Rachita Dash

Org Lett. 2025 Nov 14;27(45):12563-12568. doi: 10.1021/acs.orglett.5c03982. Epub 2025 Nov 4.

ABSTRACT

We report a chemoenzymatic strategy for generating graspeptide mimetics. This strategy exploits the compatibility of sortase with the ester group at the X position of the pentapeptide sequence (LPXTG). Six types of graspeptide mimetics, including monocyclic and bicyclic depsipeptides, were generated. Combined with phage display, we identified a bicyclic depsipeptide targeting TEAD4 with a K_D value of 2.2 μM. This study demonstrates the potential of peptiligase-based system for constructing cyclic peptide libraries with unique topologies.

PMID:41186450 | DOI:10.1021/acs.orglett.5c03982

ACS Cent Sci. 2025 Aug 27;11(10):1911-1920. doi: 10.1021/acscentsci.5c00803. eCollection 2025 Oct 22.

ABSTRACT

Electron bifurcation reactions divide electrons from two-electron donors into high- and low-energy pools by transporting charge on spatially separated low- and high-potential electron hopping pathways. Bifurcation delivers electrons at potentials that drive downstream reactions in photosynthesis, respiration, and biocatalysis. Recent theoretical studies have described the requirements for effective ground-state electron bifurcation. The aim of this study is to design synthetic bifurcation constructs that can be driven by light. We describe a strategy to bifurcate holes (oxidizing equivalents) efficiently with light, and we present an illustrative energy landscape that could support this design. The design focuses on the electrochemical potentials and distances between cofactors. The analysis finds that hole bifurcation may be driven efficiently with light, guiding the further development of bioinspired networks that bifurcate charge and deliver the charges with prescribed electrochemical potentials.

PMID:41142337 | PMC:PMC12550633 | DOI:10.1021/acscentsci.5c00803

J Med Chem. 2025 Nov 13;68(21):23459-23471. doi: 10.1021/acs.jmedchem.5c02367. Epub 2025 Oct 27.

ABSTRACT

Acquired drug resistance remains a challenge for treating melanoma. Monotherapies such as vemurafenib and dabrafenib, which target a mutant form of BRAF kinase, become ineffective within six months of treatment. Therapies that combine multiple drugs targeting the same cellular pathway have emerged as a strategy to reduce drug resistance development. To determine whether additional benefits could be achieved by combining anticancer compounds with distinct killing mechanisms, we synthesized a suite of peptide-drug conjugates (PDCs) containing vemurafenib and peptides with either membrane-disruptive anticancer activity or nondisruptive properties. The PDCs crossed membranes with the drug cargo attached and killed melanoma cells with similar or improved activity relative to the free drug. The choice of peptide carrier impacted overall PDC potency and selectivity, and we identified an optimal membrane-active carrier peptide where the Vem-containing PDC exhibited activity against both drug-naı̈ve and drug-resistant melanoma cells while maintaining selectivity over noncancer cells.

PMID:41143531 | DOI:10.1021/acs.jmedchem.5c02367

J Am Chem Soc. 2025 Nov 5;147(44):40869-40878. doi: 10.1021/jacs.5c13909. Epub 2025 Oct 22.

ABSTRACT

De novo designed proteins offer a malleable platform for the development of stereoselective transformations not found in biochemistry. Here, we report the de novo design and directed evolution of helical bundle protein catalysts for enantioselective germylation through Ge-H insertion, a transformation not previously achieved by enzymatic catalysis. Comparative computational analysis revealed that, relative to Si-H insertion, the Ge-H insertion reaction proceeds through an earlier and more flexible transition state, introducing distinct challenges for stereocontrol. Using a fully de novo designed truncated four-helix bundle scaffold as the starting point, directed evolution afforded a quadruple mutant that catalyzes Ge-H insertion with high efficiency, enantioselectivity, and broad substrate scope. Molecular dynamics simulations indicated that beneficial mutations introduced from directed evolution enhanced active-site preorganization and modulated local backbone flexibility, contributing to improved transition-state complementarity with fine-tuned binding pocket size and more stable cofactor positioning regulated by hydrogen bonding interactions. These findings showcase the excellent potential for de novo proteins to achieve stereoselective transformations previously unknown to biocatalysts and underscore the importance of active-site remodeling of de novo protein scaffolds via directed evolution in achieving selective catalysis involving flexible transition states.

