An Introduction to Fragment-Based Drug Discovery (FBDD)

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In this minireview, Dr. Romyr Dominique introduces three key concepts in fragment-based drug discovery and shares his favorite articles and resources on fragment-based drug discovery. Fragment-based drug discovery has emerged as a key tool for acquiring starting points for challenging targets like KRAS.

What is FBDD, or Fragment-Based Drug Discovery?

Although fragment-based drug discovery (FBDD) was first coined in the early 2000s, the concept of using small fragments to probe drug targets was discussed as early as 1994 (“needle screening”). Fragment-based lead discovery involves the screening of compounds that are deliberately selected to have a low atom-count (12-14 heavy atoms) in order to increase the probability of identifying a binding event. In this introduction to fragment-based drug discovery, we:

Summarize why fragment-based drug discovery is useful
Discuss what makes a good fragment starting point
Highlight methods for screening and evaluating chemical fragments
Provide a reading list of reviews and resources for more in-depth reading on FBDD

Why is Fragment-Based Drug Discovery Useful?

Chemical space is humungous - the number of possible compounds with MW of about 500 has been estimated to be around 10⁶⁰ range. Even the large compound libraries used in industry contain only 10^5-6 molecules. Though new technologies like DEL and macrocyclic peptide screening may expand library sizes by a few orders of magnitude (in reaction-restricted property space), this still amounts to miniscule coverage of potential chemical space.

Starting with a small fragment (12-14 heavy atoms) considerably reduces the size of possible molecules, allowing a fragment library screen containing only 5000 fragments to provide broader coverage of possible chemical and property space to assess the druggability of a new target. While initial hits are typically weak (high micromolar to millimolar in binding affinity), fragment-based hit generation is typically paired with methods like structure-based design or parallel synthesis to rapidly and rationally generate more potent lead molecules.

Over the years FBDD has gained considerable attention among drug hunters and is now widely viewed as a reliable method to discover starting points that can be optimized to clinical candidates. There are now over 50 molecules in clinical trials and 6 FDA-approved drugs that have originated from a fragment screen (ex: vemurafenib, venetoclax, pexidartinib, erdafitinib, sotorasib, asciminib)

What Makes a Good Chemical Fragment?

There are three main features that make a good fragment. They are:

Confirmed binding to a target by multiple orthogonal methods
A binding mode that is amenable to further potency optimization
High ligand efficiency

Most fragment-based discovery campaigns will not proceed unless the first two conditions are met. Once fragments are confirmed to bind to a target with a binding mode that appears to be optimizable (e.g. not on a shallow surface groove), fragments can be prioritized based on metrics like ligand efficiency.

What is Fragment Ligand Efficiency?

Ligand efficiency is a metric that developed alongside FBDD and is often associated with FBDD. Ligand efficiency was developed as an intuitive way to help prioritize small fragment hits, HTS hits, as well as clinical candidates without unfairly biasing compound selection towards larger molecules. Ligand efficiency, which is defined as the binding efficiency for a ligand divided by the number of heavy atoms (HA), allows the medicinal chemist to “detect” potentially important atoms or potency drivers even though all of the fragments may be inherently weak binders.

If adding a single atom results in a 10-fold improvement in potency, this is way more efficient than adding a large phenyl group to gain the same 10-fold in potency. The introduction of the single atom is also much more likely to be due to a single important binding interaction. Building off of a more efficient starting point gives the medicinal chemist more leeway during optimization – when starting with a fragment that is more potency for its size, more can be added to the molecule before it reaches a size where properties such as metabolic stability and solubility can become truly challenging to deal with.

While triaging hits, sometimes it is more convenient to simply use a “rule-of-thumb” for ligand efficiency (pIC50/#HA). This “rule-of-thumb” is easier to quickly calculate and offers the same conceptual scorecard for molecules that offer more “bang for your buck.” Similar concepts such as ligand lipophilic efficiency can help prioritize fragments as well due to the importance of LogD in lead optimization and appear in the reading list below.

How Are Chemical Fragment Libraries Screened and How Are Fragments Evaluated?

