Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches

Żołek, Teresa; Kadam, Mayur; Nadkarni, Sharmin; Yasuda, Kaori; Chodyński, Michał; Krajewski, Krzysztof; Michalak, Olga; Tobiasz, Joanna; Kubiszewski, Marek; Sakaki, Toshiyuki; Kutner, Andrzej

doi:10.3390/biom15091222

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Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches

by

Teresa Żołek

^1,*,†

,

Mayur Kadam

^2,†

,

Sharmin Nadkarni

³,

Kaori Yasuda

⁴,

Michał Chodyński

⁵,

Krzysztof Krajewski

⁵,

Olga Michalak

⁵

,

Joanna Tobiasz

⁵,

Marek Kubiszewski

⁵,

Toshiyuki Sakaki

^4,‡

and

Andrzej Kutner

^2,*,‡

¹

Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland

²

Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland

³

Sant Rawool Maharaj Mahavidyalaya S. N. Desai Chowk, Udyamnagar, Kudal, Sindhudurg, Maharashtra 416520, India

⁴

Department of Pharmaceutical Engineering, Toyama Prefectural University, Toyama 939-0398, Japan

⁵

Chemistry Section, Research Group of Pharmacy, Cosmetic Chemistry and Biotechnology, Łukaszewicz Research Network-Industrial Chemistry Institute, 8 Rydygiera, Warsaw 01-793, Poland

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

^‡

These authors contributed equally to this work as co-senior authors.

Biomolecules 2025, 15(9), 1222; https://doi.org/10.3390/biom15091222 (registering DOI)

Submission received: 23 July 2025 / Revised: 8 August 2025 / Accepted: 13 August 2025 / Published: 25 August 2025

(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog, 3rd Edition)

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Abstract

The clinical use of 1,25-dihydroxycholecalciferol (1,25D3), the active form of vitamin D₃, is limited by its calcemic side effects and rapid metabolic degradation. To overcome these limitations, we designed novel vitamin D analogs with extended, rigidified, and branched side chains. Among them, PRI-1938, featuring a 5,6-trans triene system and 22,24-all-trans side-chain geometry, demonstrated markedly enhanced resistance to enzymatic catabolism. In vitro assays revealed that metabolic conversion of PRI-1938 by the nonselective cytochrome P450 3A4 (CYP3A4) enzyme was ca. 4-fold lower than that of the previously obtained PRI-1906 and over 9-fold lower than 1,25D3. All new analogs, including PRI-1927 and PRI-1937, exhibited significantly higher stability toward mitochondrial cytochrome P450 24A1 (CYP24A1), the vitamin D-selective catabolic enzyme, than that of 1,25D3. Molecular modeling and quantum mechanical calculations indicated that PRI-1938 adopts a highly stable conformation in the CYP24A1 active site, stabilized by four hydrogen bonds and multiple hydrophobic interactions. The spatially optimized interaction network reduces access to the catalytic heme, resulting in the lowest observed metabolic conversion. These findings highlight the critical role of the side-chain geometry in modulating metabolic stability and support the further development of PRI-1938 as a promising anticancer vitamin D analog.

Keywords: vitamin D analog; cytochrome CYP3A4; cytochrome CYP24A1; computational modeling; PRI-1906; PRI-1927; PRI-1937; PRI-1938

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MDPI and ACS Style

Żołek, T.; Kadam, M.; Nadkarni, S.; Yasuda, K.; Chodyński, M.; Krajewski, K.; Michalak, O.; Tobiasz, J.; Kubiszewski, M.; Sakaki, T.; et al. Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches. Biomolecules 2025, 15, 1222. https://doi.org/10.3390/biom15091222

AMA Style

Żołek T, Kadam M, Nadkarni S, Yasuda K, Chodyński M, Krajewski K, Michalak O, Tobiasz J, Kubiszewski M, Sakaki T, et al. Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches. Biomolecules. 2025; 15(9):1222. https://doi.org/10.3390/biom15091222

Chicago/Turabian Style

Żołek, Teresa, Mayur Kadam, Sharmin Nadkarni, Kaori Yasuda, Michał Chodyński, Krzysztof Krajewski, Olga Michalak, Joanna Tobiasz, Marek Kubiszewski, Toshiyuki Sakaki, and et al. 2025. "Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches" Biomolecules 15, no. 9: 1222. https://doi.org/10.3390/biom15091222

APA Style

Żołek, T., Kadam, M., Nadkarni, S., Yasuda, K., Chodyński, M., Krajewski, K., Michalak, O., Tobiasz, J., Kubiszewski, M., Sakaki, T., & Kutner, A. (2025). Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches. Biomolecules, 15(9), 1222. https://doi.org/10.3390/biom15091222

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Metabolic Interactions of Side-chain Extended and Unsaturated Vitamin D Analogs with Cytochrome P450 Enzymes: Integrating Theoretical and Experimental Approaches

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