Unlocking New Avenues in Cancer Treatment: Targeting MYC with NT-B2R Peptide Library

Introduction
Scientists have made a groundbreaking discovery in cancer research by developing a peptide library that could pave the way for targeting the elusive cancer factor, MYC. MYC is a crucial transcription factor associated with many human cancers, but due to its disordered nature and rapid turnover rate, it has been a challenging target for oncology therapies.

The Breakthrough: NT-B2R Peptide
In a recent study, researchers reported the development of NT-B2R, a MYC-targeted peptide derived from a molecular library. This library, created using a stereo-diversified bicyclic peptide approach, explores a three-dimensional chemical space previously unexplored with conventional constructs.

Library Development Process
Cyclization using ROM-RCM Reaction: The library was cyclized in one step using the ROM-RCM reaction, resulting in a bicyclic peptide that could be easily linearized for sequencing through a one-step deallylation process.

Proline Scanning with FIVAL Model: Proline residues were strategically introduced to favor preferred conformations, aiding in the development of bicyclic structures. Racemic exo- and endo-norbornene building molecules were used for "proline scanning" using the FIVAL model peptide sequence.

Validation and Screening: The developed library underwent validation through tetrazine assessment, Edman degradation, mass spectrometry, and molecular simulations. A total of 42 beads were randomly selected, sequenced, and linearized. The resulting NT-B peptide library was then screened for MYC-binding molecular hits.

Evaluation of Binding Efficiency
ELISA Assays: Racemic exo- and endo-norbornene isomer combinations were evaluated for their binding efficiency to recombinant MYC using enzyme-linked immunosorbent assays (ELISA).

Competitive ELISA: Racemic NT-B2-Exo and NT-B2-Endo isomers were generated and assessed for their MYC-binding affinities through competitive ELISA.

Temperature-Based Circular Dichroism Spectroscopy: This method was employed to investigate the mechanisms underlying the NT-B2-MYC interactions.

Cellular Impact and Therapeutic Potential
Cellular Thermal Shifting Experiments: NT-B2R demonstrated the ability to bind to MYC in complex biological settings, as demonstrated through cellular thermal shifting experiments on U87 cellular lysates.

Suppression of MYC Transcription Activities: NT-B2R effectively suppressed MYC transcription activities and cell proliferation, indicating its potential as a therapeutic agent.

RNA-Seq Analysis: RNA-seq analysis of U87 cells treated with NT-B2R revealed considerable transcriptomic alterations, with 1,322 genes increased and 704 genes decreased, aligning with MYC's role as a master transcription factor.

Molecular Insights and Stability
Molecular Simulations: Atomistic molecular simulations unveiled that all eight isomers acquired stable conformations during the simulation time, with unique ring pucker orientations.

Binding Affinities: Library screening generated eight hits with micromolar-level binding affinities to MYC, further validated through protein thermal shift assays.

Isomer Stability: NT-B2R production yielded two isomers with different retention durations. Molecular simulations revealed that NT-B2R had higher stability than NT-B2S due to fewer conformations and higher inner-ring forces.

Therapeutic Implications
Impact on MYC Activities: NT-B2R bound to MYC resulted in reduced metabolic activities and propagation in U87 cell lines without affecting MYC production and phosphorylation.

Transcriptomic Alterations: The therapy induced significant transcriptomic alterations, showcasing its potential in altering gene expression patterns associated with MYC.

In conclusion, the development of the NT-B2R peptide library represents a significant leap in targeting the challenging MYC factor. With its demonstrated effectiveness in suppressing MYC activities and inducing transcriptomic alterations, NT-B2R opens new possibilities for the development of clinically viable therapeutics in oncology. This breakthrough brings hope for more effective cancer treatments in the future.The developed library underwent validation through tetrazine assessment, Edman degradation, mass spectrometry, and molecular simulations. A total of 42 beads were randomly selected, sequenced, and linearized. The resulting NT-B peptide library was then screened for MYC-binding molecular hits.that could pave the way for targeting the elusive cancer factor, MYC. MYC is a crucial transcription factor associated with many human cancers, but due to its disordered nature and rapid turnover rate, it has been a challenging target for oncology therapies.tetrazine assessment, Edman degradation, mass spectrometry, and molecular simulations. A total of 42 beads were randomly selected, sequenced, and linearized. The resulting NT-B peptide library was then screened for MYC-binding molecular hits.assessed for their MYC-binding affinities through competitive ELISA.induced significant transcriptomic alterations, showcasing its potential in altering gene expression patterns associated with MYC.