Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research

Abstract

Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose ‘the rule of two’: At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.

HDAC inhibitor derivatives induce differentiation of leukemic cells through two distinct and separable mechanisms

“…However, identifying suitable tool compounds is a challenging task, and indeed a systematic literature review revealed suboptimal use of chemical probes in cell-based biomedical research. 32 To control for any off-target activity of the developed molecules, an inactive close analogue is often used as a negative control. 33 This is often based on an inactive enantiomer for chiral molecules or on a small modification that completely abolishes the phenotypic effect.…”

Small-Molecule Probes as Pharmacological Tools for the Bone Morphogenetic Protein Signaling Pathway

“…Small-molecule probes can serve as valuable and versatile tools in pharmacology to investigate molecular signaling pathways in health and disease. However, their quality is decisive for devising meaningful data that can be translated to coherent molecular networks. , In biomedical research study design, active chemical probes, corresponding negative controls, and their dosing should be carefully chosen each time in view of the individual application and biological context . Unfortunately, probes with promiscuous, non-specific activities are still frequently used, simply because they have been established at times when no higher quality probe was available .…”

“…4,5 In biomedical research study design, active chemical probes, corresponding negative controls, and their dosing should be carefully chosen each time in view of the individual application and biological context. 151 Unfortunately, probes with promiscuous, non-specific activities are still frequently used, simply because they have been established at times when no higher quality probe was available. 152 Therefore, it is vital to constantly explore the availability of optimized probes for a given target or the introduction of novel probe modalities with unprecedented modes of action and targets in a specific field.…”

CK2 Chemical Probes: Past, Present, and Future

“…The adoption of SGC-CK2-1 as a CK2 chemical probe by the scientific community for use in cell-based studies is a positive step forward. We emphasize that the best practice of using a chemical probe is in parallel with its associated negative control, and/or the use of two orthogonal chemical probes [83]. Both options are currently enabled for CK2.…”