PMID:41123946 | DOI:10.1021/jacs.5c13909

J Am Chem Soc. 2025 Nov 5;147(44):40146-40157. doi: 10.1021/jacs.5c06654. Epub 2025 Oct 21.

ABSTRACT

Endothelial cells (ECs) comprise the pulmonary vascular bed and play a significant role in health and diseases. Consequently, the EC niche represents an attractive therapeutic target for treating a wide range of pulmonary vascular diseases. We have identified a new class of dicationic charge-altering releasable transporters. These single-component transporters selectively deliver mRNA to the lung upon intravenous administration without the use of a targeting ligand. Significantly, the number and spatial array of cationic charges within the repeating units of the CART polymer are found to control both mRNA delivery efficacy and tissue tropism. High-resolution imaging revealed efficient mRNA delivery to endothelial cells in pulmonary arteries, veins, and capillaries. The selective lung tropism of these new CARTs, coupled with the efficient and tunable synthesis of this new family of CART amphiphiles, represents an enabling platform for research and clinical applications.

PMID:41118665 | PMC:PMC13186261 | DOI:10.1021/jacs.5c06654

J Am Chem Soc. 2025 Oct 22;147(42):37893-37898. doi: 10.1021/jacs.5c12610. Epub 2025 Oct 9.

ABSTRACT

Peptide aminoacyl-transfer ribonucleic acid ligases (PEARLs) are amide-bond-forming enzymes that extend the main chain of peptides by using aminoacyl-tRNA (aa-tRNA) as a substrate. In this study, we investigated the substrate specificity of the PEARL BhaB_C^Ala from Bacillus halodurans, which utilizes Ala-tRNA^Ala. By leveraging flexizyme, a ribozyme capable of charging diverse acids onto a desired tRNA, we generated an array of aa-tRNAs in which we varied both the amino acid and the tRNA to dissect the substrate scope of BhaB_C^Ala. We demonstrate that BhaB_C^Ala catalyzes peptide extension with noncognate proteinogenic and noncanonical amino acids, hydroxy acids, and mercaptocarboxylic acids when attached to tRNA^Ala. For most of these, the efficiency was considerably reduced compared to Ala, indicating that the enzyme recognizes the amino acid. By variation of the different parts of the tRNA, enzyme specificity was shown to also depend on the acceptor stem and the anticodon arm of the tRNA. These findings establish the molecular determinants of PEARL specificity and provide a foundation for engineering these enzymes for broader applications in peptide synthesis.

PMID:41066767 | PMC:PMC12550832 | DOI:10.1021/jacs.5c12610

Angew Chem Int Ed Engl. 2025 Oct 4:e202517101. doi: 10.1002/anie.202517101. Online ahead of print.

ABSTRACT

Late-stage diversification of peptides via selective modification of endogenous amino acid side chains provides a powerful strategy to access analogues with enhanced bioactivity and tailored physicochemical properties, thereby facilitating peptide-based drug discovery. However, precise manipulation of short peptides comprising canonical amino acids-particularly control over backbone conformation-remains a formidable challenge. Herein, we present a robust electrochemical strategy for constructing macrocyclic peptides through direct incorporation of diverse aryl sulfur linkers. This method enables tryptophan (Trp)-selective crosslinking via electrochemical reaction with aryl thiosulfonates, leading to efficient formation of S─N bonds. The resulting sulfur-bridged multi-aryl macrocycles act as conformationally adaptive scaffolds that reshape the peptide backbone architecture. This conformational remodeling grants access to previously inaccessible structural spaces that are critical for modulating biological activity.

PMID:41045198 | DOI:10.1002/anie.202517101