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Refereed/Peer-reviewed Staphylococcus aureus, a key ESKAPE bacteria, is responsible for most blood-based infections and, as a result, is a major economic healthcare burden requiring urgent attention. Here, we report in silico docking, synthesis, and assay of N1-diphenylmethyl triazole-based analogues (7–13) designed to interact with the entire binding site of S. aureus biotin protein ligase (SaBPL), an enzyme critical for the regulation of gluconeogenesis and fatty acid biosynthesis. The second aryl ring of these compounds enhances both SaBPL potency and whole cell activity against S. aureus relative to previously reported mono-benzyl triazoles. Analogues 12 and 13, with added substituents to better interact with the adenine binding site, are particularly potent, with Ki values of 6.01 ± 1.01 and 8.43 ± 0.73 nM, respectively. These analogues are the most active triazole-based inhibitors reported to date and, importantly, inhibit the growth of a clinical isolate strain of S. aureus ATCC 49775, with minimum inhibitory concentrations of 1 and 8 μg/mL, respectively.

We previously reported potent ligands and inhibitors ofMycobacterium tuberculosisdethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumannet al.,ACS Chem Biol. 2021, 16, 2339-2347); here the unconventional origin of the fragment compound they were derived from is described for the first time. Compound1(9b-hydroxy-6b,7,8,9,9a,9b-hexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified byin silicofragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (KD0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket, when1was soaked intoMtDTBS crystals, but the density was inconsistent with the structure of1. Here we show the lactone of1hydrolyses to carboxylic acid2under basic conditions, including those of the crystallography soak, with subsequent ring-opening of the component cyclobutane ring to form cyclopentylacetic acid3. Crystals soaked directly with authentic3produced electron density that matched that of crystals soaked with presumed1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed3enabled subsequent compound development into nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.SynopsisA molecule flagged in anin silicodocking screen againstMtDTBS, was inadvertently hydrolysed in the crystal conditions used for hit validation. The resulting fragment-sized molecule bound to the DAPA substrate binding pocket of the target enzyme (MtDTBS) with millimolar affinity, as measured by surface plasmon resonance, but was later modified to a highly potent (nanomolar) ligand and promising lead for the development of novel tuberculosis treatments.Graphical Abstract

The rise of multidrug-resistant bacteria, such as Staphylococcus aureus, has highlighted global urgency for new classes of antibiotics. Biotin protein ligase (BPL), a critical metabolic regulatory enzyme, is an important target that shows significant promise in this context. Here we report the in silico docking, synthesis, and biological assay of a new series of N1- diphenylmethyl-1,2,3-triazole-based S. aureus BPL (SaBPL) inhibitors (8-19) designed to probe the adenine binding site and define whole-cell activity for this important class of inhibitor. Triazoles 13 and 14 with N1-propylamine and-butanamide substituents, respectively, were particularly potent with Ki values of 10 +/- 2 and 30 +/- 6 nM, respectively, against SaBPL. A strong correlation was apparent between the Ki values for 8-19 and the in silico docking, with hydrogen bonding to amino acid residues S128 and N212 of SaBPL likely contributing to potent inhibition. Refereed/Peer-reviewed

