In silico analysis of the interaction between Rimegepant and HRAS as a therapeutic target in Non-Small Cell Lung Cancer

Authors

  • Fabricio Jácome Campos Independent Researcher, Ambato, Ecuador
  • Anthony Fernando González Independent Researcher, Ambato, Ecuador

DOI:

https://doi.org/10.47187/perf.v1i32.298

Keywords:

therapeutic target, HRAS gen, Rimegepant, bioinformatics, MAPK

Abstract

Lung cancer accounts for 1,800,000 deaths worldwide. Lung neoplasms are divided into non-small cell lung cancer and small cell lung cancer. The first covers 80% of cases and is subdivided into adenocarcinoma, large cell carcinoma and squamous cell carcinoma. The aim of this study is to analyze a potential therapeutic molecular target in non-small cell lung cancer using an in silico approach. The methodology included a differential expression analysis using GEO2R, followed by a comparison of genes with databases such as Malacards, Harmonizome and KEGG. In addition, interaction networks were built using Cytoscape to identify interactions between cancer-related genes. Subsequently, DrugBank was used to identify a potential therapeutic target and the druggable site was recognized through DOGSiteScorer. The results indicate that the drug Rimegepant shows favorable pharmacokinetic and toxicity properties, suggesting that it could be a viable alternative for the development of drugs targeting the HRAS protein. This finding opens up new perspectives for the treatment of non-small cell lung cancer, improving its therapeutic approach.

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References

Fois SS, Paliogiannis P, Zinellu A, Fois AG, Cossu A, Palmieri G. Molecular Epidemiology of the Main Druggable Genetic Alterations in Non-Small Cell Lung Cancer. Int J Mol Sci. 2021;22(2):1–19. doi: 10.3390/IJMS22020612

Zavala-Hoppe AN, Recalde-Chávez JZ, Saldarriaga-García AJ, Quiroz-Villafuerte WA. Epidemiología y factores de riesgo asociados al cáncer de pulmón en los países de Latinoamérica y Europa. MQRInvestigar. 2024;8(1):1483–99.

Duma N, Santana-Davila R, Molina JR. Non-Small Cell Lung Cancer: Epidemiology, Screening, Diagnosis, and Treatment. Mayo Clin Proc. 2019;94(8):1623–40. doi: 10.1016/J.MAYOCP.2019.01.013

Rivas S, Armisén R. El cáncer de pulmón de células no pequeñas en la era de la medicina de precisión. Rev Médica Clínica Las Condes. 2022;33(1):25–35. doi: 10.1016/J.RMCLC.2022.01.001

Saab S, Zalzale H, Rahal Z, Khalifeh Y, Sinjab A, Kadara H. Insights Into Lung Cancer Immune-Based Biology, Prevention, and Treatment. Front Immunol. 2020;11. doi: 10.3389/FIMMU.2020.00159

Wang Y, Zou S, Zhao Z, Liu P, Ke C, Xu S. New insights into small-cell lung cancer development and therapy. Cell Biol Int. 2020;44(8):1564–76. doi: 10.1002/CBIN.11359

Hoy H, Lynch T, Beck M. Surgical Treatment of Lung Cancer. Crit Care Nurs Clin North Am. 2019;31(3):303–13. doi: 10.1016/J.CNC.2019.05.002

Hsu PC, Jablons DM, Yang CT, You L. Epidermal Growth Factor Receptor (EGFR) Pathway, Yes-Associated Protein (YAP) and the Regulation of Programmed Death-Ligand 1 (PD-L1) in Non-Small Cell Lung Cancer (NSCLC). Int J Mol Sci. 2019;20(15). doi: 10.3390/IJMS20153821

Alexander M, Kim SY, Cheng H. Update 2020: Management of Non-Small Cell Lung Cancer. Lung. 2020;198(6):897–907. doi: 10.1007/S00408-020-00407-5

Escobar P, Mercedes M, Rodríguez G, Emilio M, Moredo A, Escobar EP. Cáncer de pulmón de células no pequeñas : presentación de caso. Arch Médico Camaguey. 2017;21(2):1–6.

Lin L, Ding D, Xiao X, Li B, Cao P, Li S. Trametinib potentiates TRAIL-induced apoptosis via FBW7-dependent Mcl-1 degradation in colorectal cancer cells. J Cell Mol Med. 2020;24(12):6822–32. doi: 10.1111/JCMM.15336

Rivera C, Granados A, Ramírez J. Erlotinib vs. Gefitinib en cáncer de pulmón de células no pequeñas avanzado o metastásico: Una comparación indirecta de eficacia. Gac Mex Oncol. 2010;9(5):1–9.

Campos-Parra AD, Cruz-Rico G, Arrieta O. Genotipificación en cáncer de pulmón de células no pequeñas. Gac Mex Oncol. 2012;11(1):35–44.

Auxiliadora Castillo-Muñoz M, Abdel-Kader-Martín L, Beltrán-Calvo C, Isabel-Gómez R, Romero-Tabares A, Molina-López T. Erlotinib y gefitinib en primera línea de cáncer de pulmón no microcítico en estadio avanzado o metastásico, con mutación activadora del EGFR.

Liu J, Zhang X, Cao X. Dendritic cells in systemic lupus erythematosus: From pathogenesis to therapeutic applications. J Autoimmun. 2022;132. doi: 10.1016/J.JAUT.2022.102856

Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, et al. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother. 2020;131:110648.

Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, et al. Validation of Structures in the Protein Data Bank. Structure. 2017;25(12):1916–27. doi: 10.1016/J.STR.2017.10.009

Evans C, Hardin J, Stoebel DM. Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions. Brief Bioinform. 2018;19(5):776–92. doi: 10.1093/BIB/BBX008

Boyero Corral L. Análisis de los perfiles de expresión génica en cáncer de pulmón: Valor pronóstico en pacientes con cáncer de pulmón no microcítico sometidos a toracotomía. Universidad de Granada. 2016.

Selamat SA, Chung BS, Girard L, Zhang W, Zhang Y, Campan M, et al. Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res. 2012;22(7):1197–211. doi: 10.1101/GR.132662.111

Kareff SA, Trabolsi A, Krause HB, Samec T, Elliott A, Rodriguez E, et al. The Genomic, Transcriptomic, and Immunologic Landscape of HRAS Mutations in Solid Tumors. Cancers (Basel). 2024;16(8). doi: 10.3390/CANCERS16081572

Stephen AG, Esposito D, Bagni RG, McCormick F. Dragging ras back in the ring. Cancer Cell. 2014;25(3):272–81. doi: 10.1016/J.CCR.2014.02.017

Pylayeva-Gupta Y, Grabocka E, Bar-Sagi D. RAS oncogenes: weaving a tumorigenic web. Nat Rev Cancer. 2011;11(11):761–74. doi: 10.1038/NRC3106

Degirmenci U, Wang M, Hu J. Targeting Aberrant RAS/RAF/MEK/ERK Signaling for Cancer Therapy. Cells. 2020;9(1). doi: 10.3390/CELLS9010198

Tomasini P, Walia P, Labbe C, Jao K, Leighl NB. Targeting the KRAS Pathway in Non-Small Cell Lung Cancer. Oncologist. 2016;21(12):1450. doi: 10.1634/THEONCOLOGIST.2015-0084

Gómez-López A, Revuelta-Salgado F, García-Luján R. Cáncer de pulmón de células no pequeñas. Med - Programa Form Médica Contin Acreditado. 2022;13(67):3933–41.

