Disparities in Access to a Regular Primary Care Physician Among First-Generation Migrants with Early Psychosis in Ontario, Canada.

Disparities in primary care utilization among migrants with early psychosis may be related to lack of access to a regular primary care physician. This study aimed to investigate access to a regular primary care physician among first-generation migrants with early psychosis. People aged 14-35 years with first onset non-affective psychotic disorder in Ontario, Canada were identified in health administrative data (N = 39,440). Access to a regular primary care physician through enrollment in the year prior to diagnosis was compared between first-generation migrants (categorized by country of birth) and the general population using modified Poisson regression. Most migrant groups had a lower prevalence of regular primary care physician access relative to the general population, particularly migrants from Africa (African migrants: 81% vs. non-migrants: 89%). Adjustment for sociodemographic and clinical factors attenuated these differences, although the disparities for migrants from Africa remained (PR = 0.96, 95%CI = 0.94-0.99). Interventions aimed at improving primary care physician access in migrant groups may facilitate help-seeking and improve pathways to care in early psychosis.

Oral cannabinoid for the prophylaxis of chemotherapy-induced nausea and vomiting-a systematic review and meta-analysis.

INTRODUCTION: Chemotherapy-induced nausea and vomiting (CINV) is a burdensome adverse event frequently associated with chemotherapy treatment of cancer. Evidence suggests that cannabinoid CB2 receptors are present in brainstem neurons, and thus, there may exist a role for cannabinoids to counter CINV. The aim of this paper is to conduct a systematic review and meta-analysis of the efficacy and safety of oral cannabinoids compared with other treatments as documented in randomized controlled trials (RCTs). METHODS: A literature search was conducted using Ovid MEDLINE up until December 31, 2018; Embase Classic and Embase up until 2018 week 53; and Cochrane Central Register of Controlled Trials up until November 2018. Study data were extracted and included in this meta-analysis if they reported on at least one of the following efficacy endpoints: no nausea and no vomiting, no nausea, and no vomiting. The Mantel-Haenszel method and random effects analysis model were used, to generate odds ratio (OR) and accompanying 95% confidence intervals (CI). RESULTS: In the setting of prophylactic treatment against both nausea and vomiting, oral cannabinoid was more efficacious than placebo or other studied antiemetic treatments. When controlling for vomiting, oral cannabinoid was equally as efficacious as others. Against nausea, oral cannabinoid was equally as effective as other treatments. A greater percentage of patients administered oral cannabinoid for CINV experienced dysphoria, euphoria, and sedation. CONCLUSION: Although there exists some evidence suggesting that oral cannabinoids may have a role in controlling for emesis from a neurophysiological perspective, these conclusions are currently not mirrored in the published RCTs to date. However, there exists only a limited number of RCTs, comparisons with older treatment regimens and a lack of standard reporting practice across published literature. Further RCTs should investigate the efficacy and safety of oral cannabinoids, to secure a better picture of the efficacy of oral cannabinoids against CINV.

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

BACKGROUND: Ultra-deep next-generation sequencing of circulating tumor DNA (ctDNA) holds great promise as a tool for the early detection of cancer and for monitoring disease progression and therapeutic responses. However, the low abundance of ctDNA in the bloodstream coupled with technical errors introduced during library construction and sequencing complicates mutation detection. RESULTS: To achieve high accuracy of variant calling via better distinguishing low-frequency ctDNA mutations from background errors, we introduce TNER (Tri-Nucleotide Error Reducer), a novel background error suppression method that provides a robust estimation of background noise to reduce sequencing errors. The results on both simulated data and real data from healthy subjects demonstrate that the proposed algorithm consistently outperforms a current, state-of-the-art, position-specific error polishing model, particularly when the sample size of healthy subjects is small. CONCLUSIONS: TNER significantly enhances the specificity of downstream ctDNA mutation detection without sacrificing sensitivity. The tool is publicly available at https://github.com/ctDNA/TNER .

Predictive methods for computational metalloenzyme redesign - a test case with carboxypeptidase A.

Computational metalloenzyme design is a multi-scale problem. It requires treating the metal coordination quantum mechanically, extensive sampling of the protein backbone, and additionally accounting for the polarization of the active site by both the metal cation and the surrounding protein (a phenomenon called electrostatic preorganization). We bring together a combination of theoretical methods that jointly offer these desired qualities: QM/DMD for mixed quantum-classical dynamic sampling, quantum theory of atoms in molecules (QTAIM) for the assessment of electrostatic preorganization, and Density Functional Theory (DFT) for mechanistic studies. Within this suite of principally different methods, there are both complementarity of capabilities and cross-validation. Using these methods, predictions can be made regarding the relative activities of related enzymes, as we show on the native Zn2+-dependent carboxypeptidase A (CPA), and its mutant proteins, which are hypothesized to hydrolyze modified substrates. For the native CPA, we replicated the catalytic mechanism and the rate in close agreement with the experiment, giving validity to the QM/DMD predicted structure, the DFT mechanism, and the QTAIM assessment of catalytic activity. For most sequences of the modified substrate and tried CPA mutants, substantially worsened activity is predicted. However, for the substrate mutant that contains Asp instead of Phe at the C-terminus, one CPA mutant exhibits a reasonable activity, as predicted across the theoretical methods. CPA is a well-studied system, and here it serves as a testing ground for the offered methods.

Mysteries of metals in metalloenzymes.

Natural metalloenzymes are often the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions. However, metalloenzymes are occasionally surprising in their selection of catalytic metals, and in their responses to metal substitution. Indeed, from the isolated standpoint of producing the best catalyst, a chemist designing from first-principles would likely choose a different metal. For example, some enzymes employ a redox active metal where a simple Lewis acid is needed. Such are several hydrolases. In other cases, substitution of a non-native metal leads to radical improvements in reactivity. For example, histone deacetylase 8 naturally operates with Zn(2+) in the active site but becomes much more active with Fe(2+). For ß-lactamases, the replacement of the native Zn(2+) with Ni(2+) was suggested to lead to higher activity as predicted computationally. There are also intriguing cases, such as Fe(2+)- and Mn(2+)-dependent ribonucleotide reductases and W(4+)- and Mo(4+)-dependent DMSO reductases, where organisms manage to circumvent the scarcity of one metal (e.g., Fe(2+)) by creating protein structures that utilize another metal (e.g., Mn(2+)) for the catalysis of the same reaction. Naturally, even though both metal forms are active, one of the metals is preferred in every-day life, and the other metal variant remains dormant until an emergency strikes in the cell. These examples lead to certain questions. When are catalytic metals selected purely for electronic or structural reasons, implying that enzymatic catalysis is optimized to its maximum? When are metal selections a manifestation of competing evolutionary pressures, where choices are dictated not just by catalytic efficiency but also by other factors in the cell? In other words, how can enzymes be improved as catalysts merely through the use of common biological building blocks available to cells? Addressing these questions is highly relevant to the enzyme design community, where the goal is to prepare maximally efficient quasi-natural enzymes for the catalysis of reactions that interest humankind. Due to competing evolutionary pressures, many natural enzymes may not have evolved to be ideal catalysts and can be improved for the isolated purpose of catalysis in vitro when the competing factors are removed. The goal of this Account is not to cover all the possible stories but rather to highlight how variable enzymatic catalysis can be. We want to bring up possible factors affecting the evolution of enzyme structure, and the large- and intermediate-scale structural and electronic effects that metals can induce in the protein, and most importantly, the opportunities for optimization of these enzymes for catalysis in vitro.

Computational treatment of metalloproteins.

Metalloproteins present a considerable challenge for modeling, especially when the starting point is far from thermodynamic equilibrium. Examples include formidable problems such as metalloprotein folding and structure prediction upon metal addition, removal, or even just replacement; metalloenzyme design, where stabilization of a transition state of the catalyzed reaction in the specific binding pocket around the metal needs to be achieved; docking to metal-containing sites and design of metalloenzyme inhibitors. Even more conservative computations, such as elucidations of the mechanisms and energetics of the reaction catalyzed by natural metalloenzymes, are often nontrivial. The reason is the vast span of time and length scales over which these proteins operate, and thus the resultant difficulties in estimating their energies and free energies. It is required to perform extensive sampling, properly treat the electronic structure of the bound metal or metals, and seamlessly merge the required techniques to assess energies and entropies, or their changes, for the entire system. Additionally, the machinery needs to be computationally affordable. Although a great advancement has been made over the years, including some of the seminal works resulting in the 2013 Nobel Prize in chemistry, many aforementioned exciting applications remain far from reach. We review the methodology on the forefront of the field, including several promising methods developed in our lab that bring us closer to the desired modern goals. We further highlight their performance by a few examples of applications.

Metal-dependent activity of Fe and Ni acireductone dioxygenases: how two electrons reroute the catalytic pathway.

Two virtually identical acireductone dioxygenases, ARD and ARD', catalyze completely different oxidation reactions of the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, depending exclusively on the nature of the bound metal. Fe(2+)-dependent ARD' produces the α-keto acid precursor of methionine and formate and allows for the recycling of methionine in cells. Ni(2+)-dependent ARD instead produces methylthiopropionate, CO, and formate, and exits the methionine salvage cycle. This mechanistic difference has not been understood to date but has been speculated to be due to the difference in coordination of the substrate to Fe(2+)versus Ni(2+): forming a five-membered ring versus a six-membered ring, respectively, thus exposing different carbon atoms for the attack by O2. Here, using mixed quantum-classical molecular dynamics simulations followed by the density functional theory mechanistic investigation, we show that, contrary to the old hypothesis, both metals preferentially bind the substrate as a six-membered ring, exposing the exact same sites to the attack by O2. It is the electronic properties of the metals that are then responsible for the system following different reaction paths, to yield the respective products. We fully explain the puzzling metal-induced difference in functionality between ARD and ARD' and, in particular, propose a new mechanism for ARD'. All results are in agreement with available isotopic substitution and other experimental data.

The Role of the Flexible L43-S54 Protein Loop in the CcrA Metallo-ß-lactamase in Binding Structurally Dissimilar ß-Lactam Antibiotics.

The CcrA di-Zn ß-lactamase is a bacterial enzyme capable of efficiently hydrolyzing and thus disabling a diverse set of ß-lactam antibiotics. Understanding the factors that contribute to the efficiency of CcrA is essential for the design of new CcrA-resistant antibiotics and enzyme inhibitors. The efficacy of CcrA has been speculated to be partially attributable to the flexible protein loop located above the active site (L43-S54), which would mold around structurally different substrates, for snag binding. Confirmation of this hypothesis about the role of the loop has been a challenge, from both an experimental and a theoretical point of view. We employed our newly developed method that combines extensive sampling of the protein structure via discrete molecular dynamics (DMD) and quantum mechanical (QM) treatment of the active site, QM/DMD, to investigate the structural role of the L43-S54 loop in binding three different ß-lactam antibiotics: imipenem, ampicillin, and cephalorodine. QM/DMD sampling was followed by high level ab initio calculations for the assessment of the energy contributions to loop-substrate interactions. We show that upon binding of all three antibiotic molecules, the loop comes in direct contact with the substrates and adopts distinctly different conformations depending on the bound substrate. The loop contributes to the binding affinity of CcrA to antibiotics. The primary component of the loop-substrate interaction is hydrophobic, and nonspecific, except for cephalorodine that is capable of π-stacking with W49 via one of the two competing modes.

Why urease is a di-nickel enzyme whereas the CcrA ß-lactamase is a di-zinc enzyme.

Ureases and metallo-ß-lactamases are amide hydrolases closely related in function and structure. However, one major difference between them is that the former uses two nickel cations, and the latter uses two zinc cations to do similar catalytic jobs. What is the reason for this choice that Nature made for the catalytic metals? Is it dictated by electronic or structural reasons in the two catalyzed reactions, or some other evolutionary factors? Are both enzymes "perfect" catalysts, as far as just catalysis is concerned, and if they are, then why? Here, we address these questions through a joint quantum mechanical/molecular mechanical dynamics approach and ab initio mechanistic investigation. Five enzyme/substrate systems are considered: urease/urea, CcrA ß-lactamase/ß-lactam antibiotic model, urease/ß-lactam antibiotic model, CcrA ß-lactamase/urea, and di-Ni-substituted CcrA ß-lactamase/ß-lactam antibiotic model. The mechanisms and rates of the metal-facilitated nucleophilic attack are assessed. Both urease and Ni-substituted ß-lactamase catalyze the attack on the ß-lactam ring with the efficiency surpassing that of natural di-Zn ß-lactamase, whereas ß-lactamase is unable to hydrolyze urea. These results suggest that in ß-lactamases the use of zinc does not provide maximal possible efficiency of the enzyme. Thus, ß-lactamases operate by the principle of "good enough"; i.e., the choice for Zn in them leads to a performance that is just satisfactory for its biological purpose but can be evolutionarily improved via replacement of Zn with Ni.