Small molecule microarray (SMM) is a well-established method for identifying small molecule (SM) binding interactions with a diverse range of target types. It has proven particularly successful at identifying novel RNA-binding small molecules (RBSM),1,2 which have been challenging to identify using other high-throughput screening (HTS) technologies. For these reasons SMM is enjoying a resurgence of interest from drug discovery groups. Despite other drug modalities being on the rise (e.g. ex vivo and in vivo base editing, immunotherapies, and antibody-drug conjugates), the comparatively simple synthesis and deliverability of small molecules has helped maintain their dominance (>90% market share) since the synthesis of aspirin more than a century ago.3 SMM is a well-validated technology with more than 152 published articles to date, consistently identifying novel protein and RNA-binding SM2,4,5 and therapeutic lead molecules such as KB-0742, a CDK9 inhibitor undergoing clinical trial.6,7 Today, SMM continues to be an attractive, accessible tool for SM hit identification, exploring target disease biology and ultimately identifying novel drug candidates.
What is SMM?
A SMM can be thought of as a miniaturised compound library-on-a-chip for highly efficient drug screening. Modern ultra-low-volume printing methods can rapidly produce hundreds of SMM chips with tens of thousands of compounds in a matter of days. These are stable and can be stored and used for testing against a broad range of target types. The SMM workflow follows an adapted microarray incubation protocol, as outlined in Figure 1. First, the glass chip surface
is functionalised (typically with an isocyanate coating) to be highly reactive to allow the immobilisation of a diverse range of SMs from a selected compound library. No library preparation is necessary, as SMM uses unmodified compounds directly from standard library formats and concentrations, typically 10 mM in 100 % DMSO. Through microarray printing, each SM in the library is covalently coupled to the chip surface as an individual spot in a spatially resolved microscopic 2D grid.
The SMM chip is then incubated with a target of interest, thereby screening for binding against the whole library in parallel. SMM is compatible with various target types including proteins, structural RNA, DNA and cell lysates. Binding interactions are identified through detection of target molecule fluorescence signal at a discrete spatial position on the microscopic grid. With advances in imaging technologies, data processing is streamlined, meaning hit identification can be completed and quantitative binding data can be generated rapidly.
Milestones in the Evolution of SMM
In 1999 Stuart Schreiber’s group, notably Gavin MacBeath and Angela Koehler, (Harvard University) published the first SMM article “Printing Small Molecules as Microarrays and Detecting Protein−Ligand Interactions en Masse”.8 They recognised the need to increase the throughput of bead-based chemical screens and leveraged the arraying techniques made popular by the DNA microarray boom. As an early developer of arrays for drug screening, in 2004 Matt Disney, then a postdoc with Peter Seebergers (ETH Zurich) created aminoglycoside arrays to study antibiotic resistance.9 Three years later in 2007 the Disney lab (University at Buffalo) would go on to publish the first study using SMM to identify RNA binders.10
