Dynamic Single-Molecule Analysis for Drug Discovery

See your drugs in action at the molecular level.

Target Validation

Hit Identification

Hit-to-lead

Lead Optimization

Scientists can study how proteins interact with DNA or RNA molecules and visualize these interactions while correlating them with the mechanical properties of the system. In this way, they can characterize not only protein binding but also binding location and protein behavior after the binding, thus resolving the dynamics and functionality of the target. This additional information can help interpret the influence of different pharmaceuticals on the protein-DNA interactions to discover promising leads based on their MOA.

Probe and film DNA-protein interactions in real-time at the single-molecule level

Scientists can use optical tweezers to trap beads and catch a biomolecule, such as DNA, in between. This biomolecule can then be manipulated by moving the beads, while the force and extension are measured. Fluorescently labeled proteins can be visualized with confocal or STED fluorescence microscopy. The combination of optical tweezers with simultaneous multicolor fluorescence measurements allows correlating the mechanical properties of the DNA with the protein activity.

The C-Trap™ Optical Tweezers – Fluorescence Microscopy system provides the ability to apply and measure force and extension of the tethered DNA while simultaneously visualizing proteins as they interact with the DNA. In this way, it is possible to film proteins and directly characterize their effect. When DNA-protein interactions are measured at the single-molecule level the exact mechanisms of DNA organization, replication, translation, and repair can be studied in high detail, including conformational changes.

The film in Figure 1 shows the position of bound XRCC4 and XLF on DNA over time at protein concentrations of 5 nM. These are two repair proteins involved in non-homologous end joining which can associate with each other to form complexes capable of bridging DNA. The film shows XLF-XRCC4 protein tandems binding to double-stranded DNA and rapidly diffusing as they are searching for damage sites.

1 Film showing the dynamics of CRCC4-XLF protein complexes on DNA.

Data courtesy of Prof. Erwin Peterman and Prof. Gijs Wuite at the VU University Amsterdam

Quantify and measure the effect of drugs

Scientists can use optical tweezers or acoustic force spectroscopy to trap beads and catch a biomolecule, such as DNA, while an enzyme is interacting with it. It is then possible to study and quantify the effect of small molecules or biologics on the enzyme’s activity. The combination of optical tweezers with simultaneous multicolor fluorescence measurements allows correlation of the mechanical properties of the DNA with the drug activity.

C-Trap Drug-Protein Interaction

Here, the activity of RNA polymerase (RNAp) was investigated in the presence of different inhibitor (acinetodin, klebsidin, and microscin J25) concentrations. This was done by applying a constant force on the tethered structure to detect the activity of the RNAp in the presence of different known and unknown inhibitor molecules. The detection of transcription elongation was determined by the presence of varying concentrations of acinetodin, klebsidin and microcin J25; the last peptide being a known transcription inhibitor.

Figure 2 shows that – just as microsin J25 – both acinetodin and klebsidin inhibit transcript elongation by E. coli RNAp, with the inhibitor activity of klebsidin being comparable to that of microcin J25 and more active than the activity of acinetodin.

AFS Effect of inhibitors on enzymatic activity

1 RNAP activity at different inhibitor (acinetodin, klebsidin, and microscin J25) concentrations. Data were filtered by a 0.5 Hz low pass filter.

Figure 1 is reprinted with permission from ACS Chem. Bio., 2017, 12 (3), pp 814-824. Copyright 2018 American Chemical Society.

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