Payame Noor University Crop Biotechnology 2252-0783 13 2 2024 01 19 Analyzing the expression data (RNA-Seq) in Catharanthus roseus plant in order to identify key genes of the active substances (vinblastine and vincristine) in different organs (root, leaf and flower) and to investigate their anticancer effects using docking analysis and molecular dynamics. Analyzing the expression data (RNA-Seq) in Catharanthus roseus plant in order to identify key genes of the active substances (vinblastine and vincristine) in different organs (root, leaf and flower) and to investigate their anticancer effects using docking analysis and molecular dynamics. 1 11 10566 10.30473/cb.2024.70157.1945 FA Masoud Tohidfar Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Yousef Saeedi Honar Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Naser Farrokhi Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Journal Article 2023 10 04 Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients. Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients. https://cropbiotech.journals.pnu.ac.ir/article_10566_30c0de2d38eec3dc207cada1c4e4d87d.pdf