The fabrication of solid-state single-molecule switches with high on-off conductance ratios has been proposed to advance conventional technology in areas such as molecular electronics. Herein, we employed the scanning tunneling microscope break junction (STM-BJ) technique to modulate conductance in single-molecule junctions using mechanically induced stretching. Compound 1a possesses two dihydrobenzothiophene (DHBT) anchoring groups at the opposite ends linked with rigid alkyne side arms to form a gold-molecule-gold junction, while 1b contains 4-pyridine-anchoring groups. The incorporation of ferrocene into the backbone of each compound allows rotational freedom to the cyclopentadienyl (Cp) rings to give two distinct conductance states (high and low) for each. Various control experiments and suspended junction compression/retraction measurements indicate that these high- and low-conductance plateaus are the results of conformational changes within the junctions (extended and folded states) brought about by mechanically induced stretching. A high-low switching factor of 42 was achieved for 1a, whereas an exceptional conductance ratio in excess of 2 orders of magnitude (205) was observed for 1b. To the best of our knowledge, this is the highest experimental on-off conductance switching ratio for a single-molecule junction exploiting the mechanically induced STM-BJ method. Computational studies indicated that the two disparate conductance states observed for 1a and 1b result from mechanically induced conformational changes due to an interplay between conductance and the dihedral angles associated with the electrode-molecule interfaces. Our study reveals the structure-function relationship that determines conductance in such flexible and dynamic systems and promotes the development of a single-molecule variable resistor with high on-off switching factors.

Model light-confining Tamm plasmon cavities based on gold-coated nanoporous anodic alumina photonic crystals (TMM-NAA-PCs) with spectrally tunable resonance bands were engineered. Laplacian and Lorentzian NAA-PCs produced by a modified Gaussian-like pulse anodization approach showed well-resolved, high-quality photonic stopbands, the position of which was precisely controlled across the visible spectrum by the periodicity in the input anodization profile. These PC structures were used as a platform material to develop highly reflective distributed Bragg mirrors, the top sides of which were coated with a thin gold film. The resulting nanoporous hybrid plasmonic-photonic crystals showed strong light-confining properties attributed to Tamm plasmon resonances at three specific positions of the visible spectrum. These structures achieved high sensitivity to changes in refractive index, with a sensitivity of ∼106 nm RIU-1. The optical sensitivity of TMM-NAA-PCs was assessed in real time, using a model chemically selective binding interaction between thiol-containing molecules and gold. The optical sensitivity was found to rely linearly on the spectral position of the Tamm resonance band, for both Laplacian and Lorentzian TMM-NAA-PCs. The density of self-assembled monolayers of thiol-containing analyte molecules formed on the surface of the metallic film directly contributes to the dependence of sensitivity on TMM resonance position in these optical transducers. Our findings provide opportunities to integrate TMM modes in NAA-based photonic crystal structures, with promising potential for optical technologies and applications requiring high-quality surface plasmon resonance bands.

Mycobacterium tuberculosis dethiobiotin synthase (MtDTBS) is a crucial enzyme involved in the biosynthesis of biotin in the causative agent of tuberculosis, M. tuberculosis. Here, we report a binder of MtDTBS, cyclopentylacetic acid 2 (KD = 3.4 ± 0.4 mM), identified via in silico screening. X-ray crystallography showed that 2 binds in the 7,8-diaminopelargonic acid (DAPA) pocket of MtDTBS. Appending an acidic group to the para-position of the aromatic ring of the scaffold revealed compounds 4c and 4d as more potent binders, with KD = 19 ± 5 and 17 ± 1 μM, respectively. Further optimization identified tetrazole 7a as a particularly potent binder (KD = 57 ± 5 nM) and inhibitor (Ki = 5 ± 1 μM) of MtDTBS. Our findings highlight the first reported inhibitors of MtDTBS and serve as a platform for the further development of potent inhibitors and novel therapeutics for the treatment of tuberculosis.

Nanoporous anodic alumina optical microcavities (NAA-μQVs) with spectrally tunable resonance band and surface chemistry are used as model light-confining photonic crystal (PC) platforms to elucidate the combined effect of spectral light confinement features and surface chemistry on optical sensitivity. These model nanoporous PCs show well-resolved, spectrally tunable resonance bands (RBs), the central wavelength of which is engineered from ∼400 to 800 nm by the period of the input anodization profile. The optical sensitivity of the as-produced (hydrophilic) and dichlorodimethylsilane-functionalized (hydrophobic) NAA-μQVs is studied by monitoring dynamic spectral shifts of their RB upon infiltration with organic- and aqueous-based analytical solutions of equally varying refractive index, from 1.333 to 1.345 RIU. Our findings demonstrate that hydrophilic NAA-μQVs show ∼81 and 35% superior sensitivity to their hydrophobic counterparts for organic- and aqueous-based analytical solutions, respectively. Interestingly, the sensitivity of hydrophilic NAA-μQVs per unit of spectral shift is more than 3-fold higher in organic than in aqueous matrices upon equal change of refractive index, with values of 0.347 ± 0.002 and 0.109 ± 0.001 (nm RIU

