1. A computer-based methodology to design non-standard peptides potentially able to prevent HOX-PBX1-associated cancer diseases
- Author
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Maria Rita Gulotta, Andrea Brancale, Ugo Perricone, Justin John, and Giada De Simone
- Subjects
0301 basic medicine ,QH301-705.5 ,Non-standard amino acids ,Peptide ,Antineoplastic Agents ,Computational biology ,Molecular Dynamics ,Catalysis ,Article ,Protein–protein interaction ,Inorganic Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Neoplasms ,medicine ,Humans ,Computer Simulation ,PBX ,Physical and Theoretical Chemistry ,Biology (General) ,Hox gene ,Molecular Biology ,QD1-999 ,Spectroscopy ,MM-GBSA ,Cancer ,chemistry.chemical_classification ,Organic Chemistry ,Pre-B-Cell Leukemia Transcription Factor 1 ,Computer based ,Cooperative binding ,General Medicine ,medicine.disease ,HOX ,Residue Scanning ,Computer Science Applications ,Amino acid ,Chemistry ,030104 developmental biology ,chemistry ,Protein-Protein Interactions ,030220 oncology & carcinogenesis ,Drug Design ,Peptides ,DNA - Abstract
In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. Therefore, an increase or decrease in HOX activity has been associated with both solid and haematological cancer diseases. Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. In this work, a computational study is described to identify novel potential peptides designed by employing a database of non-natural amino acids. For this purpose, residue scanning of the HOX minimal active sequence was performed to select the mutations to be further processed. According to these results, the peptides were point-mutated and used for Molecular Dynamics (MD) simulations in complex with PBX1 protein and DNA to evaluate complex binding stability. MM-GBSA calculations of the resulting MD trajectories were exploited to guide the selection of the most promising mutations that were exploited to generate twelve combinatorial peptides. Finally, the latter peptides in complex with PBX1 protein and DNA were exploited to run MD simulations and the ΔGbinding average values of the complexes were calculated. Thus, the analysis of the results highlighted eleven combinatorial peptides that will be considered for further assays.
- Published
- 2021