Rapid-access, high-throughput synchrotron crystallography for drug discovery

doi:10.1016/j.tips.2012.03.009

Trends in Pharmacological Sciences

Volume 33, Issue 5, May 2012, Pages 261-267

https://doi.org/10.1016/j.tips.2012.03.009 Get rights and content

Synchrotron X-ray sources provide the highest quality crystallographic data for structure-guided drug design. In general, industrial utilization of such sources has been intermittent and occasionally limited. The Lilly Research Laboratories Collaborative Access Team (LRL-CAT) beamline provides a unique alternative to traditional synchrotron use by pharmaceutical and biotechnology companies. Crystallographic experiments at LRL-CAT and the results therefrom are integrated directly into the drug discovery process, permitting structural data, including screening of fragment libraries, to be routinely and rapidly used on a daily basis as part of pharmaceutical lead discovery and optimization. Here we describe how LRL-CAT acquires and disseminates the results from protein crystallography to maximize their impact on the development of new potential medicines.

Section snippets

The challenge

Pharmaceutical and biotechnology companies are currently facing enormous pressure to improve research and development productivity. This pressure reflects rapidly declining revenues due to loss of patent exclusivity and other pricing constraints, and historic lows in the number of annual approvals of new chemical and biological entities [1]. Recent estimates suggest that ∼30% of the attrition in drug discovery and development can be attributed to toxicity detected during preclinical animal

The infrastructure

The past decade has seen dramatic advances in the infrastructure available for structural guidance of drug discovery. Rapid crystallographic data collection from small samples (∼10–100 μm for the longest dimension) is now routinely available at an ever-growing number of third-generation synchrotron sources (BioSync: A structural biologist's guide to high energy data collection facilities; http://biosync.sbkb.org/). These sources exploit insertion devices to provide very small, intense and highly

Towards fully-integrated structure-guided drug discovery

At Lilly Research Laboratories (LRL), we are focused on using structure to improve the prospects of discovering molecules that engage the target with minimal binding to other, off-target proteins. Making this happen has entailed improving the odds of success for challenging de novo structure determinations and increasing the speed with which we can characterize target–ligand interactions in three dimensions. Using our proprietary LRL-Collaborative Access Team X-ray beamline (LRL-CAT), located

The what

Accomplishing this end involved:

1.
Minimizing upstream efforts in sample preparation by enabling data collection from the smallest possible crystals that exhibit acceptable diffracting power;
2.
Providing near-immediate access to the synchrotron;
3.
Sharing information regarding sample provenance between the laboratory creating the sample and the beamline;
4.
Streamlining crystal handling and mounting at the beamline;
5.
Minimizing the need for redundant data collection from replicate samples;
6.
Maximizing the

The how

Traditional modes of synchrotron utilization are not compatible with a requirement that structural data be available within days of compound synthesis or biochemical assay. Even so-called rapid access mechanisms at synchrotron sources take far too long for the lead discovery and optimization process, which ideally has a cycle time (compound design, chemical synthesis, characterization and molecular redesign) of no more than a few weeks. Figure 1 shows the structural biology process for drug

Minibeams for integral membrane proteins

Structure-based drug discovery for integral membrane proteins, including G protein-coupled receptors, is fast becoming a reality [27]. Crystals of these challenging targets tend to be quite small (<10 μm for the longest dimension), generally smaller than those produced with soluble proteins. Data quality for these systems can be improved by matching the size of the incident X-ray beam to that of the sample. Decreased beam sizes reduce the background coming from X-rays scattered by parts of the

Future X-ray beamline access limitations

During the early to mid 1990s, synchrotron access for protein crystallography was the exception, not the rule as it is today. Worldwide, there are currently more than 130 synchrotron endstations for macromolecular crystallography (http://biosync.sbkb.org). These facilities offer more than sufficient capacity to meet the needs of both academia and industry. However, most such beamlines are funded and often owned and operated by governmental agencies that are now facing or soon will face

Concluding remarks

The benefits that accrue from intensive use of high-resolution structures of protein–ligand complexes in the drug discovery process are clear. At Lilly, structural biology is now used for approximately half of the discovery portfolio. We expect that the impact of synchrotron crystallography will become even more significant as discovery targets become more challenging and the innovation imperative becomes more pressing.

Acknowledgement

We thank the members of the Lilly structural biology and chemistry design teams for their constructive feedback on LRL-CAT operations. Use of the Advanced Photon Source is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-06CH11357.

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Trends in Pharmacological Sciences

ReviewRapid-access, high-throughput synchrotron crystallography for drug discovery

Section snippets

The challenge

The infrastructure

Towards fully-integrated structure-guided drug discovery

The what

The how

Minibeams for integral membrane proteins

Future X-ray beamline access limitations

Concluding remarks

Acknowledgement

Drug Discov. Today

Curr. Opin. Struct. Biol.

Trends Biochem. Sci.

Curr. Opin. Pharmacol.

Mol. Cell

Nucl. Instrum. Methods Phys. Res. A

Lessons from 60 years of pharmaceutical innovation

Nat. Rev. Drug Discov.

Can the pharmaceutical industry reduce attrition rates?

Nat. Rev. Drug Discov.

High-throughput crystallography for lead discovery in drug design

Nat. Rev. Drug Discov.

Structural biology and drug discovery

Curr. Pharm. Des.

High-throughput crystallographic data collection at synchrotrons

Synchrotron radiation

Sci. Am.

An Introduction to Synchrotron Radiation

Determination of macromolecular structures from anomalous diffraction of synchrotron radiation

Science

Biomolecular interaction analysis in drug discovery using surface plasmon resonance technology

Curr. Pharm. Des.

CATS: a cryogenic automated transfer system installed on the beamline FIP at ESRF

J. Appl. Crystallogr.

Automation of sample mounting for macromolecular crystallograhy

Acta Crystallogr.

The finer things in X-ray diffraction data collection

Acta Crystallogr.

Processing diffraction data with Mosflm

Know your dose: RADDOSE

Acta Crystallogr.

Review
Rapid-access, high-throughput synchrotron crystallography for drug discovery