In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy

Abstract

The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3′ and 5′ ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.

Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

“…Two different model aptamers were considered herein as proof-of-principles. The first one is a 24-mer version of the anti-MUC1 aptamer ( A1 ), which has been identified by Missailidis and co-workers as a bioreceptor for breast cancer biomarker mucin 1 (MUC1) protein. , The anti-MUC1 aptamer folds into a stable structure with three binding thymine residues in the terminal loop . The second model aptamer is the well-known and widely used DNA aptamer for ATP or adenosine that was first described by Huizenga and Szostak in 1995 .…”

Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

“…These studies indicated consistent binding of the MUC1 peptide with the thymine loop of the aptamer (TTT) initiated by the arginine residue of the peptide 13 . In similar studies, atomistic molecular dynamic simulations on single and double mutants of the anti MUC1 aptamer showed increased affinity to the MUC1 ligand 14 .…”

“…Combining our approach with simulations of target binding to the aptamers (such as those of Refs. 13 and 14 for the anti-MUC1 aptamer) can shade further light into the crucial topic of aptamer immobilization effects on their target capture capabilities.…”

“…The molecular dynamics studies conducted by Rhinehardt et al have provided important information regarding the binding site location and orientation of the anti MUC1 aptamer and the MUC1 protein when solvated in an aqueous environment. While the results of Santini et al provided further details on mutants of the anti MUC1 aptamers and its relationship with binding free energies 14 . In particular, they showed that the double mutant aptamer exhibits a tight interaction with the MUC1 peptide and adopts a groove conformation that structurally favors the intermolecular contact with the peptide leaving the 3′ and 5′ ends free for further chemical conjugation 14 .…”

Outlook on the Development and Application of Molecular Simulations in Latin America

“…MD simulations proved to be one of the most popular computational chemistry tools. In this special issue, atomistic MD simulations have been applied in many studies to understand key structural and functional properties of proteins, − receptor activation, insights into the binding of ligands, − mutations, ,− protein folding, and inhibitor design . In addition, combined free energy simulations and NMR chemical-shift perturbation has been utilized to identify transient cation-π contacts in proteins .…”