How molecular architecture defines quantum yields.

Understanding the intricate relationship between molecular architecture and function underpins most challenges at the forefront of chemical innovation. Bond-forming reactions are particularly influenced by the topology of a chemical structure, both on small molecule scale and in larger macromolecular frameworks. Herein, we elucidate the impact that molecular architecture has on the photo-induced cyclisations of a series of monodisperse macromolecules with defined spacers between photodimerisable moieties, and examine the relationship between propensity for intramolecular cyclisation and intermolecular network formation. We demonstrate a goldilocks zone of maximum reactivity between the sterically hindered and entropically limited regimes with a quantum yield of intramolecular cyclisation that is nearly an order of magnitude higher than the lowest value. As a result of the molecular design of trifunctional macromolecules, their quantum yields can be deconvoluted into the formation of two different cyclic isomers, as rationalised with molecular dynamics simulations. Critically, we visualise our solution-based studies with light-based additive manufacturing. We formulate four photoresists for microprinting, revealing that the precise positioning of functional groups is critical for resist performance, with lower intramolecular quantum yields leading to higher-quality printing in most cases.

Introduction to the RSC Advances themed collection on New insights into biomolecular systems from large-scale simulations.

Megan O'Mara, Sarah Rauscher and Stacey Wetmore introduce the RSC Advances themed collection on New insights into biomolecular systems from large-scale simulations.

Self-reported determinants of COVID-19 vaccine acceptance among persons with and without autoimmune disease.

OBJECTIVE: Patients with autoimmune disease (AD) are at increased risk for complications from COVID-19 infection, so, optimizing vaccine utilization in this population is of particular importance. We compared COVID-19 vaccination perspectives among persons with and without AD. METHODS: 471 patients in the MetroHealth System and Cleveland Veteran Affairs Medical Center completed a 38-item questionnaire between August 2021 and February 2022. This survey containing questions regarding COVID-19 vaccine perceptions and demographics was administered both to unvaccinated individuals and individuals who delayed vaccination for at least 2 months. Multivariable ordinary least squares regression models were created to assess factors associated with vaccination likelihood. RESULTS: The number of reasons given for (p < 0.001) and against receiving COVID-19 vaccination (p < 0.001) were highly associated with increased and decreased vaccination likelihood respectively. Factors most closely associated with obtaining vaccine were: protecting family (p = 0.045) personal safety (p < 0.001) and preventing serious infection (p < 0.001). Reasons associated with decreased vaccination likelihood were: lack of concern of COVID-19 infection (p < 0.001), vaccine safety (p < 0.001) and beliefs that the vaccine was made too quickly (p = 0.024). AD patients were more likely to cite having a chronic condition (29.1 % vs 17.1 %, p = 0.003) and physician recommendation(s) (18.4 % vs 9.1 %, p = 0.005) as reasons for vaccination and were more concerned about potential medication interaction than non-AD respondents (22.4 % vs 3.3 %, p < 0.001). CONCLUSION: The number of benefits of vaccination identified strongly related to vaccination likelihood. Affirmative provider recommendations correlated with increased vaccination likelihood in AD patients. Clinical conversations centered on the benefits of COVID-19 vaccination may help increase vaccine acceptance.

Higher Vitamin D Levels before Methotrexate Therapy Initiation Are Associated with Lower Subsequent Mortality in Patients with Rheumatoid Arthritis.

(1) Vitamin D deficiency is associated with mortality in the general population and has been observed in one rheumatoid arthritis (RA) cohort. Here, we investigate the relationship between 25-hydroxyvitamin D (25(OH)D) levels before methotrexate (MTX) therapy initiation in patients with RA and the subsequent all-cause mortality in a national Veterans Affairs (VA) cohort. (2) This is a retrospective study on RA patients time-oriented around the initial MTX prescription and 25(OH)D levels before starting MTX. We examined survival in patients with 25(OH)D levels > 50 nmol/L and ≤50 nmol/L using the Cox Proportional Hazard Model and fully adjusted for risk factors. (3) In total, 15,109 RA patients were included in the nationwide cohort. RA patients with 25(OH)D levels > 50 nmol/L before starting MTX had a 28% reduced risk of mortality when compared to those with levels ≤ 50 nmol/L (HR: 0.72, CI: 0.64-0.80, p < 0.001) after adjusting for traditional risk factors. (4) In this national RA cohort receiving standard-of-care MTX, patients with 25(OH)D levels > 50 nmol/L have a lower subsequent mortality when compared to those with 25(OH)D levels ≤ 50 nmol/L. It remains to be determined whether increasing Vitamin D levels in RA patients initially found to be Vitamin D deficient impacts their all-cause mortality.

