Electrochemical nanoreactor provides a comprehensive view of isocitrate dehydrogenase cancer-drug kinetics

The ability to control enzyme cascades entrapped in a nanoporous electrode material (the “Electrochemical Leaf”, e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its “gain-of-function” activity—the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods

Tree biomass equations from terrestrial LiDAR : a case study in Guyana

Large uncertainties in tree and forest carbon estimates weaken national efforts to accurately estimate aboveground biomass (AGB) for their national monitoring, measurement, reporting and verification system. Allometric equations to estimate biomass have improved, but remain limited. They rely on destructive sampling; large trees are under-represented in the data used to create them; and they cannot always be applied to different regions. These factors lead to uncertainties and systematic errors in biomass estimations. We developed allometric models to estimate tree AGB in Guyana. These models were based on tree attributes (diameter, height, crown diameter) obtained from terrestrial laser scanning (TLS) point clouds from 72 tropical trees and wood density. We validated our methods and models with data from 26 additional destructively harvested trees. We found that our best TLS-derived allometric models included crown diameter, provided more accurate AGB estimates (R-2 = 0.92-0.93) than traditional pantropical models (R-2 = 0.85-0.89), and were especially accurate for large trees (diameter > 70 cm). The assessed pantropical models underestimated AGB by 4 to 13%. Nevertheless, one pantropical model (Chave et al. 2005 without height) consistently performed best among the pantropical models tested (R-2 = 0.89) and predicted AGB accurately across all size classes-which but for this could not be known without destructive or TLS-derived validation data. Our methods also demonstrate that tree height is difficult to measure in situ, and the inclusion of height in allometric models consistently worsened AGB estimates. We determined that TLS-derived AGB estimates were unbiased. Our approach advances methods to be able to develop, test, and choose allometric models without the need to harvest trees

NADP(H)-dependent biocatalysis without adding NADP(H)

Significance Within cells, enzymes and cofactors catalyzing multistep processes (cascades) are often confined together—either in enclosures (e.g., organelles) or via physical association (metabolons). Nanoconfinement, offering potential general advantages for catalysis, can also be achieved by loading enzymes and their exchangeable cofactors into a porous, electrically conducting inorganic material, thereby enabling catalysis to be channeled, energized, and investigated electrochemically. Such nanoconfinement enables a cascade comprising electroactive ferredoxin NADP+ reductase and isocitrate dehydrogenase to be active for days, catalyzing exhaustive oxidation of bulk isocitrate by recycling trapped NADP(H) carried in on isocitrate dehydrogenase. Nanoconfinement massively increases the efficiency of cofactor-dependent cascade catalysis and has conceptual relevance for prebiotic evolution where complex organic molecules might have formed in gaps and cracks of minerals. Abstract Isocitrate dehydrogenase 1 (IDH1) naturally copurifies and crystallizes in a resting state with a molecule of its exchangeable cofactor, NADP+/NADPH, bound in each monomer of the homodimer. We report electrochemical studies with IDH1 that exploit this property to reveal the massive advantage of nanoconfinement to increase the efficiency of multistep enzyme-catalyzed cascade reactions. When coloaded with ferredoxin NADP+ reductase in a nanoporous conducting indium tin oxide film, IDH1 carries out the complete electrochemical oxidation of 6 mM isocitrate (in 4mL) to 2-oxoglutarate (2OG), using only the NADP(H) that copurified with IDH1 and was carried into the electrode pores as cargo—the system remains active for days. The entrapped cofactor, now quantifiable by cyclic voltammetry, undergoes ~160,000 turnovers during the process. The results from a variety of electrocatalysis experiments imply that the local concentrations of the two nanoconfined enzymes lie around the millimolar range. The combination of crowding and entrapment results in a 102 to 103-fold increase in the efficiency of NADP(H) redox cycling. The ability of the method to drive cascade catalysis in either direction (oxidation or reduction) and remove and replace substrates was exploited to study redox-state dependent differences in cofactor binding between wild-type IDH1 and the cancer-linked R132H variant that catalyzes the “gain of function” reduction of 2OG to 2-hydroxyglutarate instead of isocitrate oxidation. The combined results demonstrate the power of nanoconfinement for facilitating multistep enzyme catalysis (in this case energized and verified electrochemically) and reveal insights into the dynamic role of nicotinamide cofactors as redox (hydride) carriers

Herpes simplex virus as a model vector system for gene therapy in renal disease

Herpes simplex virus as a model vector system for gene therapy in renal disease. The past decade has been marked by significant advances in the application of gene transfer into living cells of animals and humans. These approaches have been tested in a few animal models of inherited and acquired renal diseases, including carbonic anhydrase II deficiency 1 and experimental glomerulonephritis2,3. Gene transfer into proximal tubular cells has been successfully accomplished by intrarenal arterial infusion of a liposomal complex4 or an adenoviral vector5. Tubular cells from the papilla and medulla have been selectively transduced by retrograde infusion into the pelvi-calyceal system of an adenoviral vector containing a reporter for β-galactosidase5. Although the results of these initial studies are promising, further studies to optimize viral vectors, maximize gene delivery, minimize side-effects, and develop cell-specific and long-term regulated gene expression are critical to the success of gene therapy targeted to specific compartments of the kidney. Our recent efforts have focused on defining the cellular pathways responsible for viral entry and infection into renal epithelial cells using herpes simplex virus (HSV) as a model vector. We anticipate that a solid understanding of the basic scientific principles underlying viral entry and gene expression into specific populations of renal cells will facilitate the design of successful therapeutic viral-based gene transfer strategies

Relation of microvascular dysfunction to exercise capacity and symptoms in patients with severe aortic stenosis

Objective: The aim of this study was to assess the impact of left ventricular hypertrophy, myocardial fibrosis, myocardial perfusion reserve (MPR) and diastolic dysfunction on objectively measured aerobic exercise capacity (peak VO$_{2}$) in severe aortic stenosis (AS). Background: The management of asymptomatic patients with severe AS remains controversial and clinical practice varies. Echocardiographic measures of severity do not discriminate between symptomatic status or predict exercise capacity. The purpose of this study was to investigate the mechanisms contributing to symptom generation and exercise intolerance. This needs to be fully understood to optimise the management of asymptomatic AS. Methods: Patients were prospectively enrolