Erratum to "Optical Detection of Distal Lung Enzyme Activity in Human Inflammatory Lung Disease".

[This corrects the article DOI: 10.34133/2021/9834163.].

pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides.

The isoelectric point (pI) is a fundamental physicochemical property of peptides and proteins. It is widely used to steer design away from low solubility and aggregation and guide peptide separation and purification. Experimental measurements of pI can be replaced by calculations knowing the ionizable groups of peptides and their corresponding pKa values. Different pKa sets are published in the literature for natural amino acids, however, they are insufficient to describe synthetically modified peptides, complex peptides of natural origin, and peptides conjugated with structures of other modalities. Noncanonical modifications (nCAAs) are ignored in the conventional sequence-based pI calculations, therefore producing large errors in their pI predictions. In this work, we describe a pI calculation method that uses the chemical structure as an input, automatically identifies ionizable groups of nCAAs and other fragments, and performs pKa predictions for them. The method is validated on a curated set of experimental measures on 29 modified and 119093 natural peptides, providing an improvement of R2 from 0.74 to 0.95 and 0.96 against the conventional sequence-based approach for modified peptides for the two studied pKa prediction tools, ACDlabs and pKaMatcher, correspondingly. The method is available in the form of an open source Python library at https://github.com/AstraZeneca/peptide-tools, which can be integrated into other proprietary and free software packages. We anticipate that the pI calculation tool may facilitate optimization and purification activities across various application domains of peptides, including the development of biopharmaceuticals.

Optical Detection of Distal Lung Enzyme Activity in Human Inflammatory Lung Disease.

Objective and Impact Statement. There is a need to develop platforms delineating inflammatory biology of the distal human lung. We describe a platform technology approach to detect in situ enzyme activity and observe drug inhibition in the distal human lung using a combination of matrix metalloproteinase (MMP) optical reporters, fibered confocal fluorescence microscopy (FCFM), and a bespoke delivery device. Introduction. The development of new therapeutic agents is hindered by the lack of in vivo in situ experimental methodologies that can rapidly evaluate the biological activity or drug-target engagement in patients. Methods. We optimised a novel highly quenched optical molecular reporter of enzyme activity (FIB One) and developed a translational pathway for in-human assessment. Results. We demonstrate the specificity for matrix metalloproteases (MMPs) 2, 9, and 13 and probe dequenching within physiological levels of MMPs and feasibility of imaging within whole lung models in preclinical settings. Subsequently, in a first-in-human exploratory experimental medicine study of patients with fibroproliferative lung disease, we demonstrate, through FCFM, the MMP activity in the alveolar space measured through FIB One fluorescence increase (with pharmacological inhibition). Conclusion. This translational in situ approach enables a new methodology to demonstrate active drug target effects of the distal lung and consequently may inform therapeutic drug development pathways.

High fidelity fibre-based physiological sensing deep in tissue.

Physiological sensing deep in tissue remains a clinical challenge. Here a flexible miniaturised sensing optrode providing a platform to perform minimally invasive in vivo in situ measurements is reported. Silica microspheres covalently coupled with a high density of ratiometrically configured fluorophores were deposited into etched pits on the distal end of a 150 µm diameter multicore optical fibre. With this platform, photonic measurements of pH and oxygen concentration with high precision in the distal alveolar space of the lung are reported. We demonstrated the phenomenon that high-density deposition of carboxyfluorescein covalently coupled to silica microspheres shows an inverse shift in fluorescence in response to varying pH. This platform delivered fast and accurate measurements (±0.02 pH units and ±0.6 mg/L of oxygen), near instantaneous response time and a flexible architecture for addition of multiple sensors.

Surface Charge-Dependent Cellular Uptake of Polystyrene Nanoparticles.

The evaluation of the role of physicochemical properties in the toxicity of nanoparticles is important for the understanding of toxicity mechanisms and for controlling the behavior of nanoparticles. The surface charge of nanoparticles is suggested as one of the key parameters which decide their biological impact. In this study, we synthesized fluorophore-conjugated polystyrene nanoparticles (F-PLNPs), with seven different types of surface functional groups that were all based on an identical core, to evaluate the role of surface charge in the cellular uptake of nanoparticles. Phagocytic differentiated THP-1 cells or non-phagocytic A549 cells were incubated with F-PLNP for 4 h, and their cellular uptake was quantified by fluorescence intensity and confocal microscopy. The amount of internalized F-PLNPs showed a good positive correlation with the zeta potential of F-PLNPs in both cell lines (Pearson's r = 0.7021 and 0.7852 for zeta potential vs. cellular uptake in THP-1 cells and nonphagocytic A549 cells, respectively). This result implies that surface charge is the major parameter determining cellular uptake efficiency, although other factors such as aggregation/agglomeration, protein corona formation, and compositional elements can also influence the cellular uptake partly or indirectly.

