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Bioactive compounds from Morchella esculenta as potential inhibitors of RNA-binding protein La in ovarian cancer: a molecular modeling and quantum mechanics approach

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Abstract

La protein is significantly expressed in various malignant tumors, including ovarian cancer (OC), which is related to the poor response to platinum-based chemotherapy. Thus, inhibiting La protein could control the expression of the potential downstream genes involved in promoting proliferation and chemotherapy resistance to OC, which could serve as a therapeutic intervention. Through a molecular docking approach, 12 compounds from Morchella esculenta were screened against the crystal structure of La protein and four hit compounds were identified, including beta-carotene, p-hydroxybenzoic acid, gamma-tocopherol, and alpha-tocopherol, with a binding affinity of − 10.7, − 8.1, − 7.9, and − 7.6 kcal/mol, respectively, higher than pyridine-2-carboxylate (control), with a binding affinity of − 5.2 kcal/mol. To explore the interaction of the hit compounds with the target receptor, they were selected for a molecular dynamic simulation and post-simulation analysis for 100 ns. The result showed promising reliability of the ligands due to a stable interaction with the La protein crystal structure. Furthermore, the drug-likeness and physicochemical chemical properties of the compounds were investigated using ADMET study and density functional theory analysis, respectively, and the result shows that the hit compounds could serve as a promising starting for the development of novel LA protein inhibitors for OC therapeutics. Finally, this study compared HOMO and LUMO values from global hybrids with long-range corrected DFAs, and the result from the two followed the same qualitative pattern while calculating HOMO values; however, MO62X/cc-pVTZ could better predict LUMO values when considering a global hybrid.

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Data available upon request.

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Acknowledgements

This work used Bridges-2 at the Pittsburgh Supercomputer Center through allocation CHE220065 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by National Science Foundation Grants #2138259, #2138286, #2138307, #2137603, and #2138296.

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Authors and Affiliations

  1. Department of Biological Sciences, Western Illinois University, Macomb, IL, USA

    Gbenga Dairo

  2. Department of Chemistry, Western Illinois University, Macomb, IL, USA

    Matthew N. Ward, Mette Soendergaard & John J. Determan

  3. Department of Chemistry, The University of Memphis, Memphis, TN, USA

    Matthew N. Ward

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  1. Gbenga Dairo
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Contributions

GD designed the study. GD performed high-throughput virtual screening, chemical library curation, molecular docking, pharmacokinetic analysis, molecular dynamics simulation, and post-simulation analysis. GD, MNW, and JJD performed density functional theory calculations. GD drafted the manuscript. JJD and MS critically revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Mette Soendergaard or John J. Determan.

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Dairo, G., Ward, M.N., Soendergaard, M. et al. Bioactive compounds from Morchella esculenta as potential inhibitors of RNA-binding protein La in ovarian cancer: a molecular modeling and quantum mechanics approach. In Silico Pharmacol. 12, 32 (2024). https://doi.org/10.1007/s40203-024-00202-7

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