Rachita Dash

Nano Lett. 2023 May 24;23(10):4602-4608. doi: 10.1021/acs.nanolett.3c01090. Epub 2023 May 8.

ABSTRACT

Quantitative phase imaging (QPI) is a powerful optical imaging modality for label-free, rapid, and three-dimensional (3D) monitoring of cells and tissues. However, molecular imaging of important intracellular biomolecules such as enzymes remains a largely unexplored area for QPI. Herein, we introduce a fundamentally new approach by designing QPI contrast agents that allow sensitive detection of intracellular biomolecules. We report a new class of bio-orthogonal QPI-nanoprobes for in situ high-contrast refractive index (RI) imaging of enzyme activity. The nanoprobes feature silica nanoparticles (SiO₂ NPs) having higher RI than endogenous cellular components and surface-anchored cyanobenzothiazole-cysteine (CBT-Cys) conjugated enzyme-responsive peptide sequences. The nanoprobes specifically aggregated in cells with target enzyme activity, increasing intracellular RI and enabling precise visualization of intracellular enzyme activity. We envision that this general design of QPI-nanoprobes could open doors for spatial-temporal mapping of enzyme activity with direct implications for disease diagnosis and evaluating the therapeutic efficacy.

PMID:37154678 | PMC:PMC10798004 | DOI:10.1021/acs.nanolett.3c01090

J Med Chem. 2023 May 15. doi: 10.1021/acs.jmedchem.3c00628. Online ahead of print.

ABSTRACT

The development of cyclic peptides that exhibit pH-sensitive membrane permeation is a promising strategy for tissue-selective drug delivery. We investigated the pH-dependent interactions of designed cyclic peptides bearing noncanonical amino acids of long acidic side chains with lipid membranes, including surface binding, insertion, and translocation across the membrane. As the length of the side chain of acidic amino acid increased, the binding affinity of the peptides to phosphatidylcholine bilayer surfaces decreased, while the pH for the 50% insertion of the peptides into the bilayers increased. The pH for membrane permeation of the peptides increased with the side chain length, resulting in specific membrane permeation at pH ∼6.5. The longer side chain of acidic amino acids improved the maximum rate of membrane permeation at low pH, where both entropic and enthalpic contributions affected the permeation. Our peptide also showed intracellular delivery of cargo molecules into living cells in a pH-dependent manner.

PMID:37186548 | DOI:10.1021/acs.jmedchem.3c00628

Chembiochem. 2023 Jun 15;24(12):e202300320. doi: 10.1002/cbic.202300320. Epub 2023 May 16.

ABSTRACT

There is considerable interest in drug discovery targeting the aggregation of α-synuclein (αSyn) since this molecular process is closely associated with Parkinson's disease. However, inhibiting αSyn aggregation remains a major challenge because of its highly dynamic nature which makes it difficult to form a stable binding complex with a drug molecule. Here, by exploiting Random non-standard Peptides Integrated Discovery (RaPID) system, we identified a macrocyclic peptide, BD1, that could interact with immobilized αSyn and inhibit the formation of fibrils. Furthermore, improving the solubility of BD1 suppresses the co-aggregation with αSyn fibrils while it kinetically inhibits more effectively without change in their morphology. We also revealed the molecular mechanism of kinetic inhibition, where peptides bind to fibril ends of αSyn, thereby preventing further growth of fibrils. These results suggest that our approach for generating non-standard macrocyclic peptides is a promising approach for developing potential therapeutics against neurodegeneration.

PMID:37186077 | DOI:10.1002/cbic.202300320

Methods Mol Biol. 2023;2670:255-266. doi: 10.1007/978-1-0716-3214-7_13.

ABSTRACT

Noncanonical peptide backbone structures, such as heterocycles and non-α-amino acids, are characteristic building blocks present in peptidic natural products. To achieve ribosomal synthesis of designer peptides bearing such noncanonical backbone structures, we have devised translation-compatible precursor residues and their chemical posttranslational modification processes. In this chapter, we describe the detailed procedures for the in vitro translation of peptides containing the precursor residues by means of genetic code reprogramming technology and posttranslational generation of objective noncanonical backbone structures.

PMID:37184709 | DOI:10.1007/978-1-0716-3214-7_13

ACS Chem Biol. 2023 May 12. doi: 10.1021/acschembio.3c00085. Online ahead of print.

ABSTRACT

The characterization of microbiota mechanisms in health and disease has reinvigorated pattern recognition receptors as prominent targets for immunotherapy. Notably, our recent studies on Enterococcus species revealed peptidoglycan remodeling and activation of NOD2 as key mechanisms for microbiota enhancement of immune checkpoint inhibitor therapy. Inspired by this work and other studies of NOD2 activation, we performed in silico ligand screening and developed N-arylpyrazole dipeptides as novel NOD2 agonists. Importantly, our N-arylpyrazole NOD2 agonist is enantiomer-specific and effective at promoting immune checkpoint inhibitor therapy and requires NOD2 for activity in vivo. Given the significant functions of NOD2 in innate and adaptive immunity, these next-generation agonists afford new therapeutic leads and adjuvants for a variety of NOD2-responsive diseases.

PMID:37172210 | DOI:10.1021/acschembio.3c00085

Curr Opin Struct Biol. 2023 May 11;80:102603. doi: 10.1016/j.sbi.2023.102603. Online ahead of print.

