Sheema Yaqoob Khan , Mohd Ashraf Rather , Azra Shah , Ishtiyaq Ahmad , Irfan Ahmad , KawKabul Saba , Faisal Rashid Sofi
{"title":"利用同源建模、分子动力学模拟和对接研究探索虹鳟促性腺激素受体的三维结构","authors":"Sheema Yaqoob Khan , Mohd Ashraf Rather , Azra Shah , Ishtiyaq Ahmad , Irfan Ahmad , KawKabul Saba , Faisal Rashid Sofi","doi":"10.1016/j.endmts.2024.100171","DOIUrl":null,"url":null,"abstract":"<div><p>Reproductive processes in fishes are regulated by the hypothalamic-pituitary-gonadal (HPG) axis, much like in tetrapods. Within this system, Gonadotropin-Releasing Hormone (GnRH) is released by the hypothalamus, binding to GnRH receptors in the pituitary gland and stimulating the secretion of gonadotropin hormones. The current study aimed to analyze the GnRH receptor in <em>Oncorhynchus mykiss</em> (rainbow trout) using a computational and structural biology approach. The GnRH receptor gene of <em>O. mykiss</em> comprises a nucleotide sequence of 1707 base pairs with an open reading frame of 1251 base pairs, which is responsible for encoding 416 amino acids. It was found that the GnRH receptor contains leucine (L) as the most abundant amino acid. The secondary structure revealed that alpha helices constitute the largest percentage (36 %) with 153 residues, followed by extended strands with 77 residues (17.51 %). The GnRH receptor contains 26 negatively charged and 37 positively charged amino acid residues. The highest hydrophilicity was observed for lysine (K) at position 310, with a value of −3.900, while the highest hydrophobicity was found for leucine (L) at position 290, with a value of 3.80. Molecular docking analysis showed that the most favorable binding energy was observed for Gestrinone (−7.8 kcal/mol). Gestrinone was found to form hydrogen bonds with MET160, LUE245, LUE62, TYR216, and GLN209 residues of GnRH. Moreover, molecular dynamics revealed that the complexes form robust and enduring connections, indicating their structural integrity throughout the simulation. The results of this study provide insights into the protein modeling, molecular docking, and virtual screening of antagonist ligands against the GnRH receptor. Additionally, they may significantly aid in the advancement and improvement of therapeutic strategies targeted at treating various fish reproductive dysfunctions.</p></div>","PeriodicalId":34427,"journal":{"name":"Endocrine and Metabolic Science","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666396124000153/pdfft?md5=b9e9ba4b26db004c056baa92100c1dde&pid=1-s2.0-S2666396124000153-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Exploring 3D structure of gonadotropin hormone receptor using homology modeling, molecular dynamic simulation and docking studies in rainbow trout, Oncorhynchus mykiss\",\"authors\":\"Sheema Yaqoob Khan , Mohd Ashraf Rather , Azra Shah , Ishtiyaq Ahmad , Irfan Ahmad , KawKabul Saba , Faisal Rashid Sofi\",\"doi\":\"10.1016/j.endmts.2024.100171\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Reproductive processes in fishes are regulated by the hypothalamic-pituitary-gonadal (HPG) axis, much like in tetrapods. Within this system, Gonadotropin-Releasing Hormone (GnRH) is released by the hypothalamus, binding to GnRH receptors in the pituitary gland and stimulating the secretion of gonadotropin hormones. The current study aimed to analyze the GnRH receptor in <em>Oncorhynchus mykiss</em> (rainbow trout) using a computational and structural biology approach. The GnRH receptor gene of <em>O. mykiss</em> comprises a nucleotide sequence of 1707 base pairs with an open reading frame of 1251 base pairs, which is responsible for encoding 416 amino acids. It was found that the GnRH receptor contains leucine (L) as the most abundant amino acid. The secondary structure revealed that alpha helices constitute the largest percentage (36 %) with 153 residues, followed by extended strands with 77 residues (17.51 %). The GnRH receptor contains 26 negatively charged and 37 positively charged amino acid residues. The highest hydrophilicity was observed for lysine (K) at position 310, with a value of −3.900, while the highest hydrophobicity was found for leucine (L) at position 290, with a value of 3.80. Molecular docking analysis showed that the most favorable binding energy was observed for Gestrinone (−7.8 kcal/mol). Gestrinone was found to form hydrogen bonds with MET160, LUE245, LUE62, TYR216, and GLN209 residues of GnRH. Moreover, molecular dynamics revealed that the complexes form robust and enduring connections, indicating their structural integrity throughout the simulation. The results of this study provide insights into the protein modeling, molecular docking, and virtual screening of antagonist ligands against the GnRH receptor. Additionally, they may significantly aid in the advancement and improvement of therapeutic strategies targeted at treating various fish reproductive dysfunctions.</p></div>\",\"PeriodicalId\":34427,\"journal\":{\"name\":\"Endocrine and Metabolic Science\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-03-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2666396124000153/pdfft?md5=b9e9ba4b26db004c056baa92100c1dde&pid=1-s2.0-S2666396124000153-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Endocrine and Metabolic Science\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2666396124000153\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Medicine\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Endocrine and Metabolic Science","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2666396124000153","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Medicine","Score":null,"Total":0}
Exploring 3D structure of gonadotropin hormone receptor using homology modeling, molecular dynamic simulation and docking studies in rainbow trout, Oncorhynchus mykiss
Reproductive processes in fishes are regulated by the hypothalamic-pituitary-gonadal (HPG) axis, much like in tetrapods. Within this system, Gonadotropin-Releasing Hormone (GnRH) is released by the hypothalamus, binding to GnRH receptors in the pituitary gland and stimulating the secretion of gonadotropin hormones. The current study aimed to analyze the GnRH receptor in Oncorhynchus mykiss (rainbow trout) using a computational and structural biology approach. The GnRH receptor gene of O. mykiss comprises a nucleotide sequence of 1707 base pairs with an open reading frame of 1251 base pairs, which is responsible for encoding 416 amino acids. It was found that the GnRH receptor contains leucine (L) as the most abundant amino acid. The secondary structure revealed that alpha helices constitute the largest percentage (36 %) with 153 residues, followed by extended strands with 77 residues (17.51 %). The GnRH receptor contains 26 negatively charged and 37 positively charged amino acid residues. The highest hydrophilicity was observed for lysine (K) at position 310, with a value of −3.900, while the highest hydrophobicity was found for leucine (L) at position 290, with a value of 3.80. Molecular docking analysis showed that the most favorable binding energy was observed for Gestrinone (−7.8 kcal/mol). Gestrinone was found to form hydrogen bonds with MET160, LUE245, LUE62, TYR216, and GLN209 residues of GnRH. Moreover, molecular dynamics revealed that the complexes form robust and enduring connections, indicating their structural integrity throughout the simulation. The results of this study provide insights into the protein modeling, molecular docking, and virtual screening of antagonist ligands against the GnRH receptor. Additionally, they may significantly aid in the advancement and improvement of therapeutic strategies targeted at treating various fish reproductive dysfunctions.
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