X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

Abstract

Introduction Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. Areas covered This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. Expert opinion X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.

Fluorine Pseudocontact Shifts Used for Characterizing the Protein–Ligand Interaction Mode in the Limit of NMR Intermediate Exchange

“…High-throughput screening normally identifies initial lead compounds with mircomolar affinities that are also central to fragment-based drug discovery.T he structure-guided optimization of lead compounds requires high-resolution complex crystal structures, [1] but their availability is often limited by the dynamic nature of the targets and/or the low aqueous solubility of the lead compounds.N MR spectroscopy is an alternative and fruitful approach to depict the protein-ligand interaction modes.The interactions between proteins and weak binders in the fastexchange regime are readily interrogated using NMR chemical shift perturbations, [2] the intermolecular nuclear Overhauser effect (NOE), [3] transferred pseudocontact shifts (PCSs), [4] or transferred paramagnetic relaxation enhancement (PRE). High-throughput screening normally identifies initial lead compounds with mircomolar affinities that are also central to fragment-based drug discovery.T he structure-guided optimization of lead compounds requires high-resolution complex crystal structures, [1] but their availability is often limited by the dynamic nature of the targets and/or the low aqueous solubility of the lead compounds.N MR spectroscopy is an alternative and fruitful approach to depict the protein-ligand interaction modes.The interactions between proteins and weak binders in the fastexchange regime are readily interrogated using NMR chemical shift perturbations, [2] the intermolecular nuclear Overhauser effect (NOE), [3] transferred pseudocontact shifts (PCSs), [4] or transferred paramagnetic relaxation enhancement (PRE).…”

“…Protein-ligand interaction modes are at the heart of the rational drug discovery campaign. High-throughput screening normally identifies initial lead compounds with mircomolar affinities that are also central to fragment-based drug discovery.T he structure-guided optimization of lead compounds requires high-resolution complex crystal structures, [1] but their availability is often limited by the dynamic nature of the targets and/or the low aqueous solubility of the lead compounds.N MR spectroscopy is an alternative and fruitful approach to depict the protein-ligand interaction modes.The interactions between proteins and weak binders in the fastexchange regime are readily interrogated using NMR chemical shift perturbations, [2] the intermolecular nuclear Overhauser effect (NOE), [3] transferred pseudocontact shifts (PCSs), [4] or transferred paramagnetic relaxation enhancement (PRE). [5] Fori nstance,t he 1 HP CSs were measured on the excess ligand in fast exchange between free and bound states and used as docking restraints.…”

The role of small-angle scattering in structure-based screening applications

“…On the other hand, the lengthy process involved in establishing crystallization conditions for novel proteins imposes a significant limitation on applicability of crystallographic methods, if these have not been found in previous available studies. This biases their application towards known and well-studied systems (Zheng et al, 2015), particularly in membrane-bound scenarios such as G-protein coupled receptors (Ranganathan et al, 2017). Given that transporters and membrane-bound receptors are critical to major cellular processes and thus highly attractive targets, crystallographic screening remains an important source of structural information.…”

Non-stoichiometric inhibition in integrated lead finding – a literature review

“…Of course, depending on the number of compounds, classical and well-established but lower-throughput methods such as ITC, [117] innovative label-free readouts such as microscale thermophoresis [118] or structural techniques such as NMR [119] and X-ray [120] can also provide the essential proof of interaction with the target.…”