ABSTRACT

Membrane-traversing peptides offer opportunities for targeting intracellular proteins and oral delivery. Despite progress in understanding the mechanisms underlying membrane traversal in natural cell-permeable peptides, there are still several challenges to designing membrane-traversing peptides with diverse shapes and sizes. Conformational flexibility appears to be a key determinant of membrane permeability of large macrocycles. We review recent developments in the design and validation of chameleonic cyclic peptides, which can switch between alternative conformations to enable improved permeability through cell membranes, while still maintaining reasonable solubility and exposed polar functional groups for target protein binding. Finally, we discuss the principles, strategies, and practical considerations for rational design, discovery, and validation of permeable chameleonic peptides.

PMID:37178478 | DOI:10.1016/j.sbi.2023.102603

Chem Sci. 2023 Apr 3;14(18):4935-4944. doi: 10.1039/d3sc00231d. eCollection 2023 May 10.

ABSTRACT

Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.

PMID:37181761 | PMC:PMC10171189 | DOI:10.1039/d3sc00231d

Angew Chem Int Ed Engl. 2023 Jun 19;62(25):e202301522. doi: 10.1002/anie.202301522. Epub 2023 May 11.

ABSTRACT

The peptidoglycan cell wall is essential for bacterial survival. To form the cell wall, peptidoglycan glycosyltransferases (PGTs) polymerize Lipid II to make glycan strands and then those strands are crosslinked by transpeptidases (TPs). Recently, the SEDS (for shape, elongation, division, and sporulation) proteins were identified as a new class of PGTs. The SEDS protein FtsW, which produces septal peptidoglycan during cell division, is an attractive target for novel antibiotics because it is essential in virtually all bacteria. Here, we developed a time-resolved Förster resonance energy transfer (TR-FRET) assay to monitor PGT activity and screened a Staphylococcus aureus lethal compound library for FtsW inhibitors. We identified a compound that inhibits S. aureus FtsW in vitro. Using a non-polymerizable Lipid II derivative, we showed that this compound competes with Lipid II for binding to FtsW. The assays described here will be useful for discovering and characterizing other PGT inhibitors.

PMID:37099323 | PMC:PMC10330507 | DOI:10.1002/anie.202301522

Angew Chem Int Ed Engl. 2023 May 10:e202300647. doi: 10.1002/anie.202300647. Online ahead of print.

ABSTRACT

Although cyclic peptides have become increasingly important as drugs, the most conventional peptide cyclization using moderately active coupling agents suffers from a lot of waste, high cost as well as long reaction times and burdensome purification. Here, we report an unconventional approach to peptide cyclization that uses acylammonium species generated from inexpensive and less wasteful Me2NBn and ClCO2i-Pr. Using this approach, we observed a desired rapid activation of C-terminal of cyclization precursors by acylammonium species, and achieved a rapid and epimerization/dimerization-free cyclization of synthetically challenging peptides, which included a difficult cyclization via N-methyl amide bond formation. The ease of purification, productivities, and reaction mass efficiencies of our approach were significantly superior to those in previous reports. We synthesized a previously reported versicotide D analogue and our data indicated that its stereochemistry should be revised.

PMID:37161693 | DOI:10.1002/anie.202300647

Curr Med Chem. 2023 Apr 8. doi: 10.2174/0929867330666230408203820. Online ahead of print.

ABSTRACT

During the last few decades, several efforts have been made towards the development of biocompatible materials. Among them, peptide amphiphiles (PAs) constitute a novel nanotechnological strategy used in the field of biomedicine since they can provide tissue-specific binding and localization. PAs possess several regions combining hydrophobic and hydrophilic areas that are able to self-assemble in aqueous media forming different tertiary nanostructures able to interact with cellular membranes. Moreover, these molecules can be tuned incorporating collagen, lipids or fluorescent markers. In addition, they can also be used as carriers in order to encapsulate active compounds for drug delivery showing promising features in this area. In this review the self-assembled structures of PAs as well as their pharmacological applications have been summarized. Furthermore, their use as drug delivery systems has been highlighted and the latest advances in this field have been reviewed.

PMID:37031390 | DOI:10.2174/0929867330666230408203820

Curr Res Microb Sci. 2023 Mar 17;4:100183. doi: 10.1016/j.crmicr.2023.100183. eCollection 2023.

ABSTRACT

According to WHO, to combat the resistant strains, new effective anti-microbial agents are needed on an urgent basis and global researchers should focus their efforts and discovery programs on developing them against antibiotic-resistant pathogens or priority pathogens like ESKAPE. In this context, Cationic antimicrobial peptides (AMPs) are being explored extensively as promising next-generation antimicrobials due to their broad range, fast kinetics and multifunctional role. Despite recent advances, it is still a daunting challenge to identify and design a potent AMP with no cytotoxicity, but with broad specific antimicrobial activity, stability and efficacy under in vivo conditions in a cost-effective and robust manner. In this work, as a proof of concept, we designed novel potent AMPs using artificial intelligence based in silico programs. Shortlisted peptide sequences were synthesized using the fmoc chemistry approach, assessed their antimicrobial activity, cell selectivity, mode of action and in vivo efficacy using a series of experiments. The synthesized peptide analogues demonstrated their antimicrobial activity (MIC in the range of 2.5-80 μM) against bacteria. The identified potential lead molecules showed antibacterial activity in physiological conditions with no signs of cytotoxicity. We further tested the antimicrobial activity of peptide analogues for treating wounds infected with Pseudomonas aeruginosa in the mice burn wound model. In drug-development programs, the identification of lead antimicrobial agents is always challenging and involves screening a large number of molecules which is time-consuming and expensive. This work demonstrates the utility of artificial intelligence based in silico analysis programs in discovering novel antimicrobial agents in an economical, robust way.

PMID:37032813 | PMC:PMC10073642 | DOI:10.1016/j.crmicr.2023.100183