Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

Gkeka, Paraskevi; Eleftheratos, Stelios; Kolocouris, Antonios; Cournia, Zoe

doi:10.1021/ct300899n

Cited by 46 publications

(108 citation statements)

References 63 publications

(108 reference statements)

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“…The angle between the pore axis or the normal of the membrane and C−N bond vector was ∼11°for 1 and close to 50°for 2-R, 2-S, and 3. These angle values suggest that the ammonium group of all aminoadamantane compounds is oriented toward the C-terminus, in consistency with previous experimental findings 6,7,9 and MD simulations 13,32,36 (Table S1). The distance between the adamantyl ring and the center of mass between the four A30 (Ad-A30) for 1−3 was measured ∼1 Å, and the distance CH 3 (lig.…”

Section: Acs Medicinal Chemistry Letterssupporting

confidence: 91%

Affinity of Rimantadine Enantiomers against Influenza A/M2 Protein Revisited

Drakopoulos

Tzitzoglaki

et al. 2017

ACS Med. Chem. Lett.

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Recent findings from solid state NMR (ssNMR) studies suggested that the (R)-enantiomer of rimantadine binds to the full M2 protein with higher affinity than the (S)-enantiomer. Intrigued by these findings, we applied functional assays, such as antiviral assay and electrophysiology (EP), to evaluate the binding affinity of rimantadine enantiomers to the M2 protein channel. Unexpectedly, no significant difference was found between the two enantiomers. Our experimental data based on the full M2 protein function were further supported by alchemical free energy calculations and isothermal titration calorimetry (ITC) allowing an evaluation of the binding affinity of rimantadine enantiomers to the M2TM pore. Both enantiomers have similar channel blockage, affinity, and antiviral potency.KEYWORDS: Rimantadine enantiomers, isothermal titration calorimetry, free energy perturbation, Bennett's acceptance ratio, electrophysiology, synthesis, antiviral assay, membrane protein, influenza M2 pore A mantadine (1) and rimantadine (2) (Scheme 1) are channel blockers of proton transit by the influenza virus M2 proton channel 1,2 and long used prophylactics and therapeutics against influenza A viruses. 3 The primary binding site of 1 and 2 is the lumen of the transmembrane domain of a tetrameric M2 protein (M2TM: amino acids 22−46) that forms the proton transit path. 4 Although 1 and 2 have been used as antivirals for decades, it was only after 2008 that high resolution structures from X-ray and ssNMR experiments unveiled the structures of M2TM in complex with 1 or 2. 5−9 According to these findings, the M2TM protein channel is blocked by 1 or 2 via a pore-binding mechanism. 6−10 The adamantane cage in 1 or 2, as well as in other aminoadamantane analogues, 11−13 is tightly contacted on all sides by V27 and A30 side chains, producing a steric occlusion of proton transit 6−9 and thereby preventing the viral replication. The ssNMR results for 2 also demonstrated that the ammonium group of the drug is pointing toward the four H37 residues at the C-terminus. 9 This orientation can be stabilized either through hydrogen bonds between the ammonium group of the aminoadamantane ligand and water molecules in the channel lumen which exist between the imidazoles of H37 and the ligand, 13 and/or with A30 carbonyls in the vicinity, 14 according to experimental 9,14−16 and MD simulations data. 13,17−22 Provided that M2TM is a minimal model for M2 binding, 10 these high resolution structures can be used for the development of new ligands which may bind more effectively to the M2TM pore.The effect of ligand's chirality in its binding with a chiral receptor is of outstanding significance and the characterization of protein−ligand interactions for each enantiomer separately may identify potential stereospecific binding interactions to the receptor. While rimantadine analogues are known antiviral drugs for more than four decades, the relative potency of rimantadine enantiomers has not been studied at the molecular level. The binding affinity...

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Section: Acs Medicinal Chemistry Letterssupporting

confidence: 91%

Affinity of Rimantadine Enantiomers against Influenza A/M2 Protein Revisited

Drakopoulos

Tzitzoglaki

et al. 2017

ACS Med. Chem. Lett.

