Computational Studies on the Interactions of Inhalational Anesthetics with Proteins SATYAVANI VEMPARALA,* ,† CARMEN DOMENE, ‡ AND MICHAEL L. KLEIN § † The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai 600 113, India, ‡ Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ U.K., § Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323 RECEIVED ON MAY 13, 2009 CON SPECTUS D espite the widespread clinical use of anesthetics since the 19th century, a clear understanding of the mechanism of anesthetic action has yet to emerge. On the basis of early experiments by Meyer, Overton, and subsequent researchers, the cell’s lipid membrane was generally concluded to be the primary site of action of anes- thetics. However, later experiments with lipid-free globular proteins, such as luciferase and apoferritin, shifted the focus of anesthetic action to proteins. Recent experimen- tal studies, such as photoaffinity labeling and mutagenesis on membrane proteins, have suggested specific binding sites for anesthetic molecules, further strengthening the proteocentric view of anesthetic mechanism. With the increased availability of high-resolution crystal structures of ion channels and other integral membrane pro- teins, as well as the availability of powerful computers, the structure-function rela- tionship of anesthetic-protein interactions can now be investigated in atomic detail. In this Account, we review recent experiments and related computer simulation studies involving interactions of inhalational anesthetics and proteins, with a partic- ular focus on membrane proteins. Globular proteins have long been used as models for understanding the role of protein-anesthetic interactions and are accordingly examined in this Account. Using selected examples of membrane pro- teins, such as nicotinic acetyl choline receptor (nAChR) and potassium channels, we address the issues of anesthetic bind- ing pockets in proteins, the role of conformation in anesthetic effects, and the modulation of local as well as global dynamics of proteins by inhaled anesthetics. In the case of nicotinic receptors, inhalational anesthetic halothane binds to the hydro- phobic cavity close to the M2-M3 loop. This binding modulates the dynamics of the M2-M3 loop, which is implicated in allosterically transmitting the effects to the channel gate, thus altering the function of the protein. In potassium channels, anesthetic molecules preferentially potentiate the open conformation by quenching the motion of the aromatic residues impli- cated in the gating of the channel. These simulations suggest that low-affinity drugs (such as inhalational anesthetics) mod- ulate the protein function by influencing local as well as global dynamics of proteins. Because of intrinsic experimental limitations, computational approaches represent an important avenue for exploring the mode of action of anesthetics. Molecular dynamics simulationssa computational technique frequently used in the general study of proteinssoffer particular insight in the study of the interaction of inhalational anesthetics with membrane proteins. Introduction The molecular mechanism of general anesthetics (GA) has remained elusive despite the use of anes- thetics over 150 years. The nonspecific or lipid theory dominated the understanding of anesthe- sia for more than a century. 1 This theory was based on Meyer and Overton observations 2,3 which predicted that the potency of anesthetic molecules strongly correlates with their relative solubility in nonpolar solvents such as olive oil. Under this theory, anesthetic molecules were assumed to dissolve in the cell membrane, per- Vol. 43, No. 1 January 2010 103-110 ACCOUNTS OF CHEMICAL RESEARCH 103 Published on the Web 09/30/2009 www.pubs.acs.org/acr 10.1021/ar900149j © 2010 American Chemical Society