Main-chain Macromolecular Hydrazone Photoswitches.

Hydrazones-consisting of a dynamic imine bond and an acidic NH proton-have recently emerged as versatile photoswitches underpinned by their ability to form thermally bistable isomers, (Z) and (E), respectively. Herein, we introduce two photoresponsive homopolymers containing structurally different hydrazones as main-chain repeating units, synthesized via head-to-tail Acyclic Diene METathesis (ADMET) polymerization. Their key difference lies in the hydrazone design, specifically the location of the aliphatic arm connecting the rotor of the hydrazone photoswitch to the aliphatic polymer backbone. Critically, we demonstrate that their main photoresponsive property, i.e., their hydrodynamic volume, changes in opposite directions upon photoisomerization (λ=410 nm) in dilute solution. Further, the polymers-independent of the design of the individual hydrazone monomer-feature a photoswitchable glass transition temperature (Tg ) by close to 10 °C. The herein established design strategy allows to photochemically manipulate macromolecular properties by simple structural changes.

The efficacy of the analgesic GlyT2 inhibitor, ORG25543, is determined by two connected allosteric sites.

Glycine Transporter 2 (GlyT2) inhibitors have shown considerable potential as analgesics for the treatment of neuropathic pain but also display considerable side effects. One potential source of side effects is irreversible inhibition. In this study, we have characterized the mechanism of ORG25543 inhibition of GlyT2 by first considering three potential ligand binding sites on GlyT2-the substrate site, the vestibule allosteric site and the lipid allosteric site. The three sites were tested using a combination of molecular dynamics simulations and analysis of the inhibition of glycine transport of a series point mutated GlyT2 using electrophysiological methods. We demonstrate that the lipid allosteric site on GlyT2 is the most likely binding site for ORG25543. We also demonstrate that cholesterol derived from the cell membrane can form specific interactions with inhibitor-bound transporters to form an allosteric network of regulatory sites. These observations will guide the future design of GlyT2 inhibitors with the objective of minimising on-target side effects and improving the therapeutic window for the treatment of patients suffering from neuropathic pain.

Structural basis of promiscuous substrate transport by Organic Cation Transporter 1.

Organic Cation Transporter 1 (OCT1) plays a crucial role in hepatic metabolism by mediating the uptake of a range of metabolites and drugs. Genetic variations can alter the efficacy and safety of compounds transported by OCT1, such as those used for cardiovascular, oncological, and psychological indications. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 remain poorly understood. Here, we present cryo-EM structures of full-length human OCT1 in the inward-open conformation, both ligand-free and drug-bound, indicating the basis for its broad substrate recognition. Comparison of our structures with those of outward-open OCTs provides molecular insight into the alternating access mechanism of OCTs. We observe that hydrophobic gates stabilize the inward-facing conformation, whereas charge neutralization in the binding pocket facilitates the release of cationic substrates. These findings provide a framework for understanding the structural basis of the promiscuity of drug binding and substrate translocation in OCT1.

Rheumatoid arthritis and older age are associated with lower humoral and cellular immune response to primary series COVID-19 mRNA vaccine.

OBJECTIVE: People with autoimmune disease have worse COVID-19 infection-related outcomes, lower antibody responses to COVID-19 vaccine, and higher rates of breakthrough infection. Immunosuppressive medications used to treat rheumatoid arthritis (RA) are associated with lower COVID-19 vaccine responses, though independent contributions of comorbidities, T-cell immunity, and age are less clear. We sought to test the hypothesis that RA, immunosuppressive medications used to treat RA, and older age, contribute to reduced B and T cell response to COVID-19 vaccine. METHODS: We evaluated serum samples, taken the day of 1st vaccine dose, the day of 2nd dose, 2-6 weeks after 2nd dose, 7-12 weeks after 2nd dose, 13-24 weeks after 2nd dose, and 2-6 weeks after the 3rd dose, for anti-spike IgG and neutralizing antibody levels to Wuhan and Omicron BA.1 and peripheral blood mononuclear cells (PBMC) for spike-specific IFN-γ and IL-2 production by ELISPOT assay in 46 RA and 101 non-autoimmune control participants before and after the primary series COVID-19 mRNA vaccination. RESULTS: RA participants had lower spike-specific IgG and Wuhan-strain neutralizing antibody levels 2-6 weeks compared to controls after the second dose of primary vaccine series. Neutralizing antibody levels against Omicron BA.1 were low in both groups. IFN-γ production correlated with Wuhan neutralizing antibody levels, while older age negatively correlated with spike-specific IL-2, IFN-γ and IgG. Lower antibody levels were associated with older age, RA status, and medication usage, while lower T cell responses were associated primarily with older age. CONCLUSIONS: These data indicate lower COVID-19 mRNA vaccine-induced antibody levels in persons with RA compared to individuals without RA, likely partially attributable to immune suppressive medications. At the same time, older age is associated with lower antibody and cellular immune response to COVID-19 vaccines.

Extracellular vesicle lipids in cancer immunoevasion.

Recent studies have revealed that cancer cell-derived extracellular vesicles (EVs) modulate immunological responses. Lipids have diverse biological functions, and are known to promote tumor malignancy. However, the immunoevasive roles of EV lipids in cancer progression remain poorly understood. Nevertheless, the study of cancer cell-derived EV lipids holds great promise for diagnostic and therapeutic interventions.

Implementation of a Patient Acuity Tool and Safe Staffing Model in an Outpatient Oncology Clinical Trials Unit.

Appropriate staffing in the outpatient oncology setting contributes to the delivery of quality care. Objective measures of acuity and nursing workload can assist with developing staffing models; however, measuring acuity in a.

Endotoxemia Associated with Liver Disease Correlates with Systemic Inflammation and T Cell Exhaustion in Hepatitis C Virus Infection.

Both acute and chronic hepatitis C virus (HCV) infections are characterized by inflammation. HCV and reduced liver blood filtration contribute to inflammation; however, the mechanisms of systemic immune activation and dysfunction as a result of HCV infection are not clear. We measured circulating inflammatory mediators (IL-6, IP10, sCD163, sCD14), indices of endotoxemia (EndoCab, LBP, FABP), and T cell markers of exhaustion and senescence (PD-1, TIGIT, CD57, KLRG-1) in HCV-infected participants, and followed a small cohort after direct-acting anti-viral therapy. IL-6, IP10, Endocab, LBP, and FABP were elevated in HCV participants, as were T cell co-expression of exhaustion and senescence markers. We found positive associations between IL-6, IP10, EndoCab, LBP, and co-expression of T cell markers of exhaustion and senescence. We also found numerous associations between reduced liver function, as measured by plasma albumin levels, and T cell exhaustion/senescence, inflammation, and endotoxemia. We found positive associations between liver stiffness (TE score) and plasma levels of IL-6, IP10, and LBP. Lastly, plasma IP10 and the proportion of CD8 T cells co-expressing PD-1 and CD57 decreased after initiation of direct-acting anti-viral therapy. Although associations do not prove causality, our results support the model that translocation of microbial products, resulting from decreased liver blood filtration, during HCV infection drives chronic inflammation that results in T cell exhaustion/senescence and contributes to systemic immune dysfunction.

COVID-19 vaccination experience in patients with rheumatoid arthritis treated at a single VA medical center.

Background: Following the introduction of the COVID-19 vaccines, there has been uncertainty as to whether receiving the COVID-19 vaccine will result in overactivation of the immune system and subsequently lead to an autoimmune disease flare.The purpose of this study was to assess whether rheumatoid arthritis (RA) patients who received the mRNA COVID-19 vaccine are at increased risk for disease flare. Methods: We conducted a single-center retrospective and prospective study at the Louis Stokes Cleveland VA Medical Center between 12/2021 and 2/2022. We included 100 patients with rheumatoid arthritis (RA) who were actively on immunosuppressive therapy and received three doses of the Pfizer-BioNTech vaccine. A survey questionnaire was used to collect data about their RA and if they developed symptoms post vaccination. Our primary end point was to determine incidence of flare of RA after COVID-19 vaccine. Secondary end points were to estimate the side effect profile from the vaccine, and to check if patients developed a COVID-19 infection after they received the vaccine. Results: None of the patients reported symptoms of RA flare within two months of receiving the 3 doses of the vaccine. Most common vaccine side effects were soreness over the injection site (n = 14), headache (n = 11), fatigue(n = 7) and myalgias(n = 4). 5 patients developed a COVID-19 infection prior to receiving the vaccine, 8 after being vaccinated, 3 of the 8 within 5 months from the second dose and 5 out of the 8 within 3 months from the third vaccine dose. Conclusion: RA patients receiving the COVID-19 Pfizer mRNA vaccine do not appear to commonly develop major symptoms, flares or side effects following the vaccine. Further research with larger numbers of patients with rheumatoid arthritis as well as those with other autoimmune disease is needed to better understand the safety and effectiveness of COVID-19 vaccine.

Visible-Light-Reactive Single-Chain Nanoparticles.

We introduce a single-chain nanoparticle (SCNP) system capable of catalyzing the photooxidation of nonpolar alkenes up to three times more efficiently than an equivalent small-molecule photosensitizer at an identical concentration. Specifically, we construct a polymer chain constituted of poly(ethylene glycol) methyl ether methacrylate and glycidyl methacrylate which we compact via multifunctional thiol-epoxide ligation and functionalize with Rose Bengal (RB) in a one pot reaction, affording SCNPs with a hydrophilic shell and hydrophobic photocatalytic regions. Photooxidation of the internal alkene in oleic acid proceeds under green light. RB confined within the SCNP is three times more effective for nonpolar alkenes than free RB in solution, which we hypothesize is due to the spatial proximity of the photosensitizing units to the substrate in the hydrophobic region. Our approach demonstrates that SCNP based catalysts can afford enhanced photocatalysis via confinement effects in a homogeneous reaction environment.

The Impact of Antimicrobial Peptides on the Acinetobacter baumannii Inner Membrane Is Modulated by Lipid Polyunsaturation.

The Gram-negative pathogen Acinetobacter baumannii is a primary contributor to nosocomial multi-drug-resistant (MDR) infections. To combat the rise of MDR infections, novel features of A. baumannii need to be considered for the development of new treatment options. One such feature is the preferential scavenging of exogenous lipids, including host-derived polyunsaturated fatty acids (PUFAs), for membrane phospholipid synthesis. These alterations in membrane composition impact both the lipid chemistry and the membrane biophysical properties. In this work we examine how antimicrobial peptides (AMPs) interact with the inner membranes of A. baumannii in the presence and absence of polyunsaturated phospholipids. Using coarse-grained molecular dynamics simulations of complex A. baumannii inner membrane models derived from lipidomes of bacteria grown in the presence and absence of PUFAs, we examine the impact of the adsorption of four prototypical AMPs (CAMEL, LL-37, pexiganan, and magainin-2) on the membrane biophysical properties. Our simulations reveal that the impact of AMP adsorption on the membrane biophysical properties was dependent on both the membrane composition and the specific AMP involved. Both lipid headgroup charge and tail unsaturation played important roles in driving the interactions that occurred both within the membrane and between the membrane and AMPs. The changes to the membrane biophysical properties also showed a complex relationship with the AMP's physical properties, such as AMP charge, chain length, and charge-to-mass ratio. Cumulatively, this work highlights the importance of studying AMPs using a complex membrane environment and provides insights into the mechanistic action of AMPs in polyunsaturated lipid-rich bacterial membranes.

Membrane cholesterol regulates inhibition and substrate transport by the glycine transporter, GlyT2.

Membrane cholesterol binds to and modulates the function of various SLC6 neurotransmitter transporters, including stabilizing the outward-facing conformation of the dopamine and serotonin transporters. Here, we investigate how cholesterol binds to GlyT2 (SLC6A5), modulates glycine transport rate, and influences bioactive lipid inhibition of GlyT2. Bioactive lipid inhibitors are analgesics that bind to an allosteric site accessible from the extracellular solution when GlyT2 adopts an outward-facing conformation. Using molecular dynamics simulations, mutagenesis, and cholesterol depletion experiments, we show that bioactive lipid inhibition of glycine transport is modulated by the recruitment of membrane cholesterol to a binding site formed by transmembrane helices 1, 5, and 7. Recruitment involves cholesterol flipping from its membrane orientation, and insertion of the 3' hydroxyl group into the cholesterol binding cavity, close to the allosteric site. The synergy between cholesterol and allosteric inhibitors provides a novel mechanism of inhibition and a potential avenue for the development of potent GlyT2 inhibitors as alternative therapeutics for the treatment of neuropathic pain and therapeutics that target other SLC6 transporters.

Financial Incentives Are Associated with Lower Likelihood of COVID-19 Vaccination in Northeast Ohio.

BACKGROUND: Declining COVID-19 vaccination rates have led to implementation of monetary incentives to increase vaccine uptake. The Ohio Vax-a-Million lottery and subsequent $100 incentives were created to encourage individuals to become vaccinated. The purpose of this survey was to determine the efficacy of these monetary incentives on vaccination rates. METHODS: A 38-item questionnaire was given to outpatients at MetroHealth and Cleveland Veteran Affairs Hospitals between August 2021 and February 2022 who either waited 2 or more months to receive the COVID-19 vaccination or have not yet been vaccinated. The survey contained questions regarding demographics and perceptions of COVID-19 monetary incentives on vaccination likelihood. RESULTS: Of the 471 participants surveyed, 0.95% reported that the Ohio Vax-a-Million lottery increased their vaccination likelihood, while 29.7% reported that it decreased their likelihood. 6.8% of respondents reported the $100 incentive increased their vaccination likelihood while 17.4% reported it decreased their vaccination chances. 20.6% of participants stated news of the Delta (δ) variant increased their vaccination likelihood. CONCLUSION: Our study results suggest that monetary incentives were not associated with increased COVID-19 vaccination rates. Instead, more participants believed that these incentives decreased their vaccination likelihood. Expansion of the survey across a wider sociodemographic range can provide further evidence of the efficacy of these programs before reimplementation.

Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids.

Aryl-urea substituted fatty acids are protonophores and mitochondrial uncouplers that utilise a urea-based synthetic anion transport moiety to carry out the protonophoric cycle. Herein we show that replacement of the urea group with carbamate, a functional group not previously reported to possess anion transport activity, produces analogues that retain the activity of their urea counterparts. Thus, the aryl-carbamate substituted fatty acids uncouple oxidative phosphorylation and inhibit ATP production by collapsing the mitochondrial proton gradient. Proton transport proceeds via self-assembly of the deprotonated aryl-carbamates into membrane permeable dimeric species, formed by intermolecular binding of the carboxylate group to the carbamate moiety. These results highlight the anion transport capacity of the carbamate functional group.

Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function.

The binding of the type 1 fimbrial adhesin FimH to mannosylated receptors is allosterically regulated to enhance the fitness of uropathogenic Escherichia coli (UPEC) during urinary tract infection (UTI). Mutations in the two FimH domains (pilin and lectin) located outside the mannose binding pocket have been shown to influence mannose binding affinity, yet the details of the allostery mechanism are not fully elucidated. Here we characterised different FimH conformational states (termed low-affinity tense and high-affinity relaxed conformations) of natural FimH variants using molecular dynamics (MD) simulation techniques and report key structural dynamics differences between them. The clinically dominant FimH30 variant from the pandemic multidrug resistant E. coli ST131 lineage contains an R166H mutation that weakens FimH interdomain interactions and allows enhanced mannose interactions with pre-existing high-affinity relaxed conformations. When expressed in an isogenic ST131 strain background, FimH30 mediated high human cell adhesion and invasion, and enhanced biofilm formation over other variants. Collectively, our computational and experimental findings support a model of FimH protein allostery that is mediated by shifts in the pre-existing conformational equilibrium of FimH, additional to the sequential step-wise process of structural perturbations transmitted from one site to another within the protein. Importantly, it is the first study to shed light into how natural mutations in a clinically dominant FimH variant influence the protein's conformational landscape optimising its function for ST131 fitness at intestinal and extraintestinal niches.

