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In Silico Approach for Identification of PI3K/mTOR Dual Inhibitors for Multiple Myeloma Treatment

Year 2023, , 1 - 11, 26.06.2023
https://doi.org/10.26650/EurJBiol.2023.1178214

Abstract

Objective: Multiple myeloma is a hematologic malignancy in which targeting phosphoinositide 3 kinase (PI3K) and/or the mammalian target of rapamycin (mTOR) individually has been shown to have anti-proliferative effects, however, inhibiting both proteins simultaneously has been reported to have more effective results for its treatment. The aim of this study is to determine the molecular interactions and predicted inhibitory effects of 40 different dual inhibitors on mTOR, PI3Kδ, and PI3Kγ to propose potentially the most effective dual inhibitor that targets the PI3Kδ and PI3Kγ isoforms as well as the mTOR proteins since those isoforms are known to be predominant in multiple myeloma patients. Therefore, the focus in this study is built around the specific targeting of the PI3Kδ and PI3Kγ isoforms from the multiple myeloma perspective. Materials and Methods: In silico docking experiments were conducted to determine the binding energies for different ligands that target mTOR, PI3Kδ, and PI3Kγ. Protein-dual inhibitor complexes and the amino acids and bond types were visualized to identify molecular interactions. The absorption, distribution, metabolism, and excretion properties of dual inhibitors were analyzed and evaluated. Results: The binding affinity values were found to be between -7 and -9.9 kcal/mol. The toxicity prediction values of the selected dual inhibitors were obtained from the Pro-Tox-II web tool and classified according to the globally harmonized system of classification of labeling of chemicals. Conclusion: Correspondingly, among all dual inhibitors, Vistusertib is determined to be a promising compound against multiple myeloma cells by inhibiting both PI3Kδ and PI3Kγ as well as mTORC1/2.

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References

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  • 24. Harvey RD, Lonial S. PI3 kinase/AKT pathway as a therapeutic target in multiple myeloma. Future Oncol. 2007;3(6):639-647. google scholar
  • 25. Zhao L, Vogt PK. Class I PI3K in oncogenic cellular transformation. Oncogene. 2008;27(41):5486-5496. google scholar
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  • 28. Patidar K, Panwar U, Vuree S, et al. An in silico approach to identify high affinity small molecule targeting m-TOR inhibitors for the clinical treatment of breast cancer. Asian Pac J Cancer Prev. 2019;20(4):1229-1241. google scholar
  • 29. Sain A, Kandasamy T, Naskar D. In silico approach to target PI3K/Akt/mTOR axis by selected Olea europaea phenols in PIK3CA mutant colorectal cancer. J Biomol Struct Dyn. 2021:1-16. google scholar
  • 30. Putra PP, Abdullah SS, Rahmatunisa R, Junaidin J, Ismed F. Structure, activity, and drug-likeness of pure compounds of Sumatran lichen (Stereocaulon halei) for the targeted ACE2 protein in COVID-19 disease. Pharmaciana. 2020;10(2):135-146. google scholar
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  • 32. Tasian SK, Teachey DT, Li Y, et al. Potent efficacy of combined PI3K/ mTOR and JAK or ABL inhibition in murine xenograft models of Ph-like acute lymphoblastic leukemia. Blood. 2017;129:177-187. google scholar
  • 33. Mohd Rehan. A structural insight into the inhibitory mechanism of an orally active PI3K/mTOR dual inhibitor, PKI-179 using computational approaches. J Mol Graph Model. 2015;62:226-234. google scholar
  • 34. Ippolito T, Tang G, Mavis C, Gu JJ, Hernandez-Ilizaliturri FJ, Barth MJ. Omipalisib (GSK458), a novel Pan-PI3K/mTOR inhibitor, exhibits in vitro anti-lymphoma activity in chemotherapy-sensitive and -resistant models of burkitt lymphoma. Blood. 2016;128:5376. doi: 10.1182/blood.V128.22.5376.5376 google scholar
  • 35. Collins GP, Clevenger TN, Burke KA, et al. A phase 1/2 study of the combination of acalabrutinib and vistusertib in patients with relapsed/refractory B-cell malignancies. Leuk Lymphoma. 2021;62:2625-2636. google scholar
  • 36. Rinne N, Christie EL, Ardasheva A, et al. Targeting the PI3K/AKT/ mTOR pathway in epithelial ovarian cancer, therapeutic treatment options for platinum-resistant ovarian cancer. Cancer Drug Resist. 2021;4:573-595. google scholar
  • 37. Lipinski CA, Lombardo ational approaches to estimate solubility and permeability in drug discovery and development settings1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3-25.1. Adv Drug Deliv Rev. 2001;46:3-26. google scholar
Year 2023, , 1 - 11, 26.06.2023
https://doi.org/10.26650/EurJBiol.2023.1178214