The human sliding clamp protein known as proliferating cell nuclear antigen (PCNA) orchestrates DNA-replication and -repair and as such is an ideal therapeutic target for proliferative diseases, including cancer. Peptides derived from the human p21 protein bind PCNA with high affinity via a 310-helical binding conformation and are known to shut down DNA-replication. Here, we present studies on short analogues of p21 peptides (143–151) conformationally constrained with a covalent linker between i, i + 4 separated cysteine residues at positions 145 and 149 to access peptidomimetics that target PCNA. The resulting macrocycles bind PCNA with KD values ranging from 570 nM to 3.86 μM, with the bimane-constrained peptide 7 proving the most potent. Subsequent X-ray crystallography and computational modelling studies of the macrocyclic peptides bound to PCNA indicated only the high-affinity peptide 7 adopted the classical 310-helical binding conformation. This suggests the 310-helical conformation is critical to high affinity PCNA binding, however NMR secondary shift analysis of peptide 7 revealed this secondary structure was not well-defined in solution. Peptide 7 is cell permeable and localised to the cell cytosol of breast cancer cells (MDA-MB-468), revealed by confocal microscopy showing blue fluorescence of the bimane linker. The inherent fluorescence of the bimane moiety present in peptide 7 allowed it to be directly imaged in the cell uptake assay, without attachment of an auxiliary fluorescent tag. This highlights a significant benefit of using a bimane constraint to access conformationally constrained macrocyclic peptides. This study identifies a small peptidomimetic that binds PCNA with higher affinity than previous reported p21 macrocycles, and is cell permeable, providing a significant advance toward development of a PCNA inhibitor for therapeutic applications., A small, inherently fluorescent macrocyclic peptide constrained with a bimane-linker is cell permeable, and binds the human sliding clamp protein, PCNA, in a 310-helical conformation with nanomolar affinity.

We present a new coating procedure to prepare optical fibre sensors suitable for use with protein analytes. We demonstrate this through the detection of AlexaFluor-532 tagged streptavidin by its binding to D-biotin that is functionalised onto an optical fibre, via incorporation in a silk fibroin fibre coating. The D-biotin was covalently attached to a silk-binding peptide to provide SBP–biotin, which adheres the D-biotin to the silk-coated fibre tip. These optical fibre probes were prepared by two methods. The first involves dip-coating the fibre tip into a mixture of silk fibroin and SBP–biotin, which distributes the SBP–biotin throughout the silk coating (method A). The second method uses two steps, where the fibre is first dip-coated in silk only, then SBP–biotin added in a second dip-coating step. This isolates SBP–biotin to the outer surface of the silk layer (method B). A series of fluorescence measurements revealed that only the surface bound SBP–biotin detects streptavidin with a detection limit of 15 μg mL−1. The fibre coatings are stable to repeated washing and long-term exposure to water. Formation of silk coatings on fibres using commercial aqueous silk fibroin was found to be inhibited by a lithium concentration of 200 ppm, as determined by atomic absorption spectroscopy. This was reduced to less than 20 ppm by dialysis against water, and was found to successfully form a coating on optical fibres.

4-Aminobutanenitrile (1) is an important synthetic intermediate for neurological disorder therapeutics including Parkinson’s and Alzheimer’s diseases, and is an industrial precursor to pyrroline an...