Purba ER, Saita EI, Maruyama IN. Activation of the EGF Receptor by Ligand Binding and Oncogenic Mutations: The “Rotation Model”. Cells. 2017;6(2). doi: 10.3390/CELLS6020013

Figarol S, Delahaye C, Gence R, Doussine A, Cerapio JP, Brachais M, et al. Farnesyltransferase inhibition overcomes oncogene-addicted non-small cell lung cancer adaptive resistance to targeted therapies. Nat Commun. 2024;15(1):5345. doi: 10.1038/S41467-024-49360-4

Koch S, Claesson-Welsh L. Signal Transduction by Vascular Endothelial Growth Factor Receptors. Cold Spring Harb Perspect Med. 2012;2(7). doi: 10.1101/CSHPERSPECT.A006502

Cseh B, Doma E, Baccarini M. “RAF” neighborhood: Protein–protein interaction in the Raf/Mek/Erk pathway. Febs Lett. 2014;588(15):2398. doi: 10.1016/J.FEBSLET.2014.06.025

Veluswamy R, Mack PC, Houldsworth J, Elkhouly E, Hirsch FR. KRAS G12C-Mutant Non-Small Cell Lung Cancer: Biology, Developmental Therapeutics, and Molecular Testing. J Mol Diagn. 2021;23(5):507–20. doi: 10.1016/J.JMOLDX.2021.02.002

Uprety D, Adjei AA. KRAS: From undruggable to a druggable Cancer Target. Cancer Treat Rev. 2020;89. doi: 10.1016/J.CTRV.2020.102070

Du X, Shao Y, Qin HF, Tai YH, Gao HJ. ALK-rearrangement in non-small-cell lung cancer (NSCLC). Thorac cancer. 2018;9(4):423–30. doi: 10.1111/1759-7714.12613

Fan Z, Zhang L, Zhang S, Liu A, Li S, Cao X, et al. Farnesyltransferase (FTase) Inhibitors Increase Inhibition of KIT Mutants by Imatinib. Reports Biochem Mol Biol. 2023;12(1):74–82. doi: 10.52547/RBMB.12.1.74

Volkamer A, Kuhn D, Rippmann F, Rarey M. DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics. 2012;28(15):2074–5. doi: 10.1093/BIOINFORMATICS/BTS310

Fährrolfes R, Bietz S, Flachsenberg F, Meyder A, Nittinger E, Otto T, et al. ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. 2017;45(W1):W337–43. doi: 10.1093/NAR/GKX333

Michel M, Visnes T, Homan EJ, Seashore-Ludlow B, Hedenström M, Wiita E, et al. Computational and Experimental Druggability Assessment of Human DNA Glycosylases. ACS Omega. 2019;4(7):11642–56. doi: 10.1021/ACSOMEGA.9B00162/SUPPL_FILE/AO9B00162_SI_002.XLSX

Fitri A, Basultan H, Iryani. Hydrophobic Pocket of SARS-Cov-2 Spike Glycoprotein are Potential as Binding Pocket. J Phys Conf Ser. 2021;1788(1). doi: 10.1088/1742-6596/1788/1/012021

Salem MM, Gerges MN, Noser AA. Synthesis, molecular docking, and in-vitro studies of pyrimidine-2-thione derivatives as antineoplastic agents via potential RAS/PI3K/Akt/JNK inhibition in breast carcinoma cells. Sci Reports 2022 121. 2022;12(1):1–20. doi: 10.1038/s41598-022-26571-7

Li J, Ma X, Guo S, Hou C, Shi L, Zhang H, et al. A Hydrophobic‐Interaction‐Based Mechanism Triggers Docking between the SARS‐CoV‐2 Spike and Angiotensin‐Converting Enzyme 2. Glob Challenges. 2020;4(12). doi: 10.1002/GCH2.202000067

Varma AK, Patil R, Das S, Stanley A, Yadav L, Sudhakar A. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of Drug-Designing. PLoS One. 2010;5(8).

Mustafai A, Zubair M, Hussain A, Ullah A. Recent Progress in Proteins-Based Micelles as Drug Delivery Carriers. Polymers (Basel). 2023;15(4). doi: 10.3390/POLYM15040836

Dunga AK, Allaka TR, Kethavarapu Y, Nechipadappu SK, Pothana P, Kuppan C, et al. Design, Synthesis, Molecular Docking, ADMET, and Biological Studies of Some Novel 1,2,3-Triazole Linked Tetrazoles as Anticancer Agents. Curr Org Synth. 2022;20(5):576–87.

