Methods for Identifying Ligand Binding Sites in Drug Discovery
Understanding how a small molecule ligand binds to its target is valuable in drug discovery, because it enables more efficient optimization through structure-based design, better mechanistic understanding of molecular pharmacology, and greater confidence in the therapeutic hypothesis from both safety and efficacy perspectives. Recently, Drug Hunter highlighted methods for target identification when the target is unknown. In this Drug Hunter Minireview, we catalog common methods used in industry to determine or predict a ligand’s binding site, while highlighting advantages, disadvantages, and case studies, including:
X-ray crystallography
cryogenic electron microscopy (cryo-EM)
competition assays
nuclear magnetic resonance (NMR)
covalent labeling
photoaffinity labeling
mutational analysis and site-directed mutagenesis
hydrogen/deuterium exchange (HDX) and chemical or proteolytic stability profiling
native mass spectrometry
computational approaches
Our list begins with techniques providing the highest confidence prediction with the greatest precision and resolution (e.g., X-ray crystallography), and continues toward the other end of the spectrum with economical alternatives (Figure 1). The techniques span a range of classes: biophysical; biochemical; chemical biology; and virtual. For simplicity, proteins are assumed to be the biological target throughout the review, although this may not always be the case.
About the Authors
Daniel Beck
Daniel is a staff medicinal chemist based at Purdue University. His work includes the design and synthesis of novel small molecule potential therapeutics and oversight of outsourced synthesis projects. Daniel earned both his B.S. in biochemistry and Ph.D. in medicinal chemistry from Purdue University in West Lafayette, Indiana, and then went on to postdoctoral studies in medicinal chemistry at The Scripps Research Institute in Jupiter, Florida. He next worked for drug development C.R.O.s for several years before beginning his current position.
More from Daniel →Karson Putt
Karson received his A.S. and B.S degrees from Purdue University and pursued his Ph.D. in biochemistry at the University of Illinois at Urbana-Champaign (UIUC), where he studied cell death pathways. After graduation, he created and was the director of UIUC’s first high-throughput screening facility. Karson then took a position with Johnson & Johnson, where he created another high-throughput screening facility at their Jacksonville site. Currently, he is the managing director of the Purdue University Institute for Drug Discovery. Karson has over 40 issued patents, founded several startup companies, participates as an advisor for multiple companies, and has helped discover and develop multiple drugs in human clinical trials.
More from Karson →About the Reviewers
Pablo Martín-Gago
Pablo is currently a Principal Scientist and the head of the Hit Discovery team at LEO Pharma, where he leads chemical biology and medicinal chemistry efforts to identify, validate and develop novel molecules for treating skin diseases. Pablo Martín-Gago completed his Ph.D. at the IRB Barcelona with Prof. A. Riera. After a research stay in the Fu Lab at Caltech, he joined the Max Planck Institute as a postdoc with Prof. H. Waldmann to develop inhibitors of the KRas-PDEδ interaction. After joining Copenhagen University as an assistant professor designing covalent probes for epigenetic targets, he moved to Lundbeck, where he worked on multiple hit-finding campaigns and early-stage drug discovery projects targeting CNS disorders.
More from Pablo →Ravi Kurumbail
Dr. Ravi Kurumbail, Ph.D. is an independent structural biology and biophysics consultant who works with early stage biotechs. Ravi is a consummate drug hunter with a deep passion for innovation. Dr. Kurumbail has had a distinguished career in the pharmaceutical industry with over twenty-five years of experience in structure-based drug design, lead identification and validation and biophysical and mechanistic studies. Through biophysical and structural studies coupled with elegant application of molecular biology techniques, Ravi and his team demonstrated molecular mechanism of action and specificity in over 20 drug discovery projects. Ravi was an active member of the COX-2 project team that discovered Celebrex™, Bextra™, Dynastat™ and Deramaxx™. He has contributed to the discovery of over a dozen clinical candidates. He has a comprehensive knowledge of three-dimensional structures of macromolecules critical for the discovery of drugs and vaccines. Ravi was one of the first crystallographers to solve a membrane-protein structure (COX-2) in the pharmaceutical industry. Dr. Kurumbail helped build a strong biophysics technology platform for validation of lead matter, hit triaging and for molecular mode of action studies. Ravi demonstrated strong scientific and personal leadership as an Executive Director in big Pharma, managing an industry-leading group of approximately 50 scientists and establishing cutting-edge technologies including cryo-EM. He has a strong track record in publications and scientific/technical reviews and is a passionate teacher who has contributed to the drug discovery course at the University of Massachusetts, Amherst for over 10 years.
More from Ravi →
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