A new class of semiconductor photonic crystals composed of titanium dioxide (TiO2)-functionalized nanoporous anodic alumina (NAA) broadband-distributed Bragg reflectors (BDBRs) for visible-light-driven photocatalysis is presented. NAA-BDBRs produced by double exponential pulse anodization (DEPA) show well-resolved, spectrally tunable, broad photonic stop bands (PSBs), the width of which can be precisely tuned from 70 ± 6 to 153 ± 9 nm (in air) by progressive modification of the anodization period in the input DEPA profile. Photocatalytic efficiency of TiO2-NAA-BDBRs with tunable PSB width upon visible-NIR illumination is studied using three model photodegradation reactions of organics with absorbance bands across the visible spectral regions. Analysis of these reactions allows us to elucidate the interplay of spectral distance between red edge of TiO2-NAA-BDBRs' PSB, electronic bandgap, and absorbance band of model organics in harnessing visible photons for photocatalysis. Photodegradation reaction efficiency is optimal when the PSB's red edge is spectrally close to the electronic bandgap of the functional semiconductor coating. Photocatalytic performance decreases dramatically when the red edge of the PSB is shifted toward visible wavelengths. However, a photocatalytic recovery is observed when the PSB's red edge is judiciously positioned within the proximity of the absorption band of model organics, indicating that TiO2-NAA-BDBRs can harness visible electromagnetic waves to speed up photocatalytic reactions by drastically slowing the group velocity of incident photons at specific spectral regions. Our advances provide new opportunities to better understand and engineer light-matter interactions for photocatalysis, using TiO2-NAA-BDBRs as model nanoporous semiconductor platforms. These high-performing photocatalysts could find broad applicability in visible-NIR light harvesting for environmental remediation, green energy generation, and chemical synthesis.

Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl-ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate-ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.

The hemispherical barrier oxide layer (BOL) closing the bottom tips of hexagonally distributed arrays of cylindrical nanochannels in nanoporous anodic alumina (NAA) membranes is structurally engineered by anodizing aluminum substrates in three distinct acid electrolytes at their corresponding self-ordering anodizing potentials. These nanochannels display a characteristic ionic current rectification (ICR) signal between high and low ionic conduction states, which is determined by the thickness and chemical composition of the BOL and the pH of the ionic electrolyte solution. The rectification efficiency of the ionic current associated with the flow of ions across the anodic BOL increases with its thickness, under optimal pH conditions. The inner surface of the nanopores in NAA membranes was chemically modified with thiol-terminated functional molecules. The resultant NAA-based iontronic system provides a model platform to selectively detect gold metal ions (Au

Nitric oxide (NO) is a ubiquitous, volatile, cellular signaling molecule that operates across a wide physiological concentration range (pM-µM) in different tissues. It is a highly diffusible messenger and intermediate in various metabolic pathways. NO plays a pivotal role in maintaining optimum cardiovascular function, particularly by regulating vascular tone and blood flow. This review highlights the need for accurate, real-time bioimaging of NO in clinical diagnostic, therapeutic, monitoring, and theranostic applications within the cardiovascular system. We summarize electrochemical, optical, and nanoscale sensors that allow measurement and imaging of NO, both directly and indirectly via surrogate measurements. The physical properties of NO render it difficult to accurately measure in tissues using direct methods. There are also significant limitations associated with the NO metabolites used as surrogates to indirectly estimate NO levels. All these factors added to significant variability in the measurement of NO using available methodology have led to a lack of sensors and imaging techniques of clinical applicability in relevant vascular pathologies such as atherosclerosis and ischemic heart disease. Challenges in applying current methods to biomedical and clinical translational research, including the wide physiological range of NO and limitations due to the characteristics and toxicity of the sensors are discussed, as are potential targets and modifications for future studies. The development of biocompatible nanoscale sensors for use in combination with existing clinical imaging modalities provides a feasible opportunity for bioimaging NO within the cardiovascular system.

