Protonated form: the potent form of potassium-competitive acid blockers

Abstract

Potassium-competitive acid blockers (P-CABs) are highly safe and active drugs targeting H+,K+-ATPase to cure acid-related gastric diseases. In this study, we for the first time investigate the interaction mechanism between the protonated form of P-CABs and human H+,K+-ATPase using homology modeling, molecular docking, molecular dynamics and binding free energy calculation methods. The results explain why P-CABs have higher activities with higher pKa values or at lower pH. With positive charge, the protonated forms of P-CABs have more competitive advantage to block potassium ion into luminal channel and to bind with H+,K+-ATPase via electrostatic interactions. The binding affinity of the protonated form is more favorable than that of the neutral P-CABs. In particular, Asp139 should be a very important binding site for the protonated form of P-CABs through hydrogen bonds and electrostatic interactions. These findings could promote the rational design of novel P-CABs.

Figure 1. Chemical structures of P-CABs with their protonated form.

Figure 2. Sequence alignment results between human H⁺,K⁺-ATPase and the template Na⁺,K⁺-ATPase (2ZXE).

The residues with identical, strong and weak similarities in H⁺,K⁺-ATPase are shown in dark blue, blue and light blue color background, respectively. The alpha helical, sheet and coil of secondary structure in the template are colored by pink, light purple and light green.

Figure 3. The human gastric H⁺,K⁺-ATPase model.

Figure 4. RMSDs for the backbone atoms of the complexes: (A) P-CABs; (B) protonated form of P-CABs.

Figure 5. Time evolutions of the distances between potassium ion (K1) and nitrogen atom of P-CABs (N15475 of SCH28080 or N15494 of TAK-438-1) (A).

The distances beyond 35 Å of TAK-438-1 are not shown in plot. The interaction modes of SCH28080 system at 0 ns (B) and 7.570 ns (C), and TAK-438-1 system at 0 ns (D) and 3.180 ns (E), with the potassium ion represented by blue ball.

Figure 6. RMSF of each residue in SCH28080 and TAK-438-1 complexes.

Figure 7. Interaction modes of P-CABs with H⁺,K⁺-ATPase.

(A) SCH28080; (B) SCH28080-1; (C) TAK-438; (D) TAK-438-1; (E) Soraprazan; (F) Soraprazan-1; (G) Revaprazan; (H) Revaprazan-1; (I) AZD0865; (J) AZD0865-1

Figure 8. The relationship between binding free energy and pIC₅₀ of P-CABs at different pH.

Figure 9. The comparison of energy decomposition for residues in binding sites of P-CABs.

(A) SCH28080 and SCH28080-1; (B) TAK-438 and TAK-438-1; (C) Soraprazan and Soraprazan-1; (D) Revaprazan and Revaprazan-1; (E) AZD0865 and AZD0865-1

Figure 10. Interaction modes of SCH28080 (A) and TAK-438-1 (B) with H⁺,K⁺-ATPase after 100 ns disassociation molecular dynamics.

Water molecules into the ion channel are shown in ball & stick model and the potassium ions near P-CABs are represented by blue ball.

Figure 11. The comparison of energy decomposition for residues in binding sites of SCH28080 and TAK-438-1 after 100 ns disassociation molecular dynamics.