1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins

Abstract

Aquaporins and aquaglyceroporins (AQPs) are membrane channel proteins responsible for transport of water and for transport of glycerol in addition to water across the cell membrane, respectively. They are expressed throughout the human body and also in other forms of life. Inhibitors of human AQPs have been sought for therapeutic treatment for various medical conditions including hypertension, refractory edema, neurotoxic brain edema, and so forth. Conducting all-atom molecular dynamics simulations, we computed the binding affinity of acetazolamide to human AQP4 that agrees closely with in vitro experiments. Using this validated computational method, we found that 1,3-propanediol (PDO) binds deep inside the AQP4 channel to inhibit that particular aquaporin efficaciously. Furthermore, we used the same method to compute the affinities of PDO binding to four other AQPs and one aquaglyceroporin whose atomic coordinates are available from the protein data bank (PDB). For bovine AQP1, human AQP2, AQP4, AQP5, and Plasmodium falciparum PfAQP whose structures were resolved with high resolution, we obtained definitive predictions on the PDO dissociation constant. For human AQP1 whose PDB coordinates are less accurate, we estimated the dissociation constant with a rather large error bar. Taking into account the fact that PDO is generally recognized as safe by the US FDA, we predict that PDO can be an effective diuretic which directly modulates water flow through the protein channels. It should be free from the serious side effects associated with other diuretics that change the hydro-homeostasis indirectly by altering the osmotic gradients.

Keywords: aquaporin inhibitor; ligand-protein interaction; molecular dynamics.

Figure 1

PMF curves of bAQP1, AQP 1, 2, 5, and PfAQP. 1D PMF is shown in purple and 3D PMF in blue.

Figure 2

Fluctuations on the xy‐plane at the 1D–3D interface.

Figure 3

Illustration of binding means inhibition. Single file waters in the apo state versus water line interrupted by PDO in the holo state of the PDO‐AQP2 complex. Protein is represented as cartoons colored by residue types; PDO as licorices colored by atom names; and waters inside the channel and near the channel entry/exit as large spheres colored by atom names. Color schemes: hydrophilic, green; hydrophobic, white; negatively charged, red; positively charge, blue; hydrogen, white; oxygen, red; carbon, cyan (All molecular graphics in the article were rendered with VMD.59).

Figure 4

PDO at the binding site near the NPA motifs. (A) Protein in cartoons colored by residue types, ar/R selectivity filter Arg 187 and His 172 in large spheres colored by atom names, PDO and water in or near the channel in medium spheres colored by atom names. This panel shows PDO residing near the NPA motifs which is on the right‐hand side of the ar/R and where the two half membrane helices face each other. (B) Zoom‐in of PDO with near‐by residues (Ser 182 and Asn 184) and waters forming four hydrogen bonds (green dashed bars). (C) PDO (large spheres colored by atom names) in favorable (attractive) van der Waals contact with surrounding residues (licorices colored by atom names). Color schemes identical to Figure 3.