Chemical space as a unifying theme for chemistry.

Chemistry has diversified from a basic understanding of the elements to studying millions of highly diverse molecules and materials, which together are conceptualized as the chemical space. A map of this chemical space where distances represent similarities between compounds can represent the mutual relationships between different subfields of chemistry and help the discipline to be viewed and understood globally.

Leveraging machine learning to streamline the development of liposomal drug delivery systems.

Drug delivery systems efficiently and safely administer therapeutic agents to specific body sites. Liposomes, spherical vesicles made of phospholipid bilayers, have become a powerful tool in this field, especially with the rise of microfluidic manufacturing during the COVID-19 pandemic. Despite its efficiency, microfluidic liposomal production poses challenges, often requiring laborious, optimization on a case-by-case basis.

Chemical Space for Peptide-based Antimicrobials.

Multidrug-resistant (MDR) bacteria represent a global public health threat, and antimicrobial peptides (AMPs), derived from naturally occurring linear or cyclic peptides, can provide the solution. However, most AMPs are sensitive to proteases and have poor pharmacokinetics. The EU-funded ERC Advanced Grant SPACE4AMPS aims to identify new AMPs by applying the concepts of chemical space and ligand-based virtual screening, which are well known for small molecule drug discovery, to the world of peptides.

Stereorandomized Oncocins with Preserved Ribosome Binding and Antibacterial Activity.

We recently showed that solid-phase peptide synthesis using racemic amino acids yields stereorandomized peptides comprising all possible diastereomers as homogeneous, single-mass products that can be purified by HPLC and that stereorandomization modulates activity, toxicity, and stability of membrane-disruptive cyclic and linear antimicrobial peptides (AMPs) and dendrimers. Here, we tested if stereorandomization might be compatible with target binding peptides with the example of the proline-rich AMP oncocin, which inhibits the bacterial ribosome. Stereorandomization of up to nine -terminal residues preserved ribosome binding and antibacterial effects including activities against drug-resistant bacteria and protected against serum degradation.

Chemoenzymatic multistep retrosynthesis with transformer loops.

Integrating enzymatic reactions into computer-aided synthesis planning (CASP) should help devise more selective, economical, and greener synthetic routes. Herein we report the triple-transformer loop algorithm with biocatalysis (TTLAB) as a new CASP tool for chemo-enzymatic multistep retrosynthesis. Single-step retrosyntheses are performed using two triple transformer loops (TTL), one trained with chemical reactions from the US Patent Office (USPTO-TTL), the second one obtained by multitask transfer learning combining the USPTO dataset with preparative biotransformations from the literature (ENZR-TTL).