David A Winkler, Ira Katz, Andrew Warden, Aaron W Thornton, Géraldine Farjot
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Identifying medically relevant xenon protein targets by in silico screening of the structural proteome.
In a previous study, in silico screening of the binding of almost all proteins in the Protein Data Bank to each of the five noble gases xenon, krypton, argon, neon, and helium was reported. This massive and rich data set requires analysis to identify the gas-protein interactions that have the best binding strengths, those where the binding of the noble gas occurs at a site that can modulate the function of the protein, and where this modulation might generate clinically relevant effects. Here, we report a preliminary analysis of this data set using a rational, heuristic score based on binding strength and location. We report a partial prioritized list of xenon protein targets and describe how these data can be analyzed, using arginase and carbonic anhydrase as examples. Our aim is to make the scientific community aware of this massive, rich data set and how it can be analyzed to accelerate future discoveries of xenon-induced biological activity and, ultimately, the development of new "atomic" drugs.
期刊介绍:
Medical Gas Research is an open access journal which publishes basic, translational, and clinical research focusing on the neurobiology as well as multidisciplinary aspects of medical gas research and their applications to related disorders. The journal covers all areas of medical gas research, but also has several special sections. Authors can submit directly to these sections, whose peer-review process is overseen by our distinguished Section Editors: Inert gases - Edited by Xuejun Sun and Mark Coburn, Gasotransmitters - Edited by Atsunori Nakao and John Calvert, Oxygen and diving medicine - Edited by Daniel Rossignol and Ke Jian Liu, Anesthetic gases - Edited by Richard Applegate and Zhongcong Xie, Medical gas in other fields of biology - Edited by John Zhang. Medical gas is a large family including oxygen, hydrogen, carbon monoxide, carbon dioxide, nitrogen, xenon, hydrogen sulfide, nitrous oxide, carbon disulfide, argon, helium and other noble gases. These medical gases are used in multiple fields of clinical practice and basic science research including anesthesiology, hyperbaric oxygen medicine, diving medicine, internal medicine, emergency medicine, surgery, and many basic sciences disciplines such as physiology, pharmacology, biochemistry, microbiology and neurosciences. Due to the unique nature of medical gas practice, Medical Gas Research will serve as an information platform for educational and technological advances in the field of medical gas.