1
|
Ayasse N, Berg P, Svendsen SL, Rousing AQ, Sørensen MV, Fedosova NU, Leipziger J. Trimethoprim inhibits renal H +-K +-ATPase in states of K + depletion. Am J Physiol Renal Physiol 2024; 326:F143-F151. [PMID: 37942538 DOI: 10.1152/ajprenal.00273.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/10/2023] Open
Abstract
There is growing consensus that under physiological conditions, collecting duct H+ secretion is independent of epithelial Na+ channel (ENaC) activity. We have recently shown that the direct ENaC inhibitor benzamil acutely impairs H+ excretion by blocking renal H+-K+-ATPase. However, the question remains whether inhibition of ENaC per se causes alterations in renal H+ excretion. To revisit this question, we studied the effect of the antibiotic trimethoprim (TMP), which is well known to cause K+ retention by direct ENaC inhibition. The acute effect of TMP (5 µg/g body wt) was assessed in bladder-catheterized mice, allowing real-time measurement of urinary pH, electrolyte, and acid excretion. Dietary K+ depletion was used to increase renal H+-K+-ATPase activity. In addition, the effect of TMP was investigated in vitro using pig gastric H+-K+-ATPase-enriched membrane vesicles. TMP acutely increased natriuresis and decreased kaliuresis, confirming its ENaC-inhibiting property. Under control diet conditions, TMP had no effect on urinary pH or acid excretion. Interestingly, K+ depletion unmasked an acute urine alkalizing effect of TMP. This finding was corroborated by in vitro experiments showing that TMP inhibits H+-K+-ATPase activity, albeit at much higher concentrations than benzamil. In conclusion, under control diet conditions, TMP inhibited ENaC function without changing urinary H+ excretion. This finding further supports the hypothesis that the inhibition of ENaC per se does not impair H+ excretion in the collecting duct. Moreover, TMP-induced urinary alkalization in animals fed a low-K+ diet highlights the importance of renal H+-K+-ATPase-mediated H+ secretion in states of K+ depletion.NEW & NOTEWORTHY The antibiotic trimethoprim (TMP) often mediates K+ retention and metabolic acidosis. We suggest a revision of the underlying mechanism that causes metabolic acidosis. Our results indicate that TMP-induced metabolic acidosis is secondary to epithelial Na+ channel-dependent K+ retention. Under control dietary conditions, TMP does not per se inhibit collecting duct H+ secretion. These findings add further argument against a physiologically relevant voltage-dependent mechanism of collecting duct H+ excretion.
Collapse
Affiliation(s)
- Niklas Ayasse
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
- Vth Department of Medicine, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Peder Berg
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Samuel L Svendsen
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | | | | | - Natalya U Fedosova
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Jens Leipziger
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| |
Collapse
|
2
|
Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A. Deep learning driven de novo drug design based on gastric proton pump structures. Commun Biol 2023; 6:956. [PMID: 37726448 PMCID: PMC10509173 DOI: 10.1038/s42003-023-05334-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023] Open
Abstract
Existing drugs often suffer in their effectiveness due to detrimental side effects, low binding affinity or pharmacokinetic problems. This may be overcome by the development of distinct compounds. Here, we exploit the rich structural basis of drug-bound gastric proton pump to develop compounds with strong inhibitory potency, employing a combinatorial approach utilizing deep generative models for de novo drug design with organic synthesis and cryo-EM structural analysis. Candidate compounds that satisfy pharmacophores defined in the drug-bound proton pump structures, were designed in silico utilizing our deep generative models, a workflow termed Deep Quartet. Several candidates were synthesized and screened according to their inhibition potencies in vitro, and their binding poses were in turn identified by cryo-EM. Structures reaching up to 2.10 Å resolution allowed us to evaluate and re-design compound structures, heralding the most potent compound in this study, DQ-18 (N-methyl-4-((2-(benzyloxy)-5-chlorobenzyl)oxy)benzylamine), which shows a Ki value of 47.6 nM. Further high-resolution cryo-EM analysis at 2.08 Å resolution unambiguously determined the DQ-18 binding pose. Our integrated approach offers a framework for structure-based de novo drug development based on the desired pharmacophores within the protein structure.
Collapse
Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Mami Ozako
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Miki Inukai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoe Matsuyuki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Shinnosuke Kitayama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Chisato Kanai
- INTAGE Healthcare, Inc., 3-5-7, Kawaramachi Chuo-ku, Osaka, 541-0048, Japan
| | - Chiaki Nagai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | | | - Christoph Gerle
- RIKEN SPring-8 Center, Kouto, Sayo-gun, Hyogo, 679-5148, Japan
| | - Hideki Shigematsu
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Nariyoshi Umekubo
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-0012, Japan.
