An outlook on using serial femtosecond crystallography in drug discovery

ABSTRACT

Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process.

Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided.

Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.

KEYWORDS:

• X-ray Free Electron Laser (XFEL)
• Serial Femtosecond Crystallography (SFX)
• structure based drug discovery (SBDD)
• membrane protein
• Lipidic Cubic Phase (LCP)
• G Protein Coupled Receptor (GPCR)

Article highlights

• Over the last three decades, X-ray crystallography has contributed profoundly to successes in rational drug discovery; however, many important drug targets are not amenable to traditional SBDD approaches.

• The recent emergence of XFELs brings the promise of revolutionizing structural biology and accelerating SBDD applications through overcoming radiation damage and providing access to difficult-to-crystallize proteins, room temperature structures, and protein dynamics.

• Five hard XFEL facilities are currently available for users worldwide: LCLS in the USA, SACLA in Japan, EuXFEL in Germany, PAL-XFEL in South Korea, SwissFEL in Switzerland. Several new sources are on the way: LCLS II HE in the USA, SHINE in China.

• Data at XFEL sources are collected following the ‘diffraction-before-destruction’ principle implemented as an SFX approach that required the development of new instrumentation for crystal delivery and data acquisition, crystal preparation technologies, and data processing software.

• SFX technology has quickly matured and started to show high efficiency in the structure determination of various important drug targets, such as GPCRs, channels, enzymes, ribosomes, riboswitches, toxins, and viruses. Time-resolved SFX has been established using pump-probe and mix-and-inject approaches.

• Applications of SFX in SBDD will be contingent on further developments focused on the automation of sample preparation and delivery, optimization of data collection efficiency, and the expansion of available XFEL beam time.

This box summarizes the key points contained in the article.

Declaration of interest

All authors are supported by the non-profit academic-industrial GPCR consortium, the Russian Science Foundation, the Russian Foundation for Basic Research, and the Ministry of Science and Higher Education of the Russian Federation. V Cherezov also has received grant support from the National Institutes of General Medical Sciences and the National Institute on Drug Abuse. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Reviewer Disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This manuscript was supported by grants 18-02-40020 (A.M., A.G., A.L.,V.B.) and 18-54-00030 (E.M.) from the Russian Foundation for Basic Research (RFBR) and R35 GM127086 (V.C.) from the National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS).