Ananya Naick

Nat Microbiol. 2026 Apr 7. doi: 10.1038/s41564-026-02322-6. Online ahead of print.

ABSTRACT

Accurate division site placement is essential for bacteria to produce viable daughter cells. In the ovoid-shaped Streptococcus pneumoniae, previous work showed that division site placement depends on both the protein MapZ and chromosome segregation, although specific mechanisms remain unclear. Here we imaged fluorescently labelled S. pneumoniae, observing division site placement at the cell equator, the widest part of the cell, not at the mid-cell. Disruption of chromosome segregation neither affected MapZ nor divisome positioning, suggesting that division site selection can occur independently of chromosome segregation. MapZ localization depends on the sequential recruitment of two peptidoglycan decarboxylases, DacA and DacB, to the division site. DacA and DacB activity during early peptidoglycan synthesis generates a distinctive, tetrapeptide signature required for MapZ binding. As the cell cycle progresses, this signature becomes enriched at cell equators, recruiting MapZ so that these equators eventually serve as the division site in daughter cells. These findings update the mechanism of division site placement in S. pneumoniae.

PMID:41946898 | DOI:10.1038/s41564-026-02322-6

Angew Chem Int Ed Engl. 2026 Apr 6:e7837067. doi: 10.1002/anie.7837067. Online ahead of print.

ABSTRACT

Backbone-cyclic peptides (BMPs) are an attractive class of molecules appeared in diverse natural bioactive products. However, mRNA display technology coupled with ribosomal synthesis is intrinsically inapplicable to such peptide phenotypes due to loss of the C-terminal peptide region linking to the mRNA genotypes. To overcome this issue, we have devised a new strategy to link the sidechain-to-S-mainchain bond via an S-to-N acyl-shift to connect BMPs to the C-terminal fragment of the peptide. Here, we report the application of this strategy to construct a library of BMPs fused to cognate mRNAs. The library was applied for the selection of BMP ligands targeting Akt2, which is involved in the signal pathway to cancer pathogenesis. Consequently, BMP ligands against Akt2 were successfully uncovered from the library. The most potent Akt2 inhibitor, BMPakti-3, showed 1.3 nM of dissociation constant and 34 nM of half-maximal inhibitory concentration (IC₅₀). This system offers a unique platform for the de novo discovery of bioactive BMP ligands against various protein targets of interest.

PMID:41940682 | DOI:10.1002/anie.7837067

J Am Chem Soc. 2026 Apr 7. doi: 10.1021/jacs.5c23019. Online ahead of print.

ABSTRACT

Incorporation of α-hydrazino acid (α-Hza) into peptide chain can stabilize the secondary structures, such as helices and turns, and give rise to rigidification of peptide conformation. Consequently, such peptides potentially acquire enhanced binding affinity to target proteins. Moreover, the hydrazidic bond in α-Hza-containing peptides contributes to proteolytic resistance. Despite such favorable characteristics for therapeutic peptides, there is no example of success in screening de novo α-Hza-containing peptides against target proteins of interest. Here we report the construction of diverse, mRNA-encoded α-Hza-containing macrocyclic peptide libraries and their application to the Random nonstandard Peptides Integrated Discovery (RaPID) selection against two enzyme targets, Janus kinase 2 (JAK2) and human factor XIIa (FXIIa). The affinity-based enrichment of ligands from these libraries yielded potent binders with low-to-sub-nM dissociation constants, also exhibiting potent inhibitory activity, target specificity, proteolytic stability, and membrane permeability. Mutational studies of active macrocycles underscored critical roles of α-Hza residues in functional potencies. This study establishes a platform for de novo discovery of bioactive α-Hza-containing macrocyclic peptides against proteins of choice, thereby expanding the accessible chemical space for the RaPID system.

PMID:41944810 | DOI:10.1021/jacs.5c23019

Pathol Res Pract. 2026 Jun;282:156445. doi: 10.1016/j.prp.2026.156445. Epub 2026 Mar 19.

ABSTRACT

The growing threat of antimicrobial resistance, coupled with the challenges of developing new antibiotics, demands innovative therapeutic solutions. Antimicrobial peptides (AMPs) present a promising alternative, yet their clinical application is limited by toxicity, instability, low permeability, and high production costs. To overcome these barriers, we employed artificial intelligence (AI) and machine learning (ML) to design a fifteen-amino acid peptide, LCN-15 (RWWRRKKLKAPIWVR), with a molecular weight of 2079 Da. This short cationic peptide, rich in arginine and tryptophan residues, exhibits strong membrane interaction and antimicrobial potential. Using AI-guided de novo design, we rapidly analyzed structural features, predicted biological activities, and optimized the sequence for enhanced safety and efficacy. ML-based predictive assays indicated broad functional potential, encompassing anti-microbial, anti-biofilm, anti-cancer, and anti-oxidant properties. Subsequent analysis indicated favourable safety attributes, including low toxicity, minimal hemolytic potential, and good blood brain barrier permeability. In addition, predictive models suggested potential immunomodulatory activity, indicating that LCN-15 may enhance host defense mechanisms alongside its direct anti-microbial effects. Further, to correlate our predictive modelling of LCN-15, we used melittin (GIGAVLKVLTTGLPALISWIKRKRQQ), a 26 amino-acid cationic linear AMP which is very well studied. This comprehensive in silico predictive analysis, performed prior to peptide synthesis, ensured that only the most promising designs were advanced for consideration, thereby streamlining the workflow, minimizing experimental steps, and reducing overall costs. Furthermore, the consistency between the predicted activities of melittin and its well-established in vitro properties further supports the reliability of the computational predictions.These findings position LCN-15 as a multifunctional therapeutic candidate with potential applications in managing infections, modulating immune responses, and addressing the urgent global challenge of antimicrobial resistance.

PMID:41880932 | DOI:10.1016/j.prp.2026.156445

Chem Sci. 2026 Mar 25. doi: 10.1039/d6sc01577h. Online ahead of print.

ABSTRACT

Phage display is a powerful technology for discovering macrocyclic peptide ligands. Many phage display-revealed peptide inhibitors comprise disulfide crosslinks, which unfortunately exhibit vulnerability to reduction and proteolysis. Lanthipeptides are a family of ribosomally synthesized peptides that harbor thioether cyclization instead of disulfides. Lanthipeptide libraries have been constructed on phage; however, only with the use of the Lan enzyme that demands specific recognition sequences. Here, we present an enzyme-free strategy for constructing lanthionine-bridged macrocyclic peptide libraries on M13 phage. Our strategy involves selective and reversible masking of the N-terminal cysteine (NCys), followed by Cys-to-Dha conversion and subsequent cyclization upon NCys deprotection. We have specifically optimized the chemistry for each step to allow easy preparation of lanthipeptide libraries. The utility of such libraries is demonstrated by panning against Keap1 as a model protein. To the best of our knowledge, this is the first demonstration of a Lan enzyme-free construction of lanthipeptide libraries on phage, which presents a significant addition to the increasing collection of cyclization chemistries that expand the chemical space of phage display.

PMID:41890561 | PMC:PMC13014544 | DOI:10.1039/d6sc01577h

ACS Infect Dis. 2026 Mar 17. doi: 10.1021/acsinfecdis.5c01001. Online ahead of print.

ABSTRACT

Increasing multidrug resistance in nosocomial, opportunistic bacterial pathogens motivates a need to exploit metabolic pathways of therapeutic value. Here, we describe a one-pot reconstitution of the MurCDEF pathway from Acinetobacter baumannii, made possible by the biosynthesis and quantification of UDP-MurNAc (UM) and UM-stem peptide derivatives prepared in isotopically "heavy" and "light" isotopomer forms. The successive activity of each Mur ligase in one-pot is quantified by C18 liquid chromatography (LC). We show that the kinetics of sequential extension of the peptide stem is readily modulated by adjusting the relative Mur ligase concentrations or by adding effectors to the assay. We find that MurF generally pulls this pathway to mature the UM-pentapeptide product from UM, with other intermediates accumulating to variable degrees. Determination of the absolute concentrations of UM and UM-stem peptide intermediates in A. baumannii cells reveals, like the one-pot assay, a high relative UM-pentapeptide product, the concentration of which is decreased significantly by the antibiotic D-cycloserine. These in vitro and cellular assays collectively illustrate the promise of this toolkit to discover small molecules that target a specific Mur ligase or uncover novel aspects of peptidoglycan biosynthesis and recycling.

PMID:41844171 | DOI:10.1021/acsinfecdis.5c01001

J Am Chem Soc. 2026 Apr 1;148(12):13174-13185. doi: 10.1021/jacs.5c23173. Epub 2026 Mar 17.

ABSTRACT

Although numerous strategies for the identification of biologically active peptides are available, the methodologies to discover functional peptide pairs remain relatively scarce. The pairing of two combinatorial peptide libraries can furnish very large chemical spaces, which can be leveraged in ligand discovery to identify potent binders for proteins of interest. Here, we report the development of a library-vs-library in vitro selection platform for the discovery of heterodimeric macrocyclic peptide ligands. The platform is built upon the Random nonstandard Peptides Integrated Discovery (RaPID) system and utilizes protein-templated ligation of peptides from two mRNA display libraries to select for functional heterodimers. We report the method development and demonstrate the utility of the resulting protocols by identifying an ultrapotent heterodimeric ligand of 14-3-3ζ protein (h1.2, K_D = 120 pM), which forms via a proximity-enabled inverse electron demand Diels-Alder reaction of two cyclic peptide monomers upon binding to the protein. The formation of h1.2 from a1 and b2 monomers was accelerated 560-fold in the presence of 14-3-3ζ, and the heterodimer had a superior affinity compared to the constituent monomers [K_D(a1) = 430 pM and K_D(b2) = 700 pM]. Our strategy may be useful in drug discovery to develop high-affinity ligands against oligomeric proteins, targets without prominent binding pockets, or for disrupting protein-protein interactions characterized by large interaction areas.

PMID:41841560 | PMC:PMC13048255 | DOI:10.1021/jacs.5c23173

Proc Natl Acad Sci U S A. 2026 Mar 24;123(12):e2520462123. doi: 10.1073/pnas.2520462123. Epub 2026 Mar 16.

ABSTRACT

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a Cytosine-Adenosine-Guanine (CAG) repeat expansion in the Huntingtin (HTT) gene, with no disease-modifying therapies currently available. The precise molecular function of the HTT protein is unclear, and the lack of selective chemical tools has limited functional studies. We have identified and characterized macrocyclic peptide binders targeting HTT. These binders exhibit low-nanomolar affinity in vitro and engage distinct HTT and HTT-HAP40 interfaces, as revealed by hydrogen-deuterium exchange mass spectrometry and cryoelectron microscopy. Chemoproteomics confirmed selective binding in cell extracts from wildtype but not HTT-null cell lines. HAP40 consistently and stoichiometrically copurified with HTT across cell lines, including with HTT variants containing different CAG repeat lengths, highlighting the broad presence of the HTT-HAP40 complex.

PMID:41838909 | PMC:PMC13012115 | DOI:10.1073/pnas.2520462123

RSC Chem Biol. 2026 Mar 3. doi: 10.1039/d6cb00017g. Online ahead of print.

ABSTRACT

Precise spatiotemporal control over fluorescence labeling is a powerful approach for selective marking and tracking of proteins of interest within living systems. Here, we report a photoclickable labeling platform based on the 2,3-diaryl-indanone epoxide (DIO) photoswitch scaffold and the self-labeling protein HaloTag. Upon illumination, the protein-bound DIO undergoes reversible photoisomerization to form a metastable oxidopyrylium ylide (PY) that reacts with ring-strained dipolarophiles via [5 + 2] cycloaddition, enabling covalent spatiotemporal labeling. We synthesize and characterize a library of DIO-HaloTag and DIO-SNAP-tag ligands, systematically examining the effects of linker architecture and scaffold substitution on the photoswitching and photoclick reactivity in vitro and on living cells. We identify a naphthyl-substituted DIO ligand exhibiting superior photoswitching and photoclick efficiency, allowing fast, selective labeling of HaloTagged proteins on the surface of living cells using visible light activation (405 nm). Using this system, we achieve two- and three-color labeling of defined cell surface regions with excellent spatial and temporal precision, additionally allowing combinatorial labeling. Together, this work establishes a versatile framework for multiplexed, light-directed protein labeling compatible with living systems, with promising future applications including multiplexed long-term tracking and cellular barcoding.

PMID:41835454 | PMC:PMC12980540 | DOI:10.1039/d6cb00017g

Nat Commun. 2026 Mar 16. doi: 10.1038/s41467-026-70363-w. Online ahead of print.

ABSTRACT

In contrast to ynamides, whose chemistry has been extensively explored, ynimines remain underutilized in organic synthesis despite their rich functionalities. Here we report a general strategy to access 2-imido-1,3-dienes, synthetically challenging building blocks, through the reaction of ynimines with carboxylic acids. Leveraging this transformation, we develop a three-component reaction of ynimines, carboxylic acids and electron-deficient alkenes that enables the efficient synthesis of 1-imido-3,4-trans-disubstituted cyclohex-1-enes. The sequence proceeds via regioselective hydroacyloxylation and Mumm rearrangement to generate 2-imido-1,3-dienes, which undergo Diels-Alder cycloadditions. An intramolecular variant furnishes trans-fused tricyclic architectures reminiscent of trans-Δ⁹-tetrahydrocannabinol. Chemoselective hydrolysis further converts 2-imido-1,3-dienes into 2-amido-1,3-dienes, enabling chiral squaramide-catalysed enantioselective Diels-Alder reactions to afford 1-amido-3,4-cis-disubstituted cyclohex-1-enes with high stereocontrol. Distinct concerted and stepwise cycloaddition pathways rationalize the observed stereodivergence.

PMID:41839857 | DOI:10.1038/s41467-026-70363-w

ACS Infect Dis. 2026 Mar 13;12(3):870-872. doi: 10.1021/acsinfecdis.6c00181.

NO ABSTRACT

PMID:41821393 | DOI:10.1021/acsinfecdis.6c00181

FEMS Microbes. 2026 Feb 4;7:xtag003. doi: 10.1093/femsmc/xtag003. eCollection 2026.

ABSTRACT

The rapid emergence of multidrug-resistant (MDR) bacteria has severely compromised the efficacy of conventional antibiotics and intensified the global antimicrobial resistance crisis. Antimicrobial peptides (AMPs) have attracted considerable interest as adjunctive agents due to their membrane-active mechanisms and immunomodulatory properties; however, their clinical use as monotherapy remains limited by instability, toxicity, and pharmacokinetic constraints. Combining AMPs with conventional antibiotics has emerged as a promising strategy to enhance antibacterial efficacy, restore antibiotic susceptibility, and modulate resistance development. This review critically examines the mechanistic basis of AMP-antibiotic synergy, integrating evidence from in vitro and in vivo studies. Particular emphasis is placed on determinants that govern synergistic outcomes, including membrane permeability, porin-dependent antibiotic uptake, resistance-associated adaptations, and host-related factors that cannot be captured in vitro. In addition, we discuss key translational barriers limiting clinical implementation, such as immune modulation, pharmacokinetic mismatch, peptide instability, and strain-dependent variability in synergistic responses. By linking molecular mechanisms to experimental and translational outcomes, this review provides a focused framework for rational design and optimization of AMP-antibiotic combination therapies against MDR bacterial infections.

PMID:41769086 | PMC:PMC12947588 | DOI:10.1093/femsmc/xtag003

J Am Chem Soc. 2026 Mar 5. doi: 10.1021/jacs.5c17859. Online ahead of print.

