Biology subjects

Czekster, C. M.

Publications and source records attributed to Czekster, C. M..

8 recordsLinked to original sources

bioRxiv2026

Bacterial Aminopeptidase-Activated Peptide Prodrug Enables Species-Selective Targeting of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an adaptable organism, frequently found in chronic infections, and for which antimicrobial resistance is a growing concern. Therefore, there is an urgent need for alternative therapeutic strategies. Cationic antimicrobial peptides (AMPs) offer potent bactericidal activity but suffer from limited selectivity and potential host toxicity. To enhance species-specific targeting, we designed two prodrug variants of the AMP D-Bac8CLeu2,5 - EEEE{square}-Bac8CLeu2,5 and ELE{square} D-Bac8CLeu2,5 --engineered for activation by the P. aeruginosa extracellular aminopeptidase PaAP. While both prodrug motifs effectively neutralized the positive charge of D-Bac8CLeu2,5 and prevented DNA-peptide complex formation, EEEE{square}-Bac8CLeu2,5 showed negligible antimicrobial activity due to slow and incomplete activation. In contrast, ELEG{square}-Bac8CLeu2,5 underwent rapid PaAP{square}mediated activation, restoring bactericidal activity in planktonic cultures and biofilms. PaAP contributed significantly to complete prodrug activation, particularly within biofilms, where the accumulation of partially activated intermediates correlated with biphasic killing kinetics. The prodrug showed reduced activity against other ESKAPEE pathogens, demonstrating selective activation by P. aeruginosa. Experiments selecting resistant bacteria revealed distinct mutations in lipopolysaccharide biosynthesis pathways for D-Bac8CLeu2,5 and the prodrug, with limited cross{square}resistance. These findings establish aminopeptidase{square}activated AMP prodrugs as a promising approach for species{square}selective antimicrobial therapy and highlight the feasibility of exploiting bacterial enzymes for controlled antimicrobial peptide activation.

microbiology↗

bioRxiv2025

Dimerization and Threonine-Dependent Stabilization Govern Human YRDC Catalysis

Addition of N6-threonylcarbamoyladenosine occurs at position 37 (tA37) of five mitochondrial tRNA species, influencing translation fidelity and efficiency. Mutations in YRDC, the enzyme catalyzing the first step in tA37 synthesis, cause severe neurological and renal diseases in humans, including in Galloway-Mowatt disease (GAMOS). YRDC generates threonylcarbamoyl-AMP (TC-AMP) using ATP, threonine and bicarbonate as substrates, yet their binding order, residues involved in amino-acid selectivity, and precisely how mutations contribute to disease remain unclear. Here, we combine protein biophysics, mass spectrometry, NMR, mutagenesis and kinetics to define how the human enzyme operates. Differential scanning fluorimetry and circular dichroism identify L-threonine as the gatekeeper ligand. It binds with millimolar affinity, stabilizing YRDC and enhancing ATP binding nearly fortyfold, enabling bicarbonate association. Several amino acids can form aminoacylcarbamoyl-AMP adducts in vitro, but threonine yields superior protein stabilization and product formation. Native mass spectrometry and single-molecule mass photometry corroborate YRDCs dimeric state. GAMOS-linked mutations destabilize folding, disrupting dimerization and uncoupling substrate binding from catalysis, explaining functional losses. Supported by kinetic data and NMR, we propose a chemical mechanism for the reaction and identify dimerization and conformational stability as control points for activity. This work provides a foundation for designing selective YRDC inhibitors or enhancers.

biochemistry↗

bioRxiv2025

Improved nucleoside (2'-deoxy)ribosyltransferases maximize enzyme promiscuity while maintaining catalytic efficiency

Nucleoside analogues have been extensively used to treat viral and bacterial infections and cancer for the past 60 years. However, their chemical synthesis is complex and often requires multiple steps and a dedicated synthetic route for every new nucleoside to be produced. Wild type nucleoside 2'-deoxyribosyltransferase enzymes are promising for biocatalysis. Guided by the structure of the enzyme from the thermophilic organism Chroococcidiopsis thermalis PCC 7203 (CtNDT) bound to the ribonucleoside analogue Immucillin-H, we designed mutants of CtNDT and the psychrotolerant Bacillus psychrosaccharolyticus (BpNDT) to improve catalytic efficiency with 3'-deoxynucleosides and ribonucleosides, while maintaining nucleobase promiscuity to generate over 100 distinct nucleoside products. Enhanced catalytic efficiency towards ribonucleosides and 3'-deoxyribonucleosides occurred via gains in turnover rate, rather than improved substrate binding. We determined crystal structures of two engineered variants as well as kinetic parameters with different substrates, unveiling molecular details underlying their expanded substrate scope. Our rational approach generated robust enzymes and a roadmap for reaction conditions applicable to a wide variety of substrates. Insert Table of Contents artwork here O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/641663v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@3ef466org.highwire.dtl.DTLVardef@11f55b0org.highwire.dtl.DTLVardef@32d0dcorg.highwire.dtl.DTLVardef@2e22cc_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Immobilized Nucleoside 2'-Deoxyribosyltransferases from Extremophiles for Nucleoside Biocatalysis

The synthesis of nucleosides is crucial for pharmaceutical and biotechnological applications, acting as drugs and as essential building blocks for numerous therapeutic agents. However, most enzymes employed in nucleoside biocatalysis are not recycled, possess limit stability and strict substrate selection for ribonucleosides or 2'deoxyribonucleosides. We employed 2'deoxyribonucleoside transferase (NDT) enzymes from thermophilic and psychrophilic bacteria to demonstrate they can be immobilized to en-hance specific activity, stability, and recyclability. NDT enzymes from Chroococcidiopsis thermalis (CtNDT), and Bacillus psychrosaccharolyticus (BpNDT) were immobilized by covalent attachment to chitosan beads. A double mutant of CtNDT, capable of generating 3'deoxyribonucleosides, showed remarkable and increased stability after immobilization when compared to the same enzyme in solution. Furthermore, we demonstrated the recyclability of immobilized biocatalysts, with a tenfold improvement in reaction yield over 20 consecutive cycles, highlighting the practicality and sustainability of the developed immobilization method. We used our strategy to produce a pharmaceutically relevant 3'deoxyribonucleoside (2-fluoro-3'-deoxyadenosine). This highlights the importance of efficient immobilization techniques to enhance catalytic properties of NDT enzymes, expanding their utility in biocatalysis.

biochemistry↗

bioRxiv2024

Overcoming the challenges of cascade reactions and complex substrates in natural product biocatalysis: Immobilization of a cyclodipeptide synthase.

Cyclodipeptide synthases (CDPSs) use aminoacylated tRNAs to produce cyclic dipeptide natural products which can have anticancer and neuroprotective activity. Despite their potential, applications involving CDPSs are hindered by enzyme instability and challenges in producing aminoacylated tRNAs. Immobilizing enzymes can enhance stability and recyclability, yet studies on immobilized enzymes using aminoacylated tRNAs are lacking. Here, we immobilized the CDPS enzyme from Parcubacteria bacterium RAAC4_OD1_1 (PbCDPS) using three sustainable supports: biochar from waste materials, calcium-alginate beads, and chitosan beads. Active PbCDPS immobilization led to production of the cyclodipeptide cyclo (His-Glu) (cHE). Notably, following activation with glutaraldehyde, a five-fold increase in cHE production was observed, while the immobilized enzyme remained active for seven consecutive cycles. Furthermore, we co-immobilized three enzymes required for the cascade reaction yielding cHE, all of which require aminoacyl-tRNA substrates (PbCDPS, histidyl-tRNA synthetase, and glutamyl-tRNA synthetase). This enzymatic cascade successfully generated the cyclic dipeptide of interest, showcasing the potential of immobilizing complex enzymes operating in cascade on a single support. We demonstrated that tRNAs remained free in solution without adsorption onto beads. This work paves the way for the immobilization of enzymes utilizing tRNAs and potentially other complex substrates, expanding the spectrum of reactions exploitable with this technology. Graphical AbstractO_LIFor Table of Contents Only C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/604810v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@12794baorg.highwire.dtl.DTLVardef@1956c09org.highwire.dtl.DTLVardef@e7f800org.highwire.dtl.DTLVardef@14ac97d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament

Cyclic dipeptides are produced by organisms in all domains of life. Many possess biological activities as anticancer and antimicrobial compounds. Oxidations are frequently present in these biologically active peptides. C-C bond oxidation is catalysed by tailoring enzymes, including cyclodipeptide oxidases. These flavin-dependent enzymes are underexplored due to their complex three-dimensional arrangement involving multiple copies of two distinct small subunits and unclear mechanistic features underlying substrate selection and catalysis. Here, we determined the structure and mechanism of the cyclodipeptide oxidase from the halophile Nocardiopsis dassonvillei (NdasCDO), part of the biosynthetic pathway for nocazine natural products. We show NdasCDO forms filaments in solution with a covalently bound FMN cofactor in the interface between three distinct subunits. The enzyme is promiscuous, using many cyclic dipeptides as substrates in a distributive manner. The reaction is optimal at high pH, involving the formation of a radical intermediate. Pre-steady state kinetics, a sizeable solvent kinetic isotope effect and lack of viscosity effects support that a step coupled to FMN regeneration determines the rate of the reaction. Our work dissects the complex mechanistic and structural features of this dehydrogenation reaction. This sets the stage to utilizing NdasCDO as a biocatalyst and expands the FMN-dependent oxidase family to include enzyme filaments.

biochemistry↗

bioRxiv2021

Structure, dynamics, and inhibition of Staphylococcus aureus m1A22-tRNA methyltransferase

The enzyme m1A22-tRNA methyltransferase (TrmK) catalyses the transfer of a methyl group from SAM to the N1 of adenine 22 in tRNAs. TrmK is essential for Staphylococcus aureus survival during infection, but has no homologue in mammals, making it a promising target for antibiotic development. Here we describe the structural and functional characterisation of S. aureus TrmK. Crystal structures are reported for S. aureus TrmK apoenzyme and in complexes with SAM and SAH. Isothermal titration calorimetry showed that SAM binds to the enzyme with favourable but modest enthalpic and entropic contributions, whereas SAH binding leads to an entropic penalty compensated by a large favourable enthalpic contribution. Molecular dynamics simulations point to specific motions of the C-terminal domain being altered by SAM binding, which might have implications for tRNA recruitment. Activity assays for S. aureus TrmK-catalysed methylation of WT and position 22 mutants of tRNALeu demonstrate that the enzyme requires an adenine at position 22 of the tRNA. Intriguingly, a small RNA hairpin of 18 nucleotides is methylated by TrmK depending on the position of the adenine. In-silico screening of compounds suggested plumbagin as a potential inhibitor of TrmK, which was confirmed by activity measurements. Furthermore, LC-MS indicated the protein was covalently modified by one equivalent of the inhibitor, and proteolytic digestion coupled with LC-MS identified Cys92, in the vicinity of the SAM-binding site, as the sole residue modified. These results these results identify a cryptic binding pocket of S. aureus TrmK and lay the foundation for future structure-based drug discovery.

biochemistry↗

bioRxiv2020

The dynamic interplay of host and viral enzymes in type III CRISPR-mediated cyclic nucleotide signalling

Cyclic nucleotide second messengers are increasingly implicated in prokaryotic anti-viral defence systems. Type III CRISPR systems synthesise cyclic oligoadenylate (cOA) upon detecting foreign RNA, activating ancillary nucleases that can be toxic to cells, necessitating mechanisms to remove cOA in systems that operate via immunity rather than abortive infection. Previously, we demonstrated that the Sulfolobus solfataricus type III-D CRISPR complex generates cyclic tetra-adenylate (cA4), activating the ribonuclease Csx1, and showed that subsequent RNA cleavage and dissociation acts as an "off-switch" for the cyclase activity (Rouillon et al., 2018). Subsequently, we identified the cellular ring nuclease Crn1, which slowly degrades cA4 to reset the system, and demonstrated that viruses can subvert type III CRISPR immunity by means of a potent anti-CRISPR ring nuclease variant. Here, we present a comprehensive analysis of the dynamic interplay between these enzymes, governing cyclic nucleotide levels and infection outcomes in virus-host conflict.

biochemistry↗