Submitted:
11 November 2025
Posted:
20 November 2025
Read the latest preprint version here
Abstract
Keywords:
Introduction
The Advantages of Affinity
- Faster to measurable cellular potency.
- 2.
- Achieve greater potency.
- 3.
- Accelerate the lead optimization process.
- 4.
- Optimize selectivity against closely related targets.
- 5.
- Embolden teams to pursue synthetically challenging compounds.
- 6.
- Explore diverse chemical space.
- 7.
- Avoid the “avoid-ome.”
Possible Objections to an Emphasis on Affinity
- No. I am not suggesting that we ignore other properties! I agree that many other complex properties contribute to achieving low dose effective medicines. However, intermolecular interactions drive biological consequences; understanding binding is fundamental. I am arguing that somewhat more emphasis should be placed on optimizing these interactions.
- I agree one must be mindful of the risk that a simple biochemical measurement will not capture important subtleties of the intermolecular environment in which the drug interacts with its target. However, empirical evidence shows there is a reasonable correlation between biochemical affinity and cellular potency; biochemical measurements generally provide valuable information.
- The process is highly inefficient. Even on late-stage projects, a significant percentage (typically one-third to two-thirds) of the compounds being made do not bind with sufficient affinity and selectivity to become drug candidates [16].
- The process is painfully slow. Teams will typically spend at least a year – and usually much longer -- optimizing their lead compounds [16].
- Most teams put significant effort only into a single lead series, increasing the risk of failure.
- Many teams fail to produce a development candidate, especially when working on challenging targets.
- Yes, improved affinity puts a greater emphasis on selectivity. If we can design for affinity, we can also design away from anti-targets.
- Yes, cellular potency will help achieve an effective low-dose medicine [Figure 1], and in most cases, greater affinity will help achieve greater cellular potency. Further, for agonists, being able to optimize the precise intermolecular interactions between ligand and target will help produce the desired pharmacological effects.
- As chemical biology techniques continue to evolve, it will become increasingly common for the target(s) of our drugs to be known.
- However, even where that is not the case, understanding the binding of our drugs to the “avoid-ome” [15] will enable faster and more certain candidate optimization.
- Often the best way to assess a target is with “tool” compounds, which complement information available from human genetics or knock-out or knock-down technologies. Such tool compounds must be reasonably potent, selective, and ideally possess DMPK properties suitable (not optimized) for dosing in a target animal. Shortening the time required to produce such tool compounds would dramatically improve the target validation process.
- Optimized affinity (coupled with maintaining excellent ADME properties) will enable a lower dose, reducing the chance of random off-target toxicities.
- Improved selectivity against neighboring “anti-targets” also reduces toxicological risk.
- Having multiple structurally distinct chemotypes increases the chance of project success because toxic effects seen in preclinical studies often differ between chemical series.
- Eliminating interactions with “avoid-ome” targets will further reduce toxicological risk and improve ADME.
- The field of proximity enhancement is progressing rapidly [17]. Such drugs share a common mechanistic trait: they form ternary complexes with two biomolecules. The analysis of such three-body systems is complex and counter-intuitive [18]. Understanding the mechanisms of protein degradation are equally challenging [19]. In such complex three-body systems, a deeper understanding of the relationship between the strength of the intermolecular interactions and the resulting pharmacology will guide the design of optimal compounds. This is also why advances in chemoproteomics [20] and biophysics [21] are so crucial.
- The binding of covalent compounds depend on molecular recognition to form the necessary reaction intermediates on a reasonable time scale. Further, the binding of slow off-rate reversible inhibitors generally involves protein conformational changes which depend on favorable intermolecular interactions between drug and protein.
- As with heterobifunctional drugs and glues, the analysis is highly complex. An agonist must first bind to its target with affinity sufficient to trigger the requisite conformational changes to achieve a pharmacological response. Understanding these intermolecular interactions enables design.
- While relatively rare, this is indeed a serious medical issue. Understanding the underlying mechanisms driving such events, and learning how to avoid them, is a challenging problem that is likely to continue to plague the field for several decades.
- Indirectly, a deeper understanding of affinity enables the generation of multiple diverse chemotypes which are unlikely to suffer from the same idiosyncratic effects. However, since idiosyncratic toxicity may not appear until late in clinical trials, the availability of multiple chemotypes at the research stage may not offer immediate relief. What will have a far greater impact will be the ability to identify the potential for idiosyncratic toxicology at the preclinical stage, assisted by a deeper understanding of the avoid-ome and the ability to predict the range of possible human metabolites with greater accuracy.
- Potency and selectivity are equally relevant to the design of biologics.
- For biologic drugs that form multimeric complexes (ADCs, bispecifics, and the like) understanding the intermolecular interactions will be equally challenging – and equally important – as in small molecule proximity enhancing medicines.
- The incorporation of non-standard amino acids and post-translational modifications (sugars, phosphates, sumoyl groups, and so forth) holds the potential to greatly increase the utility of many biologic agents. However, the intermolecular interactions of these non-standard moieties with macromolecular targets will need to be extensively studied so that we may understand their potency.
- Many targets remain “undruggable” because we lack a useful chemical starting point. If a target is “un-screenable” (meaning no suitable screen can be devised and executed) or “un-ligandable” (meaning a screen is possible but fails to produce useful chemical matter), that target is de facto “undruggable.”
- Even in cases with chemical matter, discerning the structure-function relationships of complex intracellular multi-component machines will remain daunting for some time.
- In cases without information about the target structure(s), we can view them as comparable to phenotypic programs, for which structural insights into avoid-ome targets should assist with compound optimization by preventing ADME and tox challenges.
- Finally, as the field of structural biology continues to mature, and as we further improve our ability to predict structures in silico, these complex multi-component systems will become tractable.
Discussion
- Exploring refers to sampling chemical space broadly. The operative questions are, “How much of chemical space have I explored?” and “How can I prioritize my exploration?” However, in the history of medicinal chemistry we have collectively sampled only a tiny fraction of the potential “drug space” – literally less than “a drop in the ocean.” Project teams often struggle to find multiple distinct lead series and have limited insights into how best to carry out a broader search of chemical space. Fortunately, our community appears to have overcome the destructive mindset that considered only a narrow spectrum of molecules to be “drug-like” based on arbitrarily defined “rules.” Teams are more adventurous now, and a deeper understanding of affinity helps to guide exploration.
- Fine-tuning refers to our ability to make more subtle changes to optimize the properties within a lead series. The relevant question while fine-tuning is, “What fraction of the molecules I’m making are good choices?” When we choose to make specific analogs within a given series, we are attempting to optimize multiple parameters simultaneously. We must admit that we are not very effective at fine-tuning. Many project teams never produce a drug candidate, and the teams that do succeed generally make thousands of compounds during a multi-year process to select one “winner.” A deeper understanding of affinity can dramatically improve the overall efficiency of the search process.
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