The majority of the protein structures have been elucidated under equilibrium conditions. The aim herein is to provide a better understanding of the dynamic behavior inherent to proteins by fabricating a label-free nanodevice comprising a single-peptide junction to measure real-time conductance, from which their structural dynamic behavior can be inferred. This device contains an azobenzene photoswitch for interconversion between a well-defined cis, and disordered trans isomer. Real-time conductance measurements revealed three distinct states for each isomer, with molecular dynamics simulations showing each state corresponds to a specific range of hydrogen bond lengths within the cis isomer, and specific dihedral angles in the trans isomer. These insights into the structural dynamic behavior of peptides may rationally extend to proteins. Also demonstrated is the capacity to modulate conductance which advances the design and development of bioinspired electronic nanodevices.

The thiol-selective fluorescent imaging agent, dibromobimane, has been repurposed to crosslink cysteine- and homocysteine-containing peptides, with the resulting bimane linker acting as both a structural constraint and a fluorescent tag. Macrocyclisation was conducted on nine short peptides containing two cysteines and/or homocysteines, both on-resin and in buffered aqueous solution, to give macrocycles ranging in size from 16 (i,i+2) to 31 (i,i+7) atoms. The structures were defined by CD, NMR structure calculations by using Xplor-NIH, NMR secondary shift and JHαNH analyses to reveal helical structure in the i,i+4 (1, 2), and i,i+3 (5) constrained peptides. Cellular-uptake studies were conducted with three of the macrocycles. Subsequent confocal imaging revealed punctate fluorescence within the cytosol indicative of peptides trapped in endocytic vesicles. These studies demonstrate that dibromobimane is an effective tool for defining secondary structure within short peptides, whilst simultaneously introducing a fluorescent tag suitable for common cell-based experiments.

Understanding and controlling charge transport across multiple parallel molecules are fundamental to the creation of innovative functional electronic components, as future molecular devices will likely be multimolecular. The smallest possible molecular ensemble to address this challenge is a dual-molecule junction device, which has potential to unravel the effects of intermolecular crosstalk on electronic transport at the molecular level that cannot be elucidated using either conventional single-molecule or self-assembled monolayer (SAM) techniques. Herein, we demonstrate the fabrication of a scanning tunneling microscopy (STM) dual-molecule junction device, which utilizes noncovalent interactions and allows for direct comparison to the conventional STM single-molecule device. STM-break junction (BJ) measurements reveal a decrease in conductance of 10% per molecule from the dual-molecule to the single-molecule junction device. Quantum transport simulations indicate that this decrease is attributable to intermolecular crosstalk (i.e., intermolecular π-π interactions), with possible contributions from substrate-mediated coupling (i.e., molecule-electrode). This study provides the first experimental evidence to interpret intermolecular crosstalk in electronic transport at the STM-BJ level and translates the experimental observations into meaningful molecular information to enhance our fundamental knowledge of this subject matter. This approach is pertinent to the design and development of future multimolecular electronic components and also to other dual-molecular systems where such crosstalk is mediated by various noncovalent intermolecular interactions (e.g., electrostatic and hydrogen bonding).

Amyloid beta peptide (Aβ42) aggregation in the brain is thought to be responsible for the onset of Alzheimer's disease, an insidious condition without an effective treatment or cure. Hence, a strategy to prevent aggregation and subsequent toxicity is crucial. Bio-inspired peptide-based molecules are ideal candidates for the inhibition of Aβ42 aggregation, and are currently deemed to be a promising option for drug design. In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregation process. Fluorescence assays, native ion-mobility mass spectrometry (IM-MS) and cell viability assays were used to demonstrate that the peptide interacts with Aβ42 monomers and oligomers with high specificity, leading to almost complete inhibition of fibril formation, with essentially no cytotoxic effects. These data define the peptide-based inhibitor as a potentially potent anti-amyloid drug candidate for this hitherto incurable disease.

The formation of a 2:1 sandwich-type complex of 15-crown-5 with K+ has been previously used for the development of various smart materials and devices through detecting K+-induced changes in absorb...