ABSTRACT

Macrocyclic peptides (MPs) have emerged as interesting therapeutic candidates due to their ability to engage difficult protein targets with high affinity and selectivity. However, their application to intracellular targets is limited by the poor passive membrane permeability of most MPs. We previously showed that incorporation of an imidazopyridinium (IP⁺) moiety into an MP boosted passive membrane permeability significantly, as measured by the parallel artificial membrane permeability assay (PAMPA) (Li et al. (2024) J. Am. Chem. Soc. 146, 14633-14644). In this study, we report a detailed analysis of the entry of IP⁺-containing MPs into living cells. Chloroalkane penetration assay (CAPA) data show that IP⁺ MPs access the cytoplasm rapidly, often at rates approaching those of drug-like small molecules. Mechanistic studies, including live-cell imaging, ATP-depletion experiments, and organelle colocalization analyses, indicate that IP⁺ MPs traverse the plasma membrane primarily via passive diffusion, avoiding endosomal entrapment. IP⁺ MPs do not localize to the mitochondria, as is the case for many positively charged molecules. We show that the incorporation of an IP⁺ unit transforms a previously described membrane-impermeable macrocyclic antagonist of the p53-MDM2 interaction into a bioactive inhibitor of MCF-7 proliferation. Enhanced permeability is observed when the IP⁺ unit is positioned either within the macrocyclic backbone or on a side chain. Collectively, these results establish that IP⁺ incorporation is an effective strategy for the development of bioactive MPs targeting intracellular proteins.

PMID:41787884 | DOI:10.1021/jacs.5c17859

J Med Chem. 2026 Mar 26;69(6):6929-6944. doi: 10.1021/acs.jmedchem.5c03165. Epub 2026 Mar 9.

ABSTRACT

Macrocyclic peptides (MCPs) are promising drug candidates but often exhibit poor passive membrane permeability due to their polar backbone. This study demonstrates that incorporation of α-aminoisobutyric acid (Aib), a helicogenic residue, can enhance MCP permeability in a scaffold-dependent manner by enforcing γ-turns and promoting saddle-shaped conformations that stabilize intramolecular hydrogen bonds (IMHBs). Systematic Pro → Aib substitutions across several representative 6-8-residue scaffolds improved lipophilicity, reduced polar surface area, and minimized conformational rearrangements between aqueous and membrane environments, as confirmed by NMR, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulations. However, Aib incorporation did not increase permeability in all scaffolds, particularly those that were already highly preorganized. Permeability improvements were most pronounced in flexible scaffolds, with up to 8-fold gains and increased oral bioavailability in mice, primarily through enhanced absorption. Mechanistically, Aib and aromatic residues contribute additively to hydrophobic patch formation, promoting membrane affinity. These findings establish Aib as a valuable design element for optimizing passive permeability and oral exposure of macrocyclic peptides.

PMID:41797579 | DOI:10.1021/acs.jmedchem.5c03165

ACS Infect Dis. 2025 Nov 14;11(11):3298-3309. doi: 10.1021/acsinfecdis.5c00689. Epub 2025 Oct 23.

ABSTRACT

Herein, we describe the design, synthesis, and evaluation of modified cyclic peptides based upon the privileged structure of the cyclic depsipeptide natural products, ohmyungsamycin and ecumicin, that target Mycobacterium tuberculosis (Mtb) caseinolytic-like protein 1 (ClpC1). Simplified analogues featuring substitution at three sites (l-Thr-3, N-Me-l-Trp-9, and/or the N-terminus) were designed and synthesized via a novel and robust strategy, employing an oxazolidine-protected C-terminal amino acid, to enable late-stage, epimerization-free, solution-phase macrolactamization. Lead analogues had nanomolar affinity for the ClpC1 N-terminal domain (NTD), possessed potent activity against Mtb in vitro and were shown to inhibit protein degradation by the mycobacterial ClpC1:ClpP1P2 protease with an associated enhancement of ClpC1 ATPase activity. The most promising analogue from the series exhibited prolonged bactericidal killing activity against Mtb without the emergence of resistance and retained activity in an in vivo zebrafish model of mycobacterial infection.

PMID:41128295 | DOI:10.1021/acsinfecdis.5c00689

Bioconjug Chem. 2026 Mar 18;37(3):511-525. doi: 10.1021/acs.bioconjchem.5c00661. Epub 2026 Mar 3.