Infield DT, Rasouli A, Galles GD, Chipot C, Tajkhorshid E, Ahern CA. Cation-π interactions and their functional roles in membrane proteins. J Mol Biol. 2021;433(17):167035. doi: 10.1016/J.JMB.2021.167035

Vernon RMC, Chong PA, Tsang B, Kim TH, Bah A, Farber P, et al. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Elife. 2018;7. doi: 10.7554/ELIFE.31486

Hubbard RE, Kamran Haider M. Hydrogen Bonds in Proteins: Role and Strength. Encycl Life Sci. 2010; doi: 10.1002/9780470015902.A0003011.PUB2

Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC. Regulation of protein-ligand binding affinity by hydrogen bond pairing. Sci Adv. 2016;2(3). doi: 10.1126/SCIADV.1501240

Newberry RW, Raines RT. The n→π∗ Interaction. Acc Chem Res. 2017;50(8):1838–46. doi: 10.1021/ACS.ACCOUNTS.7B00121/ASSET/IMAGES/LARGE/AR-2017-001218_0009.JPEG

Pratama MRF, Poerwono H, Siswodiharjo S. ADMET properties of novel 5-O-benzoylpinostrobin derivatives. J Basic Clin Physiol Pharmacol. 2019;30(6). doi: 10.1515/JBCPP-2019-0251

Flores-Holguín N, Frau J, Glossman-Mitnik D. In Silico Pharmacokinetics, ADMET Study and Conceptual DFT Analysis of Two Plant Cyclopeptides Isolated From Rosaceae as a Computational Peptidology Approach. Front Chem. 2021;9:708364.

Pham-The H, Cabrera-Pérez MÁ, Nam NH, Castillo-Garit JA, Rasulev B, Le-Thi-Thu H, et al. In Silico Assessment of ADME Properties: Advances in Caco-2 Cell Monolayer Permeability Modeling. Curr Top Med Chem. 2018;18(26):2209–29.

Youhanna S, Lauschke VM. The Past, Present and Future of Intestinal In Vitro Cell Systems for Drug Absorption Studies. J Pharm Sci. 2021;110(1):50–65. doi: 10.1016/J.XPHS.2020.07.001

Robinson K, Tiriveedhi V. Perplexing Role of P-Glycoprotein in Tumor Microenvironment. Front Oncol. 2020;10. doi: 10.3389/FONC.2020.00265

Cox D. How not to discover a drug - integrins. Expert Opin Drug Discov. 2021;16(2):197–211. doi: 10.1080/17460441.2020.1819234

Fatima S, Gupta P, Sharma S, Sharma A, Agarwal SM. ADMET profiling of geographically diverse phytochemical using chemoinformatic tools. Future Med Chem. 2020;12(1):69–87. doi: 10.4155/FMC-2019-0206

Takomthong P, Waiwut P, Yenjai C, Sombatsri A, Reubroycharoen P, Lei L, et al. Multi-Target Actions of Acridones from Atalantia monophylla towards Alzheimer’s Pathogenesis and Their Pharmacokinetic Properties. Pharmaceuticals (Basel). 2021;14(9). doi: 10.3390/PH14090888

Sevrioukova IF, Poulos TL. Understanding the mechanism of cytochrome P450 3A4: recent advances and remaining problems. Dalton Trans. 2013;42(9):3116–26. doi: 10.1039/C2DT31833D

Published

2024-12-10

How to Cite

Jácome Campos, F., & González, A. F. . (2024). In silico analysis of the interaction between Rimegepant and HRAS as a therapeutic target in Non-Small Cell Lung Cancer. Perfiles, 1(32), 37-54. https://doi.org/10.47187/perf.v1i32.298