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Yahiro I, Barnuevo KDE, Sato O, Mohapatra S, Toyoda A, Itoh T, Ohno K, Matsuyama M, Chakraborty T, Ohta K. Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy. Front Physiol 2024; 15:1349119. [PMID: 38370015 PMCID: PMC10869568 DOI: 10.3389/fphys.2024.1349119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (Engraulis japonicus, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and in vivo validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 ų) than that in EJ CXCR4b (1,241 ų). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score -9.6) and EJ CXCR4b (Vina score -8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 105 nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.
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Affiliation(s)
- Issei Yahiro
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | | | - Oga Sato
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Sipra Mohapatra
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Takehiko Itoh
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Kaoru Ohno
- National Institute for Basic Biology (NIBB), Aichi, Japan
| | | | - Tapas Chakraborty
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Kohei Ohta
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
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