Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM.
Adamantane derivatives, such as amantadine and rimantadine, have been reported to block the transmembrane domain (TM) of the M2 protein of influenza A virus (A/M2) but their clinical use has been discontinued due to evolved resistance in humans. Although experiments and simulations have provided adequate information about the binding interaction of amantadine or rimantadine to the M2 protein, methods for predicting binding affinities of whole series of M2 inhibitors have so far been scarcely applied. Such methods could assist in the development of novel potent inhibitors that overcome A/M2 resistance. Here we show that alchemical free energy calculations of ligand binding using the Bennett acceptance ratio (BAR) method are valuable for determining the relative binding potency of A/M2 inhibitors of the aminoadamantane type covering a binding affinity range of only ∼2 kcal mol(-1). Their binding affinities measured by isothermal titration calorimetry (ITC) against the A/M2TM tetramer from the Udorn strain in its closed form at pH 8 were used as experimental probes. The binding constants of rimantadine enantiomers against M2TMUdorn were measured for the first time and found to be equal. Two series of alchemical free energy calculations were performed using 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids to mimic the membrane environment. A fair correlation was found for DPPC that was significantly improved using DMPC, which resembles more closely the DPC lipids used in the ITC experiments. This demonstrates that binding free energy calculations by the BAR approach can be used to predict relative binding affinities of aminoadamantane derivatives toward M2TM with good accuracy.
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece.
Harris
H
Ioannidis
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece.
Antonios
A
Drakopoulos
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece.
Christina
C
Tzitzoglaki
Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf, Germany.
Nadine
N
Homeyer
Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität , D-72076 Tübingen, Germany.
Felix
F
Kolarov
Biomedical Research Foundation, Academy of Athens , 11527 Athens, Greece.
Paraskevi
P
Gkeka
Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität , D-72076 Tübingen, Germany.
Kathrin
K
Freudenberger
Demokritos, National Center for Scientific Research , 15310 Athens, Greece.
Christos
C
Liolios
Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität , D-72076 Tübingen, Germany.
Günter
G
Gauglitz
Biomedical Research Foundation, Academy of Athens , 11527 Athens, Greece.
Zoe
Z
Cournia
Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf, Germany.
Holger
H
Gohlke
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens , 15771 Athens, Greece.
Antonios
A
Kolocouris
D000218:Adamantane / Q000737:chemistry* / Q000378:metabolism*; D000595:Amino Acid Sequence; D002151:Calorimetry; D002462:Cell Membrane / Q000378:metabolism*; D019277:Entropy; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072417:Protein Domains; D011522:Protons; D013237:Stereoisomerism; D013696:Temperature; D014763:Viral Matrix Proteins / Q000737:chemistry* / Q000378:metabolism*; D000086082:Viroporin Proteins
D000218:Adamantane; D011522:Protons; D014763:Viral Matrix Proteins; C488937:M2 protein, Influenza A virus; D000086082:Viroporin Proteins