A Nanoscale Forest Seen Through a Big Lens

From the discovery of living cells with an early microscope by Anton van Leeuwenhoek in 1674 to the first observation of extremely distant galaxies with the Hubble Space Telescope in 1995, optical instruments were central to many breakthroughs throughout the history of science. Today, much of the data that scientists investigate is collected and analyzed digitally. Just as Leeuwenhoek invented his own microscope to look at water samples four centuries ago, scientists nowadays are constructing new types of "digital lenses" - large, high-resolution computer displays that allow them to observe complex digital datasets too small or too large to see otherwise. My research focuses on designing visualizations of nanoscale materials to portray these tiny structures in large, high-resolution display environments. Such nanostructures are too small to be seen in a microscope, yet too complex to be visualized on traditional computer screens. This image shows a 320-degrees panoramic visualization of a nanoscale glass fissure comprising 5 million atoms. The red and blue balls represent oxygen and silicon atoms, respectively. The green clouds represent electron charge densities. With big digital lenses like this, scientists can immerse themselves in their data and observe complex phenomena that would otherwise remain largely unseen

Broadly Applicable and Comprehensive Synthetic Method for <i>N</i>‑Alkyl-Rich Drug-like Cyclic Peptides

We report a versatile and durable method for synthesizing highly N-alkylated drug-like cyclic peptides. This is the first reported method for synthesizing such peptides in parallel with a high success rate and acceptable purity that does not require optimizations for a particular sequence. We set up each reaction condition by overcoming the following issues: (1) diketopiperazine (DKP) formation, (2) insufficient peptide bond formation due to the steric hindrance of the N-alkylated amino acid, and (3) instability of highly N-alkylated peptides under acidic conditions. Using this newly established method, we successfully synthesized thousands of cyclic peptides to explore the scope of this modality in drug discovery. We here demonstrate the syntheses of a hundred representative examples, including our first clinical N-alkyl-rich cyclic peptide (LUNA18) that inhibits an intracellular tough target (RAS), in 31% total yield and 97% purity on average after 23 or 24 reaction steps

Broadly Applicable and Comprehensive Synthetic Method for <i>N</i>‑Alkyl-Rich Drug-like Cyclic Peptides

We report a versatile and durable method for synthesizing highly N-alkylated drug-like cyclic peptides. This is the first reported method for synthesizing such peptides in parallel with a high success rate and acceptable purity that does not require optimizations for a particular sequence. We set up each reaction condition by overcoming the following issues: (1) diketopiperazine (DKP) formation, (2) insufficient peptide bond formation due to the steric hindrance of the N-alkylated amino acid, and (3) instability of highly N-alkylated peptides under acidic conditions. Using this newly established method, we successfully synthesized thousands of cyclic peptides to explore the scope of this modality in drug discovery. We here demonstrate the syntheses of a hundred representative examples, including our first clinical N-alkyl-rich cyclic peptide (LUNA18) that inhibits an intracellular tough target (RAS), in 31% total yield and 97% purity on average after 23 or 24 reaction steps

Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor

Cyclic peptides as a therapeutic modality are attracting a lot of attention due to their potential for oral absorption and accessibility to intracellular tough targets. Here, starting with a drug-like hit discovered using an mRNA display library, we describe a chemical optimization that led to the orally available clinical compound known as LUNA18, an 11-mer cyclic peptide inhibitor for the intracellular tough target RAS. The key findings are as follows: (i) two peptide side chains were identified that each increase RAS affinity over 10-fold; (ii) physico-chemical properties (PCP) including Clog P can be adjusted by side-chain modification to increase membrane permeability; (iii) restriction of cyclic peptide conformation works effectively to adjust PCP and improve bio-activity; (iv) cellular efficacy was observed in peptides with a permeability of around 0.4 × 10–6 cm/s or more in a Caco-2 permeability assay; and (v) while keeping the cyclic peptide’s main-chain conformation, we found one example where the RAS protein structure was changed dramatically through induced-fit to our peptide side chain. This study demonstrates how the chemical optimization of bio-active peptides can be achieved without scaffold hopping, much like the processes for small molecule drug discovery that are guided by Lipinski’s rule of five. Our approach provides a versatile new strategy for generating peptide drugs starting from drug-like hits