In situ identification of Gram-negative bacteria in human lungs using a topical fluorescent peptide targeting lipid A.

Respiratory infections in mechanically ventilated patients caused by Gram-negative bacteria are a major cause of morbidity. Rapid and unequivocal determination of the presence, localization, and abundance of bacteria is critical for positive resolution of the infections and could be used for patient stratification and for monitoring treatment efficacy. Here, we developed an in situ approach to visualize Gram-negative bacterial species and cellular infiltrates in distal human lungs in real time. We used optical endomicroscopy to visualize a water-soluble optical imaging probe based on the antimicrobial peptide polymyxin conjugated to an environmentally sensitive fluorophore. The probe was chemically stable and nontoxic and, after in-human intrapulmonary microdosing, enabled the specific detection of Gram-negative bacteria in distal human airways and alveoli within minutes. The results suggest that pulmonary molecular imaging using a topically administered fluorescent probe targeting bacterial lipid A is safe and practical, enabling rapid in situ identification of Gram-negative bacteria in humans.

Bimodal fluorogenic sensing of matrix proteolytic signatures in lung cancer.

Optical biosensing based on the activation of fluorescent reporters offers a powerful methodology for the real-time molecular interrogation of pathology. Here we report a first-in-class, bimodal fluorescent reporter strategy for the simultaneous and highly specific detection of two independent proteases (thrombin and matrix metalloproteases (MMPs)) pivotal in the fibroproliferative process surrounding lung cancer, based on a dual, multiplexing, peptide FRET system. This sophisticated synthetic smartprobe, with a molecular weight of 6 kDa, contains two independent fluorophores and quenchers that generate photonic signatures at two specific wavelengths upon activation by target enzymes within human lung cancer tissue.

Intracellular delivery of a catalytic organometallic complex.

A homogeneous carbene-based palladium catalyst was conjugated to a cell-penetrating peptide, allowing intracellular delivery of catalytically active Pd complexes that demonstrated bioorthogonal activation of a profluorophore within prostate cancer cells.

Highly selective and rapidly activatable fluorogenic Thrombin sensors and application in human lung tissue.

A library of FRET-based peptides were prepared and studied as Thrombin substrates. This identified probes that showed selective activation by Thrombin, low fluorescent background signals, stability to Factor Xa, matrix metalloproteases, and primary human inflammatory cell lysates and supernatant. These were selected for further optimization, creating a second generation of fluorogenic probes with improved solubility and Plasmin resistance. The optimised probe allowed the detection of Thrombin activity in ex vivo fibrotic human tissue.

In-Cell Dual Drug Synthesis by Cancer-Targeting Palladium Catalysts.

Transition metals have been successfully applied to catalyze non-natural chemical transformations within living cells, with the highly efficient labeling of subcellular components and the activation of prodrugs. In vivo applications, however, have been scarce, with a need for the specific cellular targeting of the active transition metals. Here, we show the design and application of cancer-targeting palladium catalysts, with their specific uptake in brain cancer (glioblastoma) cells, while maintaining their catalytic activity. In these cells, for the first time, two different anticancer agents were synthesized simultaneously intracellularly, by two totally different mechanisms (in situ synthesis and decaging), enhancing the therapeutic effect of the drugs. Tumor specificity of the catalysts together with their ability to perform simultaneous multiple bioorthogonal transformations will empower the application of in vivo transition metals for drug activation strategies.

Palladium-mediated in situ synthesis of an anticancer agent.

As a novel prodrug activation strategy Pd(0) nanoparticles, entrapped within a modular polymeric support, were used in cell culture, to synthesise the anticancer agent PP-121 from two non-toxic precursors, thereby inducing cell death in the first example of in situ mediated drug synthesis.

Dual contribution of surface charge and protein-binding affinity to the cytotoxicity of polystyrene nanoparticles in nonphagocytic A549 cells and phagocytic THP-1 cells.

Knowledge that links the physicochemical properties of nanoparticles (NP) to their toxicity is key to evaluating and understanding mechanisms underlying toxicity and developing appropriate testing methods for NP; however, this is currently limited since only a small set of NP have been used, with typically poor control of their physical properties. In this study, eight types of polystyrene NP (PLNP) were synthesized with different functional groups, but all based on an identical core. In vitro cell-based assays were performed to determine the influence of changes in physicochemical properties, such as charge, hydrodynamic size, and protein binding potential, in relation to NP-mediated toxicity. The PLNP were incubated with nonphagocytic A549 cells or phagocytic differentiated THP-1 cells for 4 h with/without fetal bovine serum (FBS), followed by incubation for 20 h in FBS-supplemented medium with/without a washing step, to assess cell-type specificity and impact of protein corona formation. The effect of surface charge on cytotoxicity differed between A549 cells and THP-1 cells. In nonphagocytic A549 cells, the zeta potential of PLNP exhibited a negative correlation with cytotoxicity, partly due to the level of coronated protein that might affect cellular uptake. In phagocytic THP-1 cells, the zeta potential of PLNP showed a positive correlation with cytotoxicity but coronated protein levels displayed no marked association with cytotoxicity, owing to the professional uptake efficacy of phagocytic cells. The consistency of our data with THP-1 cells with the surface charge paradigm in nanotoxicology suggests that phagocytic cells are the predominant targets for lung inflammatory reactions induced by PLNP.

Surface charge determines the lung inflammogenicity: A study with polystyrene nanoparticles.

Surface functionalization is a routine process to improve the behavior of nanoparticles (NPs), but the induced surface properties, such as surface charge, can produce differential toxicity profiles. Here, we synthesized a library of covalently functionalized fluorescent polymeric NPs (F-PLNPs) to evaluate the role of surface charge on the acute inflammation and the localization in the lung. Guanidinium-, acetylated-, zwitterionic-, hydroxylated-, PEGylated-, carboxylated- and sulfated-F-PLNPs were synthesized from aminated-F-PLNP. The primary particle sizes were identical, but the hydrodynamic sizes ranged from 210 to 345 nm. Following surface functionalization, the F-PLNPs showed diverse zeta potentials from -41.2 to 31.0 mV, and each F-PLNP showed a single, narrow peak. Pharyngeal aspiration with these eight types of F-PLNPs into rats produced diverse acute lung inflammation, with zeta potentials of the F-PLNPs showing excellent correlation with acute pulmonary inflammation parameters including the percentage of polymorphonuclear leukocytes (R(2) = 0.90, p < 0.0001) and the levels of interleukin-1ß (R(2) = 0.83, p < 0.0001) and of cytokine-induced neutrophil chemoattractant-3 (R(2) = 0.86, p < 0.0001). These results imply that surface charge is a key factor influencing lung inflammation by functionalized polymeric NPs, which further confirms and extends the surface charge paradigm that we reported for pristine metal oxide NPs. This demonstrates that the surface charge paradigm is a valuable tool to predict the toxicity of NPs.

Optical molecular imaging of lysyl oxidase activity - detection of active fibrogenesis in human lung tissue.

Aberrant fibrogenesis is a feature of many diseases in multiple organ systems. The lysyl oxidase family of enzymes are central to tissue homeostasis and elevated lysyl oxidase activity is implicated in fibroproliferation as well as in cancer stroma. We have synthesised a novel fluorogenic reporter for monitoring lysyl oxidase activity that generates a 3-5 fold increase in fluorescence following probe activation in ventilating fibrotic ex vivo asinine lung and ex vivo human lung tissue. The probe termed "oLOX" can provide real-time measurement of lysyl oxidase activity in a number of biological settings and is tractable from an in vitro setting to man.

A labelled-ubiquicidin antimicrobial peptide for immediate in situ optical detection of live bacteria in human alveolar lung tissue.

The in situ immediate detection of the presence of bacteria in the distal human lung is of significant clinical utility. Herein we describe the development and optimization of a bacterial binding fragment (UBI29-41) of the antimicrobial peptide, ubiquicidin (UBI), conjugated to an environmentally sensitive fluorophore to enable rapid live bacterial imaging within human lung tissue. UBI29-41 was modified for stability in the presence of human lung bronchoalveolar lavage fluid, for affinity to bacterial membranes and functionality in human lung tissue. The optimized cyclic structure yields an optical molecular Smartprobe for bacterial detection in human lung tissue.

Palladium-mediated chemistry in living cells.

