Questions and Answers

DELs are significant in drug discovery because they provide an efficient way to screen very large compound libraries for new druglike molecules.

DEL screening works by identifying molecules in the DEL that binds to a drug target. Vipergen uses a proprietary process, Binder Trap Enrichment, to do the binding in solution and avoid matrix effects that are often seen when solid phase binding is employed. In the newest version, the binding is performed in the inside of a living cell. The molecules binding to the target are identified by Next Generation Sequencing.

Yes, Vipergen has successfully identified molecular glue compounds from DELs.

Before screening, Vipergen performs a feasibility study to ensure that the target is expressed appropriately. In our experience, most cytoplasmic proteins, including membrane proteins accessible from the cytoplasm, can be screened in cells.

Most cytoplasmic proteins, including membrane proteins accessible from the cytoplasm, can be screened in cells. Vipergen has experience with several protein classes, including enzymes, protein-protein interaction targets, and many more.

Yes, Vipergen has successfully screened heteromultimers up to a size of 2.6 MDa in cells. In principle, there is no theoretical limit to the size or complexity of heteromultimer that can be screened in cells.

A small molecule drug is an organic compound with low molecular weight (typically <900 Daltons) that can regulate biological processes. They are often used as drugs because they can easily enter cells and interact with internal targets.

In 1997 Christopher Lipinski published a set of guidelines on how to make compounds with a high probability of being orally active. To do so Lipinski defined the infamous rule of 5, which sets out to balance solubility and permeability with the goal of dissolving the compound in the stomach or gut followed by traversing the cell membrane of the gut. Lipinski’s rule of 5 describes that the molecular mass should be 500 Da or less, have no more than 5 hydrogen-bond donors, no more than 10 hydrogen-bond acceptors and a logP value of 5 or less. As stated, the rule of 5 should not be considered rules, but only as guidelines. Small-pocket binding sites of proteins work well with these drugs of this size, but larger shallow binding pockets will most likely require larger drugs. Similarly CNS active drugs most often need to have a smaller polar surface area. 

Small molecules are designed or selected to interact with specific proteins, enzymes or pathways involved in disease. In small molecule drug discovery screening libraries, such as DNA encoded libraries, small molecules help identify promising candidates for further development into therapeutics.

Small molecule drugs can typically be taken orally as a pill. From here they are dissolved in the stomach before being taken up in the gut from where they enter the bloodstream. From the bloodstream they can cross cell membranes to reach intracellular targets. Small molecules are often easier and less expensive to manufacture compared to biologics like antibodies.

Small molecules are chemically synthesized and small enough to enter cells. Biologics are larger, protein-based therapies (e.g. antibodies) and usually act only on extra cellular targets such as cell surface receptors.

Through careful design and optimization typically through structure activity relationship (SAR) studies, small molecules are tailored to bind tightly and specifically to their target’s unique structure, minimizing effects on other proteins. 

A chemical library is a curated collection of diverse chemical compounds used in screening campaigns to discover new small molecule drugs targeting specific biological pathways.

Chemical libraries are built using combinatorial chemistry or curated selections of diverse structures, aiming to maximize chemical space coverage for better hit rates in screening.

A DEL library, or DNA-Encoded Library, is a collection of small molecules individually tagged with unique DNA sequences that act as molecular barcodes. These libraries can contain billions of compounds and are used to efficiently screen for molecules that bind to a specific biological target. DEL technology enables massively parallel screening in a single assay, making it a powerful tool in chemical library screening and small molecule drug discovery. Hits from DEL screening can reveal high-affinity binders to proteins, accelerating the path to novel therapeutics.

Diverse chemical libraries increase the likelihood of finding active small molecules that bind novel drug targets, which is crucial for identifying new treatment options.

High-throughput screening is a technique where thousands of compounds from a chemical library are rapidly tested against a biological target to find potential small molecule drug candidates.

A drug target is a specific molecule, typically a protein, in the body that is closely related to a particular disease process. Furthermore, the drug target should have the possibility to be influenced by a drug to produce a desired therapeutic outcome.

A drug target is typically identified by combining existing literature with genomics, proteomics, disease pathway analysis, and experimental validation. Combining these should lead to proteins essential for disease progression.

Small molecules typically bind to specific proteins (e.g. enzymes or receptors), either inhibiting or activating them, to correct biological imbalance or block disease processes.

A receptor is a protein on a cell’s surface or inside the cell that binds specific molecules. Small molecule drugs can mimic or block the receptor’s natural ligands, altering cell behavior. Unlike biologics such as antibodies, small molecules can interact with a receptor both extracellular and intracellular.

Many small molecules act by binding to an enzymes active site, hereby preventing it from catalyzing a chemical reaction that is critical for disease progression. Besides targeting active sites inhibitors can also be allosteric.

