Lead Generation: Methods, Strategies, and Case Studies

Lead generation refers to that point in drug discovery when initial screening hits against a target are wrought into compelling chemical matter. This chemical matter is often plagued with deficiencies in terms of potency, pharmacokinetics, or novelty, yet it provides a starting point for further optimization. This is the subject of a massive (800+ pages!) new two-volume work edited by Jörg Holenz (GlaxoSmithKline, formerly AstraZeneca) as part of Wiley’s Methods and Principles in Medicinal Chemistry series. Readers of this blog will not be surprised to find that fragments play a major role; indeed, the molecule on the cover of the book came out of FBLD. I won’t attempt to summarize all 25 chapters here, but will simply highlight those most relevant to FBLD.

Mike Hann (GlaxoSmithKline) sets the stage in chapter 1 by briefly describing the characteristics of successful leads. He emphasizes the importance of physicochemical properties and avoiding molecular obesity, and how judicious use of metrics can help navigate away from perilous chemical space. He also summarizes internal programs that again demonstrate that fragment-derived leads tend to be smaller and less lipophilic than those from other lead discovery techniques.

In chapter 3, Udo Bauer (AstraZeneca) and Alex Breeze (University of Leeds) discuss the concept of ligandability – the ability of a target to bind to a small molecule with high affinity. Fragments are ideally suited for assessing ligandability, and the researchers briefly describe fragment-based experimental and computational approaches to do so. They also include a nice 11-point summary of factors to consider when starting lead generation on a new target, ranging from the presence of small-molecule binding sites to the number of patent applications.

Chapter 6, by Ivan Efremov (Pfizer) and me, is entirely about fragment-based lead generation. I'm undoubtedly biased, but I think it provides a self-contained and fairly detailed guide to FBLD, including topics such as screening methods, hit validation, metrics, hit optimization, fragment growing vs fragment linking, and case studies on vemurafenib, BACE, MMP-2, LDHA, venetoclax, MCL-1, and GPCRs.

Helmut Buschmann and colleagues at RD&C Research, Development, and Consulting, focus in chapter 9 on optimizing side effects of known molecules to develop new drugs, but they also discuss some interesting older work reporting that 418 of 1386 drugs contain other drugs as internal fragments.

Chapter 12, by Dean Brown (AstraZeneca), is devoted to the hit-to-lead stage, and much of his advice is applicable to FBLD. Dean also includes a fantastic metaphor to illustrate the size of chemical space: "if a typical corporate screening collection were to fit on a postcard, the rest of the earth is the amount of available drug-like space." This assumes a million-compound library and a conservative estimate of 10²³ drug-sized molecules, so if anything it is an understatement.

Molecular recognition is critical for both FBLD and lead generation in general, and this is the topic Thorsten Nowak (C4X Discovery Holdings) tackles in chapter 13. He covers key areas such as thermodynamics, emphasizing the importance of enthalpy while acknowledging the difficulty of prospectively using thermodynamic data. The role of water and halogen bonds are covered, along with some freakishly high ligand efficiency values. There are a couple errors: one paper is categorized as using dynamic combinatorial chemistry when in fact it actually used static libraries, and Tethering is confused with Chemotype Evolution, but overall there's lots of good stuff here.

Biophysical methods are covered in chapter 14, by Stefan Geschwindner (AstraZeneca). These include NMR, SPR, ITC, thermal shift assays, native mass spectrometry, microscale thermophoresis, and more.

Chapter 16, by Ken Page and colleagues at AstraZeneca, discusses "lead quality." This often entails various metrics, from simple ones such as ligand efficiency and LLE to more complicated attempts to predict clinical dosages. Although it is easy to poke fun at metrics, most thoughtful scientists find them useful for making sense of the reams of data generated in lead optimization campaigns.

Chapter 17, by Steven Wesolowski and Dean Brown (both AstraZeneca), is arguably the most entertaining. Entitled "The strategies and politics of successful design, make, test, and analyze (DMTA) cycles in lead generation," it is replete with pithy quotes and even an original (and highly geeky) cartoon. Along with multiple examples, the chapter formulates plenty of questions to consider during lead optimization, and ends with a particularly relevant quote by Billings Learned Hand: “Life is made up of a series of judgments on insufficient data, and if we waited to run down all our doubts, it would flow past us.”

In chapter 23, Sven Ruf and colleagues at Sanofi-Aventis Deutschland describe a success story generating leads against cathepsin A, a target for cardiovascular disease. HTS yielded three different chemical series with sub-micromolar activities, each with different liabilities. Crystallography revealed their binding modes, and this allowed the team to mix and match fragments across the different series to generate a molecule that ultimately went into the clinic. Although this may not be classic FBLD, it does seem to be a good case of using concepts from the field, or fragment-assisted drug discovery.

A similar, if less directed, approach is the subject of chapter 25, the last in the book. Pravin Iyer and Manoranjan Panda (both AstraZeneca) describe "fragmentation enumeration," in which known drugs or clinical candidates are fragmented into component fragments and recombined. On some level the fragments themselves are likely to be privileged; the researchers cite the famous quote by Sir James Black that "the most fruitful basis of the discovery of a new drug is to start with an old drug." Most of the work is computational, although one molecule derived from the approach has encouraging cellular activity against Mycobacterium tuberculosis.

There's far more to this book than could be listed even in this relatively long post, including multiple case studies, so for those of you who are interested in lead generation definitely check it out!