Loss, Gain and Altered Function of GlyR α2 Subunit Mutations in Neurodevelopmental Disorders.

Glycine receptors (GlyRs) containing the α2 subunit govern cell fate, neuronal migration and synaptogenesis in the developing cortex and spinal cord. Rare missense variants and microdeletions in the X-linked GlyR α2 subunit gene (GLRA2) have been associated with human autism spectrum disorder (ASD), where they typically cause a loss-of-function via protein truncation, reduced cell-surface trafficking and/or reduced glycine sensitivity (e.g., GLRA2Δex8-9 and extracellular domain variants p.N109S and p.R126Q). However, the GlyR α2 missense variant p.R323L in the intracellular M3-M4 domain results in a gain-of-function characterized by slower synaptic decay times, longer duration active periods and increases in channel conductance. This study reports the functional characterization of four missense variants in GLRA2 associated with ASD or developmental disorders (p.V-22L, p.N38K, p.K213E, p.T269M) using a combination of bioinformatics, molecular dynamics simulations, cellular models of GlyR trafficking and electrophysiology in artificial synapses. The GlyR α2V-22L variant resulted in altered predicted signal peptide cleavage and a reduction in cell-surface expression, suggestive of a partial loss-of-function. Similarly, GlyR α2N38K homomers showed reduced cell-surface expression, a reduced affinity for glycine and a reduced magnitude of IPSCs in artificial synapses. By contrast, GlyR α2K213E homomers showed a slight reduction in cell-surface expression, but IPSCs were larger, with faster rise/decay times, suggesting a gain-of-function. Lastly, GlyR α2T269M homomers exhibited a high glycine sensitivity accompanied by a substantial leak current, suggestive of an altered function that could dramatically enhance glycinergic signaling. These results may explain the heterogeneity of clinical phenotypes associated with GLRA2 mutations and reveal that missense variants can result in a loss, gain or alteration of GlyR α2 function. In turn, these GlyR α2 missense variants are likely to either negatively or positively deregulate cortical progenitor homeostasis and neuronal migration in the developing brain, leading to changes in cognition, learning, and memory.

Dynamics of the Acinetobacter baumannii inner membrane under exogenous polyunsaturated fatty acid stress.

Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using coarse grained MARTINI simulations of chemically representative membrane models developed from mass-spectrometry datasets of an untreated, arachidonic acid (AA) treated and docosahexaenoic acid (DHA) treated A. baumannii membranes. Enzymatic integration of AA or DHA into phospholipids of the A. baumannii membrane resulted in modulation of membrane biophysical properties. Membrane thickness decreased slightly following PUFA treatment, concomitant with changes in the lateral area per lipid of each lipid headgroup class. PUFA treatment resulted in a decrease in membrane ordering and an increase in lipid lateral diffusion. Changes in lateral membrane organisation were observed in the PUFA treated membranes, with a concurrent increase in ordered cardiolipin domains and disordered PUFA-containing domains. Notably, separation between ordered and disordered domains was enhanced and was more pronounced for DHA relative to AA, providing a possible mechanism for greater antimicrobial action of DHA relative to AA observed experimentally. Furthermore, the membrane active antimicrobial, pentamidine, preferentially adsorbs to cardiolipin domains of the A. baumannii model membranes. This interaction, and membrane penetration of pentamidine, was enhanced following PUFA treatment. Cumulatively, this work explores the wide-ranging effects of PUFA incorporation on the A. baumannii membrane and provides a molecular basis for bacterial inner membrane disruption by PUFAs.