ABSTRACT

While DNA-encoded libraries (DELs) are well recognized as valuable tools for the development of novel small-molecule therapeutics, their significant potential for developing new imaging probes initially received less attention. However, as DEL technology develops and novel screening modalities are introduced, several robust strategies for generating imaging probes from DEL screening campaigns have emerged. The current topical review aims to provide an overview of DEL technology as it relates to the discovery of new molecular probes and to present recent contributions that highlight innovative ways DELs are advancing the field. Approaches to harnessing DEL-derived probes for therapeutic applications, including their conversion into integrated theranostic modalities, will also be discussed.

PMID:41773585 | DOI:10.1021/acs.bioconjchem.5c00661

J Med Chem. 2026 Mar 12;69(5):6179-6198. doi: 10.1021/acs.jmedchem.5c03707. Epub 2026 Feb 27.

ABSTRACT

To investigate how ring size and backbone flexibility influence antimicrobial potency and cytotoxicity, we synthesized a series of macrocyclic peptides of lead peptide p1 (c[Arg-Arg-arg-arg-dip-Trp-dip]) by incorporating Gly, 2-aminoethoxyacetic acid (EAA), or 2,4-diaminobutyric acid (Dab). Two optimized peptides, 6b and 10b, retained broad-spectrum activity against drug-resistant Gram-positive (MIC, 1.5-6.2 μg/mL) and Gram-negative bacteria (MIC, 4-25 μg/mL), as well as pathogenic fungi, while exhibiting enhanced selectivity for microbial cells. Their therapeutic indices (TI ∼407 and ∼394, respectively) were ∼2-fold higher than p1, indicating improved safety. Both peptides remained effective against Gram-negative pathogens beyond the reach of daptomycin, were rapidly bactericidal, and eradicated bacterial and fungal biofilms. Mechanistic studies (e.g., calcein-leakage and extracellular ATP leakage assays) confirmed a membranolytic mode of action. NMR analysis revealed a distinct "sandwich" conformation in 6b that rationalizes its improved selectivity. Both peptides exhibited high plasma stability (t₁/₂ ∼ 6-8 h), supporting their therapeutic potential.

PMID:41755744 | PMC:PMC12990034 | DOI:10.1021/acs.jmedchem.5c03707

Antibiotics (Basel). 2026 Feb 13;15(2):208. doi: 10.3390/antibiotics15020208.

ABSTRACT

BACKGROUND: Natural antimicrobial peptides (AMPs) present a promising solution to address the global threat of drug-resistant infections; however, their clinical translation is challenged by limitations in stability, cytotoxicity, and production costs.

METHODS: In the present study, a linear Battacin-derived peptide (DDLFD) was modified at the N-terminus with lipid chains, cinnamic acid, or lipoic acid. The lipoic acid-modified variant was further crosslinked by UV irradiation to form stable nanoparticles. The antibacterial performance against planktonic and biofilm bacteria was systematically evaluated in vitro.

RESULTS: The results demonstrated that lauric acid-modified pentapeptide (C₁₂-5) and crosslinked lipoic acid-modified pentapeptide (cLA-5) exhibited potent and rapid-acting effects against various pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). Moreover, they showed enhanced efficacy in eradicating bacterial biofilms. Biosafety assessments based on hemolysis and cytotoxicity assays indicated favorable biocompatibility profiles of cLA-5. Mechanistic investigations confirmed that the modified pentapeptides retained a membrane-targeting mode of action characteristic of natural AMPs, involving membrane depolarization and increased permeability. This physical mechanism effectively prevented the development of resistance in sequential passaging assays and showed strong synergistic effects with ciprofloxacin against ciprofloxacin-resistant strains, effectively restoring their antibiotic susceptibility.

CONCLUSIONS: Together, these findings underscore the strategic potential of rational structural modification, especially the crosslinked nanostructure, in advancing engineered AMPs toward clinical application.

PMID:41750505 | PMC:PMC12937389 | DOI:10.3390/antibiotics15020208