Abstract

Project Number

-

References

  • 1. Wang L, Lin N, Li Y. The PI3K/AKT signaling pathway regulates ABCG2 expression and confers resistance to chemotherapy in human multiple myeloma. Oncol Rep. 2019;41:1678- 1690. google scholar
  • 2. McKenna M, McGarrigle S, Pidgeon GP. The next generation of PI3K-Akt-mTOR pathway inhibitors in breast cancer cohorts. Bio-chim Biophys Acta Rev Cancer. 2018;1870:185-197. google scholar
  • 3. John L, Krauth MT, Podar K, Raab MS. Pathway-directed therapy in multiple myeloma. Cancers. 2021;13(7):1668. google scholar
  • 4. Ramakrishnan V, Kumar S. PI3K/AKT/mTOR pathway in multiple myeloma: from basic biology to clinical promise. Leuk Lymphoma. 2018;59(11):2524-2534. google scholar
  • 5. Tarantelli C, Lupia A, Stathis A, Bertoni F. Is there a role for dual PI3K/mTOR inhibitors for patients affected with lymphoma? Int J Mol Sci. 2020;21(3):1060. doi: 10.3390/ijms21031060. google scholar
  • 6. Jourdan M, Caraux A, De Vos J, et al. An in vitro model of differentiation of memory B cells into plasmablasts and plasma cells including detailed phenotypic and molecular characterization. Blood. 2009;114(25):5173-5181. google scholar
  • 7. Corre J, Munshi NC, Avet-Loiseau H. Risk factors in multiple myeloma: is it time for a revision? Blood. 2021;137(1):16-19. google scholar
  • 8. Clinical pathways to address the challenges of treatment resistance and relapse in multiple myeloma. J Clin Pathw. Accessed March 16, 2023. https://www.journalofclinicalpathways.com/ white-paper/clinical-pathways-address-challenges-treatment-re-sistance-and-relapse-multiple google scholar
  • 9. Zitvogel L, Kroemer G. Bortezomib induces immunogenic cell death in multiple myeloma. Blood Cancer Discov. 2021;2(4):405-407. google scholar
  • 10. Robak P, Szemraj J, Mikulski D, Drozdz I, Robak T. Prognostic value of resistance proteins in plasma cells from multiple myeloma patients treated with bortezomib. J Clin Med. 2021;10(21):5028. Published 2021 Oct 28. doi:10.3390/jcm10215028 google scholar
  • 11. Teicher BA, Tomaszewski JE. Proteasome inhibitors. Biochem Pharmacol. 2015;96:1-9. google scholar
  • 12. Painuly U, Kumar S. Efficacy of bortezomib as first-line treatment for patients with multiple myeloma. Clin Med Insights Oncol. 2013;7:53-73. google scholar
  • 13. Mologni L, Marzaro G, Redaelli S, Zambon A. Dual kinase targeting in leukemia. Cancers. 2021;13. doi:10.3390/cancers13010119. google scholar
  • 14. Abramson HN. Kinase inhibitors as potential agents in the treatment of multiple myeloma. Oncotarget. 2016;7:81926-81968. google scholar
  • 15. Musiol R. An overview of quinoline as a privileged scaffold in cancer drug discovery. Expert Opin Drug Discov. 2017;12:583-597. google scholar
  • 16. BIOVIA Discovery Studio - BIOVIA - Dassault Systèmes®. Dassault Systèmes. Accessed July 18, 2022. https://www.3ds.com/prod-ucts-services/biovia/products/molecular-modeling-simulation/ biovia-discovery-studio/ google scholar
  • 17. Thompson MA. molecular docking using ArgusLab, an efficient shape-based search algorithm and the a score scoring function. ACS meeting, Philadelphia. Scientific Research Publishing. Accessed July 18, 2022. https://www.scirp.org/(S(lz5mqp453edsn-p55rrgjct55))/reference/ReferencesPapers.aspx?Referen-ceID=1994078 google scholar
  • 18. Wong SE, Lightstone FC. Accounting for water molecules in drug design. Expert Opin Drug Discov. 2011;6:65-74. google scholar
  • 19. Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. doi:10.1038/srep42717 google scholar
  • 20. Banerjee P, Eckert AO, Schrey AK, Preissner R. ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res. 2018;46:W257-W263. google scholar
  • 21. Fareed MM, El-Esawi MA, El-Ballat EM, et al. In silico drug screening analysis against the overexpression of PGAM1 gene in different cancer treatments. Biomed Res Int. 2021;2021:5515692. doi: 10.1155/2021/5515692 google scholar
  • 22. Bojarska J, Remko M, Breza M, et al. A supramolecular approach to structure-based design with a focus on synthons hierarchy in ornithine-derived ligands: review, synthesis, experimental and in silico studies. Molecules. 2020;25(5):1135. doi: 10.3390/mole-cules25051135 google scholar
