The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design

Rawson, Shaun; McPhillie, Martin J.; Johnson, Rachel M.; Fishwick, Colin W. G.; Muench, Stephen P.

doi:10.1107/s2059798317004077

Cited by 11 publications

(6 citation statements)

References 64 publications

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“…This is especially important for proteins isolated from scarce sources such as patient tissue [ 93 ], or from pathogens which are difficult or dangerous to cultivate [ 94 ]. In this respect, cryo-EM also opens new possibilities in obtaining structural information of cyt bc complexes to develop novel human medications as well as agrochemicals [ 95–98 ].…”

Section: Inhibitors Bound At Q O or Q I ...mentioning

confidence: 99%

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy

Kao

Hunte

2022

Biochemical Society Transactions

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Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.

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Section: Inhibitors Bound At Q O or Q I ...mentioning

confidence: 99%

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy

Kao

Hunte

2022

Biochemical Society Transactions

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“…Higher resolution has been achieved in the case of - 50 which reportedly resolved not only the bound inhibitor but also co-ordinating waters. The ability to resolve inhibitor density and see how compounds interact with their target protein, means that EM has the potential to be used as a tool in SBDD 48,51 . Because of this improvement in resolution, it is now feasible that EM can play a role in elucidating structural information for parasitic proteins which have so far evaded structural characterisation.…”

Section: Resurgence In Electron Microscopymentioning

confidence: 99%

The Growing Role of Electron Microscopy in Anti-parasitic Drug Discovery

Johnson

Rawson

McPhillie

et al. 2019

CMC

Self Cite

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Parasitic diseases are a huge burden on human health causing significant morbidity and mortality. However, parasitic structure based drug discovery programmes have been hindered by a lack of high resolution structural information from parasitic derived proteins and have largely relied upon homology models from mammalian systems. The recent renaissance in electron microscopy (EM) has caused a dramatic rise in the number of structures being determined at high resolution and subsequently enabled it to be thought of as a tool in drug discovery. In this review, we discuss the challenges associated with the structural determination of parasitic proteins. We then discuss the reasons behind the resurgence in EM, how it may overcome some of these challenges and provide examples of EM derived parasitic protein structures. Finally, we discuss the challenges which EM needs to overcome before it is used as a mainstream technique in parasitic drug discovery.

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“…The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from the company ‘FEI’ ( https://www.fei.com/life-sciences/structural-biology/ ) have an overwhelming lead in terms of usage.” A review of the potential uses, and challenges facing single-particle electron microscopy as a tool for structure-based inhibitor design is described in [ 24 ].…”

Section: Technologies and Instrumentationmentioning

confidence: 99%

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

Helliwell

2017

Bioscience Reports

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Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

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The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design

Cited by 11 publications

References 64 publications

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy

Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy

The Growing Role of Electron Microscopy in Anti-parasitic Drug Discovery

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

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