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In silico studies of interactions of peptide-conjugated cholesterol metabolites and betulinic acid with EGFR, LDR, and N-terminal fragment of CCKA receptors

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Abstract

In this work, we designed three new ligands by conjugating cholesterol metabolites 3-hydroxy-5-cholestenoic acid (3-HC) and 3-oxo-4-cholestenoic acid (3-OC) and the natural tri-terpenoid betulinic acid with the tumor-targeting peptide YHWYGYTPQNVI. Molecular interactions with the unconjugated peptide and the conjugates were examined with three receptors that are commonly overexpressed in pancreatic adenocarcinoma cells using ligand docking and molecular dynamics. This study demonstrated the utility of the designed conjugates as a valuable scaffold for potentially targeting EGFR and LDLR receptors. Our results indicate that the conjugates showed strong binding affinities and formation of stable complexes with EGFR, while the unconjugated peptide, BT-peptide conjugate, an 3-HC-peptide conjugate showed the formation of fairly stable complexes with LDLR receptor. For EGFR, two receptor kinase domains were explored. Interactions with the N-terminal domain of CCKA-R were relatively weaker. For LDLR, binding occurred in the beta-propeller region. For the N-terminal fragment of CCKA-R, the conjugates induced significant conformational changes in the receptor. The molecular dynamic simulations for 100 ns demonstrate that BT-peptide conjugates and the unconjugated peptide had the highest binding and formed the most stable complexes with EGFR. RMSD and trajectory analyses indicate that these molecules transit to a dynamically stable configuration in most cases within 60 ns. NMA analysis indicated that amongst the conjugates that showed relatively higher interactions with the respective receptors, the highest potential for deformability was seen for the N-terminal-47 amino acid region of the CCKA-R receptor with and the lowest for the LDLR-receptor. Thus, the newly designed compounds may be evaluated in the future toward developing drug delivery materials for targeting tumor cells overexpressing LDLR or EGFR.

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Authors and Affiliations

  1. Department of Chemistry, Fordham University, 441 East Fordham Road, Bronx, NY, 10458, USA

    Madeline M. Bashant, Saige M. Mitchell, Lucy R. Hart, Charlotta G. Lebedenko & Ipsita A. Banerjee

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  1. Madeline M. Bashant
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  2. Saige M. Mitchell
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  3. Lucy R. Hart
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  4. Charlotta G. Lebedenko
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  5. Ipsita A. Banerjee
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Contributions

Conception and design of study: I. A. Banerjee; Acquisition of data: M. M. Bashant, S. M. Mitchell, C. G. Lebedenko and L. R. Hart. Analysis and interpretation of data: I. A. Banerjee, M. M. Bashant and C. G. Lebedenko.

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Correspondence to Ipsita A. Banerjee.

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Bashant, M.M., Mitchell, S.M., Hart, L.R. et al. In silico studies of interactions of peptide-conjugated cholesterol metabolites and betulinic acid with EGFR, LDR, and N-terminal fragment of CCKA receptors. J Mol Model 28, 16 (2022). https://doi.org/10.1007/s00894-021-05007-5

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  • DOI: https://doi.org/10.1007/s00894-021-05007-5

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