Fragment-based methods in drug discovery

FBLD generates a plethora of reviews, as evidenced by Practical Fragments’ annual round-ups (see for example 2014, 2013, and 2012). However, for the past three years there have been no new books. The drought has now ended, starting with the publication of Methods in Molecular Biology Volume 1289, edited by Anthony E. Klon of Pennsylvania Drug Discovery Institute. Computational chemistry is probably one of the most rapidly changing disciplines within FBLD, and thus it is appropriate that this is the primary focus.

The book is part of the Springer Protocols series, which offers highly specific step-by-step instructions. Many of the chapters have a common organization: Introduction, Materials, Methods, and Notes. While this can work well for established molecular biology techniques such as cloning, it can be trickier to apply to computational approaches. Some of the chapters are quite brief and assume extensive specialized knowledge, while others are extremely detailed. Of course, it is impossible to satisfy everyone; hopefully the following summary will help you find what is most useful for you.

Part I (Preparation) consists of five short chapters. The first is by Rachelle Bienstock, editor of the most recent (and also computationally intensive) book. As we’ve noted, water plays a pivotal role in protein-ligand interactions, and Rachelle concisely but thoroughly summarizes available computational methods. Chapter 2, by Yu Zhou and Niu Huang at the National Institute of Biological Sciences in Beijing, outlines how to use DOCK to assess binding site druggability. In chapter 3, Raed Khashan (King Faisal University, Saudi Arabia) describes a free software tool called FragVLib for generating virtual fragment libraries to compare different ligand binding pockets. Chapter 4, by Jennifer Ludington (formerly of Locus Pharmaceuticals), discusses practical issues in preparing a virtual fragment library, such as conformer and partial charge assignment. Finally, in chapter 5 Peter Kutchukian discusses how he and his Merck colleagues enlisted medicinal chemists to help fill the gaps in their fragment collection.

The second section is titled Simulation. In chapter 6, Kevin Teuscher and Haitao Ji (University of Utah) summarize “fragment hopping,” including an extensive table of available software tools. Chapter 7, by Olgun Guvench (University of New England), Alexander MacKerrel (University of Maryland), and coworkers describes SILCS: site identification by ligand competitive saturation. This program, developed by SilcsBio LLC, soaks proteins in virtual solutions containing very tiny fragments (think propane and methanol) to look for binding sites. Molecular dynamics simulations include methods to prevent aggregation of the ligands or denaturation of the protein.

Chapter 8, by Álvaro Cortés-Cabrera, Federico Gago (Universidad de Alcalá, Madrid) and Antonio Morreale (Repsol Technology Center, Madrid), describes how ligand efficiency indices can be used to guide fragment growing. Of course, metric skeptics will still ask, “sure it works in practice, but does it work in theory?” And in chapter 9, Jui-Chih Wang and Jung-Hsin Lin (Academia Sinica, Taipei) introduce a new scoring function for fragment-docking, including several pages of detailed instructions for implementing it in AutoDock. As we’ve noted, calculating binding affinities for fragments can be difficult, and the new function seems to be accurate to about ±2.1 kcal/mol for a series of compounds tested

Part III, Design, begins with another chapter by Rachelle Bienstock in which she outlines the process of fragment-based ligand design, highlighting various software tools available at each stage. This includes library design, growing, linking, and downstream considerations such as ADME. Chapter 11, by Zenon Konteatis of Agios, is a brief primer of the process, including an example for the kinase TGF-beta. The last chapter in this section, by Jennifer Ludington, focuses on binding site analysis to assess whether a protein site is druggable (or at least ligandable). She focuses on the procedure used at Locus Pharmaceuticals, which involved soaking a virtual protein in a solution containing fragments and then lowering the chemical potential of the system until only the tightest fragments remain bound. Clusters of probe fragments indicate possible hot spots.

Finally, Part IV consists of Case Studies, starting with a chapter on kinase inhibitors by Jon Erickson (Lilly). More than a third of FBLD-derived clinical candidates target kinases, so it is always good to have an updated overview, though there is at least one structural error.

The last two chapters are both by Frank Guarnieri, founder of Locus Pharmaceuticals and currently at Virginia Commonwealth University School of Medicine. These are highly opinionated (with lots of first-person singular pronouns) and fun to read. They both describe the simulated annealing of chemical potential (SACP) approach that formed the basis of Locus (and is also discussed by Jennifer Ludington above). Chapter 14 describes a small molecule erythropoietin (EPO) mimetic program. The protein EPO binds to and activates a dimeric receptor, and a small molecule functional mimetic would indeed be an exciting breakthrough. Unfortunately, the primary data presented are not compelling, and I remain unpersuaded, though perhaps readers are aware of more convincing evidence.

Chapter 15 describes the Locus program to develop a highly selective orally available p38 inhibitor. The discussion offers a rare window into life at a small biotech, including disagreements over strategies and interpretation of data. It now appears that p38 is probably not a good target for inflammation, which had unfortunate repercussions:

The business decision at Locus to put so many resources into this program along with other questionable business decisions resulted in the company going bankrupt after about 10 years in existence.

Some of the most important lessons are negative, and it’s nice to see these appear in print. Success stories are inspirational, but this chapter is a healthy reminder of the very many things that must succeed for fragment-based approaches to yield new drugs.