Site-specific protein labeling in the pharmaceutical industry: experiences from novartis drug discovery

Construction of a CRISPR-Biolayer Interferometry Platform for Real-Time, Sensitive, and Specific DNA Detection

The clustered regularly interspaced short palindromic repeats (CRISPR) technology has been widely applied for nucleic acid detection because of its high specificity. By using the highly specific and irreversible bond between HaloTag and its alkane chlorine ligand, we modified dCas9 (deactivated CRISPR/Cas9) with biotin as a biosensor to detect nucleic acids. The CRISPR biosensor was facilely prepared to adequately maintain its DNA-recognition capability. Furthermore, by coupling biolayer interferometry (BLI) with the CRISPR biosensor, a real-time, sensitive, and rapid digital system called CRISPR-BLI was established for the detection of double-stranded DNA. The CRISPR biosensor immobilised on the biolayer could recruit the target DNA onto the biosensor surface and change its optical thickness, resulting in a shift in the interference pattern and responding signal of the BLI. The CRISPR-BLI system was further applied to detect the ALP gene of Escherichia coli DH5α combined with a polymerase chain reaction, which demonstrated a linear range from 20 to 20 000 pg and a low detection limit (1.34 pg). The CRISPR-BLI system is a promising approach for rapid and sensitive detection of target DNA analytes.

Establishment of inhibitor screening and validation system for tryptophanyl tRNA synthetase using surface plasmon resonance

With the increase in throughput and sensitivity, biophysical technology has become a major component of the early drug discovery phase. Surface plasmon resonance technology (SPR) is one of the most widely used biophysical technologies. It has the advantages of circumventing labeling, molecular weight limitations, and neglect of low affinity interactions, etc., and provides a robust platform for hit to lead discovery and optimization. Here, we successfully established a reliable and repeatable tryptophanyl tRNA synthetase (TrpRS) SPR high-throughput screening and validation system by optimizing the TrpRS tag, TrpRS immobilization methodology, and the buffer conditions. When TrpRS was immobilized on Streptavidin (SA) sensor chip, the substrate competitive inhibitor indolmycin exhibited the best binding affinity in HBS-P (10 mM HEPES, 150 mM NaCl, 0.05% surfactant P-20, pH 7.4), 1 mM ATP and MgCl₂, with a K_D (dissociation equilibrium constant) value of 0.6 ± 0.1 μM. The Z-factor values determined in the screening assays were all larger than 0.9. We hope that our proposed research ideas and methods may provide a scientific basis for establishing SPR analysis of other drug targets, accelerate the discovery and optimization of target lead compounds, and assist the clinical application of next-generation drugs.

Rapid no-wash labeling of PYP-tag proteins with reactive fluorogenic ligands affords stable fluorescent protein conjugates for long-term cell imaging studies

Covalent labeling systems that employ protein-tags or chemical probes to convert proteins into fluorescent conjugates are powerful tools for carrying out real time imaging and pulse-chase tracking studies that enable the spatiotemporal role of proteins in complex biological systems to be investigated. In this study, we have covalently modified a specific nucleophilic cysteine residue of the PYP-tag protein with weakly fluorescent α,β-unsaturated ketone (conjugate addition) and α-halomethyl ketone (SN2 reaction) acceptors to afford highly fluorescent PYP-tag-dimethylaminocoumarin (DMAC) conjugates, whose ligands are covalently bound to the PYP-protein through stable thioether linkers. A chloromethylketone derived DMAC-CMK reagent was found to afford the best kinetic and stability profile for labeling the PYP-tag in cellular systems, with in vitro studies demonstrating that PYP-DMAC-CMK conjugates exhibit excellent photostability and cellular stability profiles which enables them to be used for long-term protein imaging studies in cellular systems. The potential of using this no wash fluorescent labeling PYP-tag-DMAC system to visualise dividing cells undergoing mitosis and for imaging a PYP-tag fused telomere binding protein bound to chromatin in cell nuclei has been demonstrated.

Chemical Modification of Proteoglycanases with Biotin

Biotinylation is a versatile technique that has been used to label proteins for a variety of applications. Under alkaline conditions, the N-hydroxylsuccinimide (NHS) ester present on the biotinylation reagent reacts with primary amines such as the side chain of lysine residues or the N-termini of proteins to yield stable amide bonds. However, the effect of biotinylation on enzyme structure and function has not been generally appreciated. In this chapter, I describe specific issues involving biotinylation of proteoglycanases (e.g., ADAMTS-1, -4, and -5). Taking ADAMTS-5 as an example, I show how high incorporation of biotin molecules causes a decrease in aggrecanase activity, most likely by disrupting exosites present in the cysteine-rich and spacer domains. Such an effect is not evident when enzymatic activity is measured with synthetic peptides, since exosites are not strictly required for peptidolytic activity. Therefore, extreme care must be taken when labeling proteoglycanases and the appropriate enzyme/biotin ratio must be determined experimentally for each enzyme.

Photoactive yellow protein and its chemical probes: an approach to protein labelling in living cells

Labelling technologies developed over the past few years have changed the way of looking at biomolecules and have made a considerable contribution to our understanding of the functions and regulation of dynamic biological processes. One of the robust technologies employed to image proteins in a cellular environment is based on the use of chemical tags and their fluorescent probes, which provides flexibility in developing probes with a wide range of synthetic fluorophores. A variety of chemical tags, ranging from short amino acid sequences to small proteins, have been employed to generate protein-labelling systems. One such chemical tag is the photoactive yellow protein (PYP)-tag, which is a small bacterial protein, developed for the selective labelling and imaging of proteins. Herein, we briefly discuss the protein-labelling system developed based on PYP-tag technology, with a focus on the design strategy for PYP-tag labelling probes and their applications in protein imaging.

Screening for Inhibitors of Kinase Autophosphorylation

Autophosphorylation of kinases influences their conformational state and can also regulate enzymatic activity. Recently, this has become an area of interest for drug discovery. Using Alk2 as an example, we present two protocols - one based on phosphate-binding Alphascreen beads, the other on coupled luminescence measurements of ADP formation - that can be used to screen for inhibitors of autophosphorylation.

Tetrazole-Based Probes for Integrated Phenotypic Screening, Affinity-Based Proteome Profiling, and Sensitive Detection of a Cancer Biomarker

Target-identification phenotypic screening has been a powerful approach in drug discovery; however, it is hindered by difficulties in identifying the underlying cellular targets. To address this challenge, we have combined phenotypic screening of a fully functionalized small-molecule library with competitive affinity-based proteome profiling to map and functionally characterize the targets of screening hits. Using this approach, we identified ANXA2, PDIA3/4, FLAD1, and NOS2 as primary cellular targets of two bioactive molecules that inhibit cancer cell proliferation. We further demonstrated that a panel of probes can label and/or image annexin A2 (a cancer biomarker) from different cancer cell lines, thus providing opportunities for potential cancer diagnosis and therapy.