Overcome Costly Hit-Finding Challenges Using an Integrated Platform

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Thomas Meins, global head of protein production, HitS Unit, WuXi AppTec.

Meins reflected that WuXi AppTec established the HitS Unit 15 years ago to facilitate drug discovery for protein biologics. Today, the unit provides a rapid and cost-effective platform for protein generation, screening, biophysical and biochemical analysis, structural determination, and “hit” confirmation. As of July 2022, the unit has produced assays for more than 1,500 recombinant proteins, including multisubunit complexes, DNA- and RNA-modifying proteins, and membrane proteins. Around 1,200 have been produced at assay grade and verified for biophysical methods. More than 150 crystallization-grade proteins are available for structural analysis.

The HitS production process comprises steps for construct design, cloning and expression studies, purification evaluation, and quality control (QC) assessment. Protein engineering is tailored to the needs of subsequent screening — e.g., if a protein must be tagged or produced using a specific QC standard. Assay-grade proteins can be expressed using microbial, insect, or mammalian cell lines, and regardless of host, production activities typically can be performed in four to eight weeks.

What distinguishes the HitS production process from that of other companies, Meins explained, is its early application of biophysical and biochemical analytical methods. The goal at this stage is to determine whether a candidate is stable and of high enough quality to advance to FBDD/DEL screening. That requires comprehensive QC assessment, including evaluation of assay conditions. For instance, the HitS team performs buffer optimization to identify suitable parameters for a given protein. Detailed reports are generated to evaluate a protein’s homogeneity in culture, postseparation purity, and so on. Collecting high-confidence data across early activities, Meins noted, helps to ensure that a candidate protein exhibits the requisite quality attributes.

HitS customers can select between fragment-based drug discovery (FBDD) and DNA-encoded libraries (DELs) for protein screening. The former can be performed using WuXi AppTec’s library of ~3,100 fragments and/or a customer-supplied library. Available methods include microscale thermophoresis (MST), surface plasmon resonance (SPR), and TRIC data analytics. Those can be used, for instance, to measure protein binding characteristics. After FBDD, “hits” can advance to biophysical evaluation, in which methods such as nuclear magnetic resonance (NMR) and X-ray crystallography are used to confirm or dismiss earlier findings. All such methods are performed with high-throughput instruments to accelerate the workflow.

Sponsors that choose the DEL screening pathway can leverage one of three service options. The DELpro solution provides access to a library of >41 billion compounds, and it comes with customized data analysis and reporting, including a compound recommendation. The DELlight package offers >10.8 billion compounds, and results are presented in a generalized report. WuXi AppTec also has developed open-access library for academic researchers, which grants free access to >4.2 billion compounds. As with FBDD, DEL hits advance to biophysical evaluation.

Meins highlighted that his company has developed “ready-to-go” assays based on a wide range of targets. Drug developers can leverage such assays for focused screening activities — e.g., to determine whether a chemical entity binds with a given protein. Four orthogonal methods are available, and results are generated within two to three weeks.

The HitS program provides comprehensive capabilities for structural characterization by X-ray crystallography, including production of crystallization-grade proteins, assay development and optimization, and data collection and refinement. Three service offerings are available: the Xpress option, which features access to 150 off-the-shelf targets and generates results within four to six weeks; the Xpedite solution, which reproduces previously published structures within four months; and the Xpert offering, which elucidates unpublished structures. That option requires at least four months. Meins added that WuXi AppTec also can perform NMR and now cryogenic electron microscopy (cryo-EM) to characterize protein and ligand structures.

Meins concluded by noting that the HitS platform is designed for customizability. It features several entry and exit points to ensure that sponsors receive support for what activities they want. Customers also are empowered at several stages to use their own materials and resources, such as internal DELs.

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