A single-fiber-based probe with a diameter of $\boldsymbol{125 \mu \mathrm{m}}$ , capable of combined imaging and sensing, was developed and applied in an in vitro fertilization setting. The probe can resolve a cumulus oocyte complex within an ovarian follicle, and measure a pH change of 0.04 units.

The antioxidant nuclear factor erythroid 2-related factor 2 (Nrf2) is a desirable therapeutic target for a broad range of pathologies, including chronic diseases of the lung and liver, and autoimmune, neurodegenerative, and cardiovascular disorders. However, current Nrf2 activators are limited by unwanted effects due to non-specificity, and systemic distribution and action. Here we report that a 1,2-dicarbonyl moiety masks the electrophilic reactivity of the Nrf2 activator monomethyl fumarate (MMF), otherwise responsible for its non-specific effects. The 1,2-dicarbonyl compound is highly susceptible to Baeyer-Villiger oxidation, with generation of MMF specifically on exposure to pathological levels of hydrogen peroxide or peroxynitrite. Oral treatment with the MMF generating 1,2-dicarbonyl compound reversed chronic neuropathic and osteoarthritis pain in mice, and selectively activated Nrf2 at sites of oxidative stress. This 1,2-dicarbonyl platform may be used to treat additional disorders of oxidative stress, and to selectively target other therapeutics to sites of redox imbalance.

An i-i+4 or i-i+3 bimane-containing linker was introduced into a peptide known to target Estrogen Receptor alpha (ERα), in order to stabilise an α-helical geometry. These macrocycles were studied by CD and NMR to reveal the i-i+4 constrained peptide adopts a 310 -helical structure in solution, and an α-helical conformation on interaction with the ERα coactivator recruitment surface in silico. An acyclic bimane-modified peptide is also helical, when it includes a tryptophan or tyrosine residue; but is significantly less helical with a phenylalanine or alanine residue, which indicates such a bimane modification influences peptide structure in a sequence dependent manner. The fluorescence intensity of the bimane appears influenced by peptide conformation, where helical peptides displayed a fluorescence increase when TFE was added to phosphate buffer, compared to a decrease for less helical peptides. This study presents the bimane as a useful modification to influence peptide structure as an acyclic peptide modification, or as a side-chain constraint to give a macrocycle.

The primary sequence and secondary structure of a peptide are crucial to charge migration, not only in solution (electron transfer, ET), but also in the solid-state (electron transport, ETp). Hence, understanding the charge migration mechanisms is fundamental to the development of biomolecular devices and sensors. We report studies on four Aib-containing helical peptide analogues: two acyclic linear peptides with one and two electron-rich alkene-based side chains, respectively, and two peptides that are further rigidified into a macrocycle by a side bridge constraint, containing one or no alkene. ETp was investigated across Au/peptide/Au junctions, between 80 and 340 K in combination with the molecular dynamic (MD) simulations. The results reveal that the helical structure of the peptide and electron-rich side chain both facilitate the ETp. As temperature increases, the loss of helical structure, change of monolayer tilt angle, and increase of thermally activated fluctuations affect the conductance of peptides. Specifically, room temperature conductance across the peptide monolayers correlates well with previously observed ET rate constants, where an interplay between backbone rigidity and electron-rich side chains was revealed. Our findings provide new means to manipulate electronic transport across solid-state peptide junctions.

Proliferating cell nuclear antigen (PCNA) is an excellent inhibition target to shut down highly proliferative cells and thereby develop a broad-spectrum cancer therapeutic. It interacts with a wide variety of proteins through a conserved motif referred to as the PCNA-interacting protein (PIP) box. There is large sequence diversity between high-affinity PCNA binding partners, but with conservation of the binding structure-a well-defined 310 -helix. Herein, all current PIP-box peptides crystallised with human PCNA are collated to reveal common trends between binding structure and affinity. Key intra- and intermolecular hydrogen-bonding networks that stabilise the 310 -helix of PIP-box partners are highlighted and related back to the canonical PIP-box motif. High correlation with the canonical PIP-box sequence does not directly afford high affinity. Instead, we summarise key interactions that stabilise the binding structure that leads to enhanced PCNA binding affinity. These interactions also implicate the "non-conserved" residues within the PIP-box that have previously been overlooked. Such insights will allow a more directed approach to develop therapeutic PCNA inhibitors.