Traditionally, enzymes are inhibited with reversible inhibitors, which have a fast-on-fast-off type kinetics where both the association and dissociation are relatively fast. In the case of active-site inhibitors, these will be classified as competitive inhibitors where the inhibitor will bind at the same place as the substrate. Besides classical methods of inhibition today there have been a rise in the development of covalent inhibitors also referred to as suicide inhibitors.

An ideal small molecule drug target is central to disease pathology, has a defined and accessible binding site, and offers the potential for high selectivity to minimize side effects. Structural knowledge, such as X-ray crystallography or cryo-EM data, greatly aids drug discovery efforts. Crucial for a good drug target is a strong connection to disease progression, which should be supported by biochemical, genetic, and/or pharmacological data. Finally, the targets expression profile should be well understood to anticipate potential risks.

Typical drug targets for small molecule drugs includes enzymes (especially kinases), G-protein-coupled receptors (GPCRs), ion channels, transporters, as well as protein-protein interactions critical for diseases.

Kinases are enzymes that transfer phosphate groups from ATP to proteins, regulating critical processes including cell growth, division, and survival. In many diseases, particularly cancer and autoimmune disorders, kinase signaling becomes dysregulated, leading to uncontrolled cell behavior. Kinases are highly druggable using small molecule inhibitors because they have a well-defined ATP-binding pocket. Targeting kinases with small molecules can block overactive signaling, which can slow or stop disease progression. Many successful kinase inhibitors have been approved by FDA highlighting the therapeutic power of this strategy.

G-protein-coupled receptors (GPCRs) are a large family of cell surface proteins that transmit signals from outside the cell to the inside, affecting countless biological functions such as sensory perception, immune responses, and neurotransmission. About 30–40% of all approved drugs act on GPCRs, making them one of the most successful drug target classes. GPCRs are attractive for small molecule drug discovery because they are easily accessible on the cell surface, have well-understood ligand-binding pockets, and modulate critical disease pathways.

Novel modes of action refer to innovative ways that small molecule drugs influence biological systems beyond traditional inhibition. New strategies like targeted protein degradation, modulation of protein–protein interactions, and allosteric regulation are expanding therapeutic possibilities.

PROTACs (Proteolysis Targeting Chimeras) are bifunctional small molecules that recruit a target protein to an E3 ubiquitin ligase, leading to the protein’s degradation by the proteasome. This approach allows the elimination of disease-causing proteins rather than simply inhibiting their activity.

Traditional small molecule drugs block a protein’s function temporarily by binding to its active site. In contrast, PROTACs cause the permanent degradation of the target protein, potentially offering longer lasting and more complete therapeutic effects.

Molecular glues are small molecules that promote or stabilize interaction between two proteins that normally would not interact, often leading to degradation or functional modulation of a disease-related protein. They offer an elegant and highly selective mechanism for drug action.

While PROTACs are larger, bifunctional molecules with two binding domains, molecular glues are typically small, single-entity compounds that induce protein–protein interactions without the need for a linker. Molecular glues often result in simpler, more drug-like properties.

Targeted protein degradation, via PROTACs or molecular glues, enables the removal of previously “undruggable” proteins, such as scaffolding proteins or transcription factors. It offers therapeutic approaches for diseases where inhibition alone is insufficient.

One early example is thalidomide and its derivatives, which act as molecular glues by modifying the substrate specificity of the E3 ligase cereblon. This leads to degradation of disease-driving transcription factors in certain blood cancers.

Emerging technologies are exploring RNA-targeted degradation using small molecules, but currently, PROTAC and molecular glue strategies are primarily applied to protein targets. Research in this field is rapidly growing.

Challenges include optimizing pharmacokinetics, reducing molecule size for better bioavailability, and ensuring high selectivity to avoid degrading unintended proteins, which could cause toxicity.

DNA-encoded library screening enables rapid discovery of small molecules that can act as degraders or molecular glues by identifying binders to E3 ligases or other novel targets, accelerating the development of targeted protein degradation therapies. At Vipergen, we have successfully discovered molecular glues by direct screening in cells.

Allosteric modulators are small molecules that bind to a site on a protein different from the active site (an allosteric site) to enhance or inhibit the protein’s function. They can offer higher selectivity and fewer side effects compared to active-site inhibitors.

Covalent inhibitors form a permanent bond with their target protein, typically at a reactive amino acid. This irreversible binding can result in very potent, long-lasting drug effects, making them attractive for targeting enzymes and cancer-driving mutations.

Beyond targeted protein degradation, small molecule drugs are now being designed to induce proximity between proteins to trigger beneficial effects, such as activating enzymes, modifying epigenetic marks, or inducing signaling pathways selectively.

Non-traditional binding sites, such as allosteric sites, shallow pockets, or transient interaction surfaces, are key to developing drugs for “undruggable” targets. Advances in structural biology and DNA-encoded libraries help uncover these opportunities.