| |
Collapse
|
3
|
Ayasse N, Berg P, Andersen JF, Svendsen SL, Sørensen MV, Fedosova NU, Lynch IJ, Wingo CS, Leipziger J. Benzamil-mediated urine alkalization is caused by the inhibition of H +-K +-ATPases. Am J Physiol Renal Physiol 2021; 320:F596-F607. [PMID: 33554781 DOI: 10.1152/ajprenal.00444.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epithelial Na+ channel (ENaC) blockers elicit acute and substantial increases of urinary pH. The underlying mechanism remains to be understood. Here, we evaluated if benzamil-induced urine alkalization is mediated by an acute reduction in H+ secretion via renal H+-K+-ATPases (HKAs). Experiments were performed in vivo on HKA double-knockout and wild-type mice. Alterations in dietary K+ intake were used to change renal HKA and ENaC activity. The acute effects of benzamil (0.2 µg/g body wt, sufficient to block ENaC) on urine flow rate and urinary electrolyte and acid excretion were monitored in anesthetized, bladder-catheterized animals. We observed that benzamil acutely increased urinary pH (ΔpH: 0.33 ± 0.07) and reduced NH4+ and titratable acid excretion and that these effects were distinctly enhanced in animals fed a low-K+ diet (ΔpH: 0.74 ± 0.12), a condition when ENaC activity is low. In contrast, benzamil did not affect urine acid excretion in animals kept on a high-K+ diet (i.e., during high ENaC activity). Thus, urine alkalization appeared completely uncoupled from ENaC function. The absence of benzamil-induced urinary alkalization in HKA double-knockout mice confirmed the direct involvement of these enzymes. The inhibitory effect of benzamil was also shown in vitro for the pig α1-isoform of HKA. These results suggest a revised explanation of the benzamil effect on renal acid-base excretion. Considering the conditions used here, we suggest that it is caused by a direct inhibition of HKAs in the collecting duct and not by inhibition of the ENaC function.NEW & NOTEWORTHY Bolus application of epithelial Na+ channel (EnaC) blockers causes marked and acute increases of urine pH. Here, we provide evidence that the underlying mechanism involves direct inhibition of the H+-K+ pump in the collecting duct. This could provide a fundamental revision of the previously assumed mechanism that suggested a key role of ENaC inhibition in this response.
Collapse
Affiliation(s)
- Niklas Ayasse
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Peder Berg
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | | | | | - Mads V Sørensen
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Natalya U Fedosova
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - I Jeanette Lynch
- Division of Nephrology, Hypertension and Renal Transplantation, University of Florida, Gainesville, Florida.,North Florida/South Georgia Veterans Health System, Gainesville, Florida
| | - Charles S Wingo
- Division of Nephrology, Hypertension and Renal Transplantation, University of Florida, Gainesville, Florida.,North Florida/South Georgia Veterans Health System, Gainesville, Florida
| | - Jens Leipziger
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| |
Collapse
|
4
|
Yamamoto K, Dubey V, Irie K, Nakanishi H, Khandelia H, Fujiyoshi Y, Abe K. A single K +-binding site in the crystal structure of the gastric proton pump. eLife 2019; 8:47701. [PMID: 31436534 PMCID: PMC6706254 DOI: 10.7554/elife.47701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
The gastric proton pump (H+,K+-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H+ and K+ coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K+ bound to the cation-binding site of the H+,K+-ATPase, indicating an exchange of 1H+/1K+ per hydrolysis of one ATP molecule. This fulfills the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K+ recognition is resolved and supported by molecular dynamics simulations, establishing how the H+,K+-ATPase overcomes the energetic challenge to generate an H+ gradient of more than a million-fold-one of the highest cation gradients known in mammalian tissue-across the membrane.
Collapse
Affiliation(s)
- Kenta Yamamoto
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Vikas Dubey
- Department of Physics, Chemistry and Pharmacy, PHYLIFE, University of Southern Denmark, Odense, Denmark
| | - Katsumasa Irie
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hanayo Nakanishi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Himanshu Khandelia
- Department of Physics, Chemistry and Pharmacy, PHYLIFE, University of Southern Denmark, Odense, Denmark
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,CeSPIA Inc, Tokyo, Japan
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
5
|
Abe K, Shimokawa J, Naito M, Munson K, Vagin O, Sachs G, Suzuki H, Tani K, Fujiyoshi Y. The cryo-EM structure of gastric H +,K +-ATPase with bound BYK99, a high-affinity member of K +-competitive, imidazo[1,2-a]pyridine inhibitors. Sci Rep 2017; 7:6632. [PMID: 28747707 PMCID: PMC5529566 DOI: 10.1038/s41598-017-06698-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/21/2017] [Indexed: 12/13/2022] Open
Abstract
The gastric proton pump H+,K+-ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K+-competitive acid blockers (P-CABs), have potential application as acid-suppressing drugs. We determined the electron crystallographic structure of H+,K+-ATPase at 6.5 Å resolution in the E2P state with bound BYK99, a potent P-CAB with a restricted ring structure. The BYK99 bound structure has an almost identical profile to that of a previously determined structure with bound SCH28080, the original P-CAB prototype, but is significantly different from the previously reported P-CAB-free form, illustrating a common conformational change is required for P-CAB binding. The shared conformational changes include a distinct movement of transmembrane helix 2 (M2), from its position in the previously reported P-CAB-free form, to a location proximal to the P-CAB binding site in the present BYK99-bound structure. Site-specific mutagenesis within M2 revealed that D137 and N138, which face the P-CAB binding site in our model, significantly affect the inhibition constant (Ki) of P-CABs. We also found that A335 is likely to be near the bridging nitrogen at the restricted ring structure of the BYK99 inhibitor. These provide clues to elucidate the binding site parameters and mechanism of P-CAB inhibition of gastric acid secretion.
Collapse
Affiliation(s)
- Kazuhiro Abe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan. .,Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan. .,Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Chiyoda, Tokyo, 100-0004, Japan.
| | - Jun Shimokawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Mao Naito
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.,Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan
| | | | | | | | - Hiroshi Suzuki
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, 10065, USA
| | - Kazutoshi Tani
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Chiyoda, Tokyo, 100-0004, Japan.,CeSPIA Inc., 2-1-1, Otemachi, Chiyoda, Tokyo, 100-0004, Japan
| |
Collapse
|