Because of the weakly-binding nature of fragments, FBDD requires very sensitive biophysical methods, with the most popular nowadays being SPR, NMR, and X-ray co-crystallization. Though FBDD was originally conducted in elegant studies using NMR and 15N-labeled protein, SPR is an increasingly preferred method due to its often simpler execution and throughput.

Most campaigns will still use multiple orthogonal detection methods, even if screening is done by SPR, to help triage the hits and identify the “real” hits from the inevitable false positives. For difficult targets, lowering the threshold for what counts as a “hit” can result in several months of characterizing only false positives. It is normal for a true positive to have a potency in the high micromolar range or even millimolar range, but who would not rather start with a well-validated hit with weak affinity over a nanomolar hit that is a false positive?

One challenge for starting with weakly-binding starting points is that it can be difficult to conduct SAR when small changes or small losses in potency essentially put binding affinity outside the limit of detection. It can be hard to tell what SAR is meaningful when even a 3-fold drop in potency would return the same value as a 100-fold drop (no binding detected!). However, for a fragment with confirmed binding to the target in a tractable binding pocket, it is not uncommon to make huge leaps in potency (100-1000x+) through small (even single atom changes) such as a chlorine or methyl addition.

Final Thoughts on the History and Future of Fragment-Based Drug Discovery

Industry drug hunters have had a profound impact in developing FBDD, most notably at companies such as Abbott (original implementation of SAR by NMR) and the discovery of venetoclax, Astex with the discovery of erdatifinib and Sunesis (origin of tethering-based fragment screening). The future of FBDD is even brighter, with emerging technologies like fragment screens in cells and covalent fragments.

We hope this brief introduction was helpful, and below are some recommended resources for further reading.

Reading List of Some of the Best References and Resources on Fragment-Based Drug Discovery

Fragment-to-Lead Medicinal Chemistry Publications in 2020
Iwan J. P. de Esch,* Daniel A. Erlanson, Wolfgang Jahnke, Christopher N. Johnson, and Louise Walsh J. Med. Chem. 65, 84−99 (2022). https://doi.org/10.1021/acs.jmedchem.1c01803
Twenty years on: the impact of fragments on drug discovery. Erlanson, D., Fesik, S., Hubbard, R. et al. Nat Rev Drug Discov 15, 605–619 (2016). https://doi.org/10.1038/nrd.2016.109
Fragment screening to predict druggability (ligandability) and lead discovery success
Fredrik N.B. Edfeldt, Rutger H.A. Folmer and Alexander L. Breeze Drug Discovery Today 16, 284-287 (2011). https://doi.org/10.1016/j.drudis.2011.02.002
Molecular complexity and fragment-based drug discovery: ten years on. Andrew R Leach, Michael M Hann Current Opinion in Chemical Biology, 15, 489-496 (2011). https://doi.org/10.1016/j.cbpa.2011.05.008
The 'rule of three' for fragment-based drug discovery: where are we now?. Jhoti, H., Williams, G., Rees, D. et al. Nat Rev Drug Discov 12, 644-645. (2013). 10.1016/s1359-6446(03)02831-9
Drugging challenging targets using fragment-based approaches. Anthony G Coyne, Duncan E Scott and Chris Abell Current Opinion in Chemical Biology 14, 299-307. (2010) https://doi.org/10.1016/j.cbpa.2010.02.010
The influence of drug-like concepts on decision-making in medicinal chemistry. Leeson, P., Springthorpe, B. Nat Rev Drug Discov 6, 881–890 (2007). 10.1038/nrd2445
Validity of Ligand Efficiency Metrics. Christopher W. Murray, Daniel A. Erlanson, Andrew L. Hopkins, György M. Keserü, Paul D. Leeson, David C. Rees, Charles H. Reynolds, and Nicola J. Richmond. ACS Medicinal Chemistry Letters 6, 616-618 (2014). https://doi.org/10.1021/ml500146d
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity, James Tsai, John T. Lee, Weiru Wang et al. Proc Natl Acad Sci U S A 105,3041-3046 (2008). https://doi.org/10.1073/pnas.0711741105
http://practicalfragments.blogspot.com/ Excellent blog site edited by Dan Erlanson covering recent literature, conferences and interesting discussion topics about FBDD from 2008 to today