albert Antolin, PhD
Sir Henry Welcome Postdoctoral Fellow, Institute of Cancer Research
1Arrowsmith CH, Audia JE, Austin C, et al. The promise and peril of chemical probes. Nat Chem Biol. 2015: 11: 536 541. Full text
2Blagg J, Workman P. Choose and use your chemical probe wisely to explore cancer biology. Cancer Cell. 2017; 32: 9 25. Full text
3A conversation on using chemical probes to study protein function in cells and organisms. Nat Commun. 2022; 13: 3757. Full text
4Lin A, Giuliano CJ, Palladino A, et al. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci Transl Med. 2019; 11: 509. Full text
5Wagner BK. Introduction to chemical probes. In Brennan P, Rodriguez SV (eds.), The discovery and utility of chemical probes in target discovery. 2020; Royal Society of Chemistry, pp. 1 13. Full text
6Antolin AA, Workman P, Al-Lazikani B. Public resources for chemical probes: The journey so far and the road ahead. Future Med Chem. 2019; 13: 731-747. Full text
Resources for chemical probes
This section includes Thermo Fisher Scientific as well as selected external resources for chemical probes. For generic chemical resources, consult the Chemical Resource Library.
Thermo Fisher Scientific resources
Key articles
Arrowsmith et al (2015), The promise and peril of chemical probes
Antolin et al (2019), Public resources for chemical probes
For Research Use Only. Not for use in diagnostic procedures.