Abstract

Advancements in platform technologies have facilitated the production of libraries consisting of macrocyclic peptides composed of natural and non-canonical amino acids for more drug-like characteristics. Identification of macrocyclic peptide ligands against targets of interest can be accomplished using mRNA display. Despite numerous successful in vitro selections for macrocyclic peptide ligands against extracellular targets, identifying macrocyclic peptide hits that can reach intracellular targets continue to be a challenge. Breakthroughs in defining the features of a macrocyclic peptide that promote cell permeability have recently been disclosed. Here, we review the successful selections of non-standard macrocyclic peptide ligands using mRNA display in the last five years and chemical optimization of a drug-like macrocyclic peptide ligand for targeting intracellular KRAS.

Abstract

Lipidation stands as a pivotal strategy for enhancing the metabolic stability of target peptides. Prenyltransferases in cyanobactin biosynthesis have garnered significant attention as potential peptide lipidation biocatalysts because of their exceptional regio- and chemoselectivity. However, these enzymes often exhibit a biased preference for certain acceptor substrates, requiring specific amino acids adjacent to the modifying residue. In this study, we demonstrate the structure-guided engineering of LimF, a His-C-geranyltransferase, to broaden its peptide substrate tolerance. By altering key residues in the peptide-binding pocket, we created a LimF variant capable of modifying sequence motifs previously inaccessible to the wildtype enzyme. The variant successfully modified some previously unfavored sequence motifs in artificial peptide substrates and bioactive peptide agents, validating the engineered substrate scope. With the discovery of novel peptide prenyltransferases, this approach would lead to a more comprehensive toolbox of peptide prenylation biocatalysts.

Abstract

The amyloidoses are diseases caused by accumulation of amyloid fibrils from over 40 different human misfolded proteins in various organs of the body depending on precursor protein. Amyloidogenesis is a self-perpetuating reaction with deleterious consequences causing degeneration in cells and organs where depositions occur. Transthyretin, TTR, is an amyloidogenic protein causing sporadic disease from the wild-type protein during aging and from numerous different autosomal dominant familial mutations at earlier ages depending on the sequence of the hereditary variant. Until recently the disease process was poorly understood, and therapies were scarce. Over the past decades, spurred by clinical data, using chemical biology research, the mechanisms of TTR production and misfolding have been elucidated affording almost complete coverage of the TTR amyloidogenesis pathway to be targeted. This translational science success has provided a plethora of therapeutic options for the TTR amyloidoses providing an inspiring example for success in previously intractable diseases.

Abstract

The addition of various chemical modifications to RNA introduces an additional layer of complexity to the regulation of gene expression. Among all RNA modifications, N ⁶-methyladenosine (m⁶A) has earned its status as the most abundant and well-studied post-transcriptional modification in mammalian mRNA. Nevertheless, understanding the role of m⁶A in shaping the fate of RNA molecules and its influence on gene expression heavily depends on the development and application of detection technologies. Among all m⁶A detection methods, chemical-based sequencing methods show unique advantages. Our group recently developed an absolute quantification method named GLORI, which employs nitrite and glyoxal to convert adenosine to inosine efficiently. With its potential to emerge as the gold standard for m⁶A detection, GLORI showcases the promise of nitrite-based approaches. This review provides a comprehensive overview of m⁶A detection techniques based on deamination or nitrosation, evaluating their strengths and limitations. Furthermore, we offer insights into the future directions of innovative approaches in m⁶A profiling.

Abstract

RNA-guided RNA modifications, including pseudouridylation and 2′-O-methylation, are naturally occurring processes that introduce pseudouridines (Ψ) and 2’-O-methylated residues (2’-O−Me) into various types of RNA. This modification is orchestrated by two distinct families of ribonucleoprotein complexes: Box H/ACA RNP and Box C/D RNP. Each complex comprises a unique guide (g)RNA (Box H/ACA gRNA or Box C/D gRNA) and a set of core proteins responsible for pseudouridylation and 2’-O-methylation, respectively. The specificity of these modifications is conferred by base-pairing of Box H/ACA gRNA and Box C/D gRNA with their RNA substrates. Here, we discuss the mechanism and function of RNA-guided pseudouridylation and 2’-O-methylation.

Abstract

In recent decades, electro-organic synthesis is indubitably emerging as a cornerstone of modern organic chemistry. Electrochemical organic transformations especially reduction reactions have made massive advancements in the last few years because of their sustainable and environ-friendly nature. Electro-reductive protocols can be used as a promising substitute for conventional reductants by expelling the requirement of the stoichiometric amount of metal reductants. The major challenges for these electro-reductive reactions are primarily the use of a sacrificial electrode and divided cells. These limitations can be resolved through smart reaction planning by employing cheap sacrificial reagents or paired electrolysis without compromising the sustainable viewpoint. Considering the rapid enhancement in this field, imparting an intangible understanding of this evolving area is essential and substantial. In this review, we portrayed the electrochemical reductive transformations of C−C and C−O bonds after 2015 along with detailed mechanistic insights.

The cover picture shows a cyclic voltammogram and catalytically active intermediates, highlighting the importance of a rationale for innovations in the rapidly evolving field of molecular electrosynthesis. Also, as a product structure, a C7 substituted indole, derived through electrocatalysis, is depicted.

Abstract

Nucleic acids are considered as fundamental molecules of living systems, which serve as universal genetic information messengers and repositories. To uncover the multifaceted aspects of nucleic acid function and metabolism within cells, labeling has become indispensable. This labeling technique enables the visualization, isolation, characterization, and even quantification of specific nucleic acid species. This review delves into cellular metabolic approaches for nucleic acid labeling, wherein enzymatic steps are employed to introduce nucleic acid modifications before conjugation with a label for detection or isolation. The discussion begins with metabolic labeling for DNA, RNA with various reactive groups and post-transcriptional RNA labeling for RNA methylation and acetylation sites, emphasizing recent advancements in the field and then, we spotlighted pertinent applications for cellular imaging and sequencing. of labeling.