The rapidly expanding field of photoswitchable biomolecules is a major frontier in scientific research and provides unparalleled opportunities for studying biological pathways and disease progression. In particular, the development of photochromic peptides has delivered both scientific tools and candidates for photopharmaceuticals. The action and function of the peptide can be remotely altered using light, allowing detection of its biological role in complex biological settings, while also enabling folding studies that provide greater understanding of protein structure dynamics. In this review we provide a key, comprehensive overview of the different types of photoswitches that have been used to control peptide structure, excluding the already extensively reviewed azobenzene. This will help address the question as to which synthetic photoswitch to use in a given study.

Here, we report the design, synthesis, and evaluation of a series of inhibitors of Staphylococcus aureus BPL (SaBPL), where the central acyl phosphate of the natural intermediate biotinyl-5′-AMP (1) is replaced by a sulfonamide isostere. Acylsulfamide (6) and amino sulfonylurea (7) showed potent in vitro inhibitory activity (Ki = 0.007 ± 0.003 and 0.065 ± 0.03 μM, respectively) and antibacterial activity against S. aureus ATCC49775 with minimum inhibitory concentrations of 0.25 and 4 μg/mL, respectively. Additionally, the bimolecular interactions between the BPL and inhibitors 6 and 7 were defined by X-ray crystallography and molecular dynamics simulations. The high acidity of the sulfonamide linkers of 6 and 7 likely contributes to the enhanced in vitro inhibitory activities by promoting interaction with SaBPL Lys187. Analogues with alkylsulfamide (8), β-ketosulfonamide (9), and β-hydroxysulfonamide (10) isosteres were devoid of significant activity. Binding free energy estimation using computational methods suggests deprotonated 6 and 7 to be the best binders, which is consistent with enzyme assay results. Compound 6 was unstable in whole blood, leading to poor pharmacokinetics. Importantly, 7 has a vastly improved pharmacokinetic profile compared to that of 6 presumably due to the enhanced metabolic stability of the sulfonamide linker moiety. Refereed/Peer-reviewed

A series of dipeptide aldehydes containing different N-terminal heterocycles was prepared and assayed in vitro against α-chymotrypsin to ascertain the importance of the heterocycle in maintaining a β-strand geometry while also providing a hydrogen bond donor equivalent to the backbone amide nitrogen of the surrogate amino acid. The dipeptide containing a pyrrole constraint (10) was the most potent inhibitor, with >30-fold improved activity over dipeptides which lacked a nitrogen hydrogen bond donor (namely thiophene 11, furan 12 and pyridine 13). Molecular docking studies of 10 bound to α-chymotrypsin demonstrates a hydrogen bond between the pyrrole nitrogen donor and the backbone carbonyl of Gly216 located in the S3 pocket which is proposed to be critical for overall binding.

A comprehensive study on the engineering of titanium dioxide-functionalized nanoporous anodic alumina distributed Bragg reflectors (TiO2–NAA-DBRs) for photocatalysis enhanced by the “slow photon” effect is presented. The photocatalytic performance of these composite photonic crystals (PCs) is assessed by monitoring photodegradation of a variety of organic molecules with absorbance bands across the spectral regions. This study demonstrates that photocatalytic performance of TiO2–NAA-DBRs is enhanced by the “slow photon” effect when the edges of the PC’s photonic stopband (PSB) fall within the absorbance band of the organic molecules. The photocatalytic performance is significantly enhanced when the PSB’s red edge is in close proximity to the absorbance band of the organic molecules. Overall photocatalytic degradation is also dependent on the total pore length of the PC structure, charge of the organic molecules, percentage of vis–near-IR irradiation, and matrix complexity (i.e., interfering ions and molecules) when the PC’s PSB is partially or entirely misaligned with respect to the absorbance band of the organic molecules. Finally, the real-life application of TiO2–NAA-DBRs to degrade pollutants such as pesticides in environmental matrices is demonstrated. This study provides new insights into the development of rationally engineered, high-performing, safe, and reusable photocatalyst systems. This is peer-reviewed version of the article: ACS Applied Energy Materials, 2019, 2, 2, 1169-1184, [https://doi.org/10.1021/acsaem.8b01721] [http://cer.ihtm.bg.ac.rs/handle/123456789/2988]

We present a study on optical and surface chemistry engineering of nanoporous photonic crystals as sensing platforms for detection of ionic copper. The optical sensing system combines glutaraldehyde-crosslinked double-layered polyethyleneimine (PEI-GA-PEI)-functionalized nanoporous anodic alumina gradient-index filters (NAA-GIFs) with reflection spectroscopy for label-free, selective detection of ionic copper in water matrices. The spectral position of the photonic stopband (PSB) of PEI-GA-PEI-functionalized NAA-GIFs is tuned across the visible-NIR spectral region to assess the impact of this optical parameter on the sensing performance of the system. Spectral shifts in the characteristic PSB (ΔλPSB) of PEI-GA-PEI-functionalized NAA-GIFs upon exposure to analytical solutions of ionic copper are used as a sensing parameter. Shifts in ΔλPSB of these photonic crystals are monitored in real-time under dynamic flow conditions. Calibration of the sensing system with analytical solutions of ionic copper from 0.1 to 100 mM shows a dual sensing regime, at low (from 1 to 10 mM) and high (from 10 to 100 mM) concentrations, which is associated with conformational changes of the PEI-GA-PEI functional layer. The binding mechanism of Cu2+ in PEI-GA-PEI-modified NAA-GIFs follows a Freundlich isotherm model. The performance of the PEI-GA-PEI-NAA-GIFs for real-life applications is demonstrated using environmental water. The system shows excellent correlation in both environmental and analytical water solutions. This study provides new opportunities to engineer portable optical sensing systems with tailor-designed features to detect ionic copper for environmental applications.

An extensive study on the structural engineering of titanium dioxide-functionalized nanoporous anodic alumina optical microcavities (TiO2-NAA-μQVs) for photocatalysis enhanced by light confinement is presented. The architecture of NAA-μQVs – composed of two highly reflective NAA-based gradient index filters (NAA-GIFs) with a physical cavity layer in between – is engineered by sinusoidal pulse anodization to tune the characteristic resonance band of these photonic crystals (PCs) across the visible-NIR spectrum. NAA-μQVs are chemically functionalized with photo-active layers of TiO2 by the sol–gel method. Photocatalytic enhancements in TiO2-NAA-μQVs are identified by monitoring the photodegradation of model organics with absorbance bands at specific positions within the visible spectral region. The performance of TiO2-NAA-μQVs under controlled visible-NIR irradiation is enhanced by resonant recirculation of light within the semiconductor PC's structure. These enhancements are found to rely strongly on the relative position between the resonance band of TiO2-NAA-μQVs and the absorbance band of model organics, and on the light confinement quality. Overall photocatalytic degradation is also dependent on the total thickness of the PC structure and the molecular steric structure of organics. Reusability and effect of the crystallographic phase of photo-active TiO2 layers in TiO2-NAA-μQVs to degrade a model organic are also demonstrated. This study provides new opportunities to develop highly performing, cost-effective, industrially scalable and reusable photocatalyst materials capable of achieving an efficient management of photons at the nanoscale to accelerate photocatalytic reactions by light confinement effect.