Bioorthogonal metal catalysed chemistry is the application of biocompatible transition metals to catalyse conventional synthetic organic chemistry reactions within a biological environment. Over the past decade, metals which were previously restricted to conventional organic synthesis have begun to be used in an increasing number of biological settings. This has been dominated by copper mediated catalysis of the azide-alkyne Huisgen cycloaddition (1,3-dipolar addition) chemistry but other, less toxic, metals such as palladium are now beginning to establish themselves in the chemical biology/chemical medicine arenas. The potential of palladium mediated chemistry in living systems now ranges from protein modifications to in cellulo synthesis or activation of drugs and suggests that palladium chemistry has the potential to become a powerful tool. In this review we highlight recent advances in Pd-mediated reactions in living systems.

Influence of spacer length on the cellular uptake of polymeric nanoparticles.

Nanotechnology is finding ever increasing application in the life science arena where nanoparticles can be used to deliver cargoes in cells. However, a clear understanding of the relationship between the chemical properties of the particle and its uptake efficiency is lacking. Herein, the effects on particle cellular uptake following modification with a variety of spacers, all bearing a positive charge, but differing in length, and the influence on formation of the protein corona are investigated. Although no significant differences in the composition of the protein corona are detected, the spacer length influences the cellular uptake of the nanoparticles. These findings will allow the target-orientated functionalisation of particles to increase the specificity of cellular uptake.

Polymerizable fluorescein derivatives: synthesis of fluorescent particles and their cellular uptake.

Fluorescent particles are used for a diverse number of biochemical assays including intracellular imaging, cellular tracking, as well as detection of a variety of biomolecules. They are typically prepared by postpolymerization conjugations of dyes onto preformed particles. Herein we report the synthesis of aminomethyl-functionalized fluorescent particles via the synthesis and application of polymerizable fluorescein monomers. These monomers allowed high and controllable fluorophore loading into the particles, resulting in enhanced fluorescence properties in comparison with more commonly used carboxyfluorescein conjugated particles. Furthermore, the particles were rapidly taken up by cells with enhanced fluorescence. The herein presented results demonstrate the advantages of dye polymerization in contrast with more conventional conjugation strategies for fluorescent particle generation with applications in the life sciences.

Protic acid immobilized on solid support as an extremely efficient recyclable catalyst system for a direct and atom economical esterification of carboxylic acids with alcohols.

A convenient and clean procedure of esterification is reported by direct condensation of equimolar amounts of carboxylic acids with alcohols catalyzed by an easy to prepare catalyst system of perchloric acid immobilized on silica gel (HClO(4)-SiO(2)). The direct condensation of aryl, heteroaryl, styryl, aryl alkyl, alkyl, cycloalkyl, and long-chain aliphatic carboxylic acids with primary/secondary alkyl/cycloalkyl, allyl, propargyl, and long-chain aliphatic alcohols has been achieved to afford the corresponding esters in excellent yields. Chiral alcohol and N-t-Boc protected chiral amino acid also resulted in ester formation with the representative carboxylic acid or alcohol without competitive N-t-Boc deprotection and detrimental effect on the optical purity of the product demonstrating the mildness and chemoselectivity of the procedure. The esters of long-chain (>C(10)) acids and alcohols are obtained in high yields. The catalyst is recovered and recycled without significant loss of activity. The industrial application of the esterification process is demonstrated by the synthesis of prodrugs of ibuprofen and a few commercial flavoring agents. Other protic acids such as H(2)SO(4), HBr, TfOH, HBF(4), and TFA that were adsorbed on silica gel were less effective compared to HClO(4)-SiO(2) following the order HClO(4)-SiO(2) >> H(2)SO(4)-SiO(2) > HBr-SiO(2) > TfOH-SiO(2) >> HBF(4)-SiO(2) approximately TFA-SiO(2). When HClO(4) was immobilized on other solid supports the catalytic efficiency followed the order HClO(4)-SiO(2) > HClO(4)-K10 > HClO(4)-Al(2)O(3) (neutral) > HClO(4)-Al(2)O(3) (acidic) > HClO(4)-Al(2)O(3) (basic).

Counterattack mode differential acetylative deprotection of phenylmethyl ethers: applications to solid phase organic reactions.

A counterattack protocol for differential acetylative cleavage of phenylmethyl ether has been developed. The phenylmethyl moiety is liberated as benzyl bromide that is isolated and reused providing advantages in terms of waste minimization/utilization and atom economy. The applicability of this methodology has been extended for solid phase organic reactions with the feasibility of reuse of the solid support.