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“…Particularly compelling in this regard are proton channels, such as the M2 proton channel of influenza A virus and Hv1, because waters represent the vehicle with which to achieve proton conduction (91)(92)(93)(94)(95)(96). Notably, in the case of M2, the drug amantadine and other hydrophobic scaffolds were shown to displace clusters of hydrogenbonded waters from main hydration sites (52,54).…”

Section: S1mentioning

confidence: 99%

“…In addition, positively charged fragment-like molecules, such as amantadine (44) and 2-guanidinobenzimidazole (2GBI) (30), are known to act as pore blockers of M2 and Hv1, respectively. Many groups, including ours, have successfully pursued drug discovery projects with M2 as a target (45)(46)(47)(48)(49)(50)(51)(52)(53). In particular, we have recently shown that scaffold replacement of hydrogen-bonded Significance Hv1, a voltage-gated proton channel, is an emerging pharmacological target implicated in many pathological conditions, including cancer and ischemic brain damage.…”

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confidence: 99%

On the role of water density fluctuations in the inhibition of a proton channel

Gianti

Delemotte

Klein

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.Hv1 | drug design | pore waters | binding site discovery | confined waters

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“…[7][8][9] An M2 fragment comprising only the transmembrane segment (M2TM, residues 22-46, Figure 1A, B) forms stable tetramers, which transport protons and bind the aminoadamantane drug Amt (1). [10][11][12][13][14] Hence, this M2 fragment has served as a model system [15][16][17] for drug binding. M2 is highly sensitive to environmental conditions, especially pH.…”

Section: Introductionmentioning

confidence: 99%

“…A subset of these compounds was also studied recently by rigorous free energy calculations for M2TM in the low pH, open state. 17 Here, we analyzed the binding properties of a similar set of compounds (Scheme 1) for M2TM Weybridge under high pH conditions, at which M2TM tetramers are stable, 10, 11 by MD simulations and free energy calculations with the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. 34 We validated the calculations by comparing energy contributions that are accessible by both MM-PBSA and isothermal titration calorimetry (ITC) experiments reported here on the binding of the aminoadamantane compounds.…”

Section: Introductionmentioning

confidence: 99%

Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations

Homeyer

Ioannidis

Kolarov

et al. 2016

J. Chem. Inf. Model.

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The development of novel anti-influenza drugs is of great importance because of the capability of influenza viruses to occasionally cross interspecies barriers and to rapidly mutate. One class of anti-influenza agents, aminoadamantanes, including the drugs amantadine and rimantadine now widely abandoned due to virus resistance, bind to and block the pore of the transmembrane domain of the M2 proton channel (M2TM) of influenza A. Here, we present one of the still rare studies that interprets thermodynamic profiles from isothermal titration calorimetry (ITC) experiments in terms of individual energy contributions to binding, calculated by the computationally inexpensive implicit solvent/implicit membrane molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach, for aminoadamantane compounds binding to M2TM of the avian "Weybridge" strain. For all eight pairs of aminoadamantane compounds considered, the trend of the predicted relative binding free energies and their individual components, effective binding energies and changes in the configurational entropy, agrees with experimental measures (ΔΔG, ΔΔH, TΔΔS) in 88, 88, and 50% of the cases. In addition, information yielded by the MM-PBSA approach about determinants of binding goes beyond that available in component quantities (ΔH, ΔS) from ITC measurements. We demonstrate how one can make use of such information to link thermodynamic profiles from ITC with structural causes on the ligand side and, ultimately, to guide decision making in lead optimization in a prospective manner, which results in an aminoadamantane derivative with improved binding affinity against M2TM(Weybridge).

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Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

Cited by 46 publications

References 63 publications

Affinity of Rimantadine Enantiomers against Influenza A/M2 Protein Revisited

Affinity of Rimantadine Enantiomers against Influenza A/M2 Protein Revisited

On the role of water density fluctuations in the inhibition of a proton channel

Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations

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