  • 23. Han K, Xu X, Chen G, et al. Identification of a promising PI3K inhibitor for the treatment of multiple myeloma through the structural optimization. J Hematol Oncol. 2014;7:9. doi: 10.1186/1756-87227-9 google scholar
  • 24. Harvey RD, Lonial S. PI3 kinase/AKT pathway as a therapeutic target in multiple myeloma. Future Oncol. 2007;3(6):639-647. google scholar
  • 25. Zhao L, Vogt PK. Class I PI3K in oncogenic cellular transformation. Oncogene. 2008;27(41):5486-5496. google scholar
  • 26. Thorpe LM, Yuzugullu H, Zhao JJ. PI3K in cancer: divergent roles of isoforms, modes of activation and therapeutic targeting. Nat Rev Cancer. 2015;15(1):7-24. google scholar
  • 27. Baumann P, Schneider L, Mandl-Weber S, Oduncu F, Schmid-maier R. Simultaneous targeting of PI3K and mTOR with NVP-BGT226 is highly effective in multiple myeloma. Anticancer Drugs. 2012;23(2):131-138. google scholar
  • 28. Patidar K, Panwar U, Vuree S, et al. An in silico approach to identify high affinity small molecule targeting m-TOR inhibitors for the clinical treatment of breast cancer. Asian Pac J Cancer Prev. 2019;20(4):1229-1241. google scholar
  • 29. Sain A, Kandasamy T, Naskar D. In silico approach to target PI3K/Akt/mTOR axis by selected Olea europaea phenols in PIK3CA mutant colorectal cancer. J Biomol Struct Dyn. 2021:1-16. google scholar
  • 30. Putra PP, Abdullah SS, Rahmatunisa R, Junaidin J, Ismed F. Structure, activity, and drug-likeness of pure compounds of Sumatran lichen (Stereocaulon halei) for the targeted ACE2 protein in COVID-19 disease. Pharmaciana. 2020;10(2):135-146. google scholar
  • 31. Schult C, Dahlhaus M, Glass A, et al. The dual kinase inhibitor NVP-BEZ235 in combination with cytotoxic drugs exerts anti-proliferative activity towards acute lymphoblastic leukemia cells. Anticancer Res. 2012;32:463-74. google scholar
  • 32. Tasian SK, Teachey DT, Li Y, et al. Potent efficacy of combined PI3K/ mTOR and JAK or ABL inhibition in murine xenograft models of Ph-like acute lymphoblastic leukemia. Blood. 2017;129:177-187. google scholar
  • 33. Mohd Rehan. A structural insight into the inhibitory mechanism of an orally active PI3K/mTOR dual inhibitor, PKI-179 using computational approaches. J Mol Graph Model. 2015;62:226-234. google scholar
  • 34. Ippolito T, Tang G, Mavis C, Gu JJ, Hernandez-Ilizaliturri FJ, Barth MJ. Omipalisib (GSK458), a novel Pan-PI3K/mTOR inhibitor, exhibits in vitro anti-lymphoma activity in chemotherapy-sensitive and -resistant models of burkitt lymphoma. Blood. 2016;128:5376. doi: 10.1182/blood.V128.22.5376.5376 google scholar
  • 35. Collins GP, Clevenger TN, Burke KA, et al. A phase 1/2 study of the combination of acalabrutinib and vistusertib in patients with relapsed/refractory B-cell malignancies. Leuk Lymphoma. 2021;62:2625-2636. google scholar
  • 36. Rinne N, Christie EL, Ardasheva A, et al. Targeting the PI3K/AKT/ mTOR pathway in epithelial ovarian cancer, therapeutic treatment options for platinum-resistant ovarian cancer. Cancer Drug Resist. 2021;4:573-595. google scholar
  • 37. Lipinski CA, Lombardo ational approaches to estimate solubility and permeability in drug discovery and development settings1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3-25.1. Adv Drug Deliv Rev. 2001;46:3-26. google scholar
There are 37 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Research Articles
Authors

İlke Maşalacı This is me 0000-0002-7989-7767

Yaren Akdoğan This is me 0000-0002-5930-2113

Özge Mutlu This is me 0000-0001-5237-7887

Hande Eyvaz This is me 0000-0002-4642-3442

Yağmur Kiraz 0000-0003-3508-5617

Project Number -
Publication Date June 26, 2023
Submission Date September 21, 2022
Published in Issue Year 2023

Cite

AMA Maşalacı İ, Akdoğan Y, Mutlu Ö, Eyvaz H, Kiraz Y. In Silico Approach for Identification of PI3K/mTOR Dual Inhibitors for Multiple Myeloma Treatment. Eur J Biol. June 2023;82(1):1-11. doi:10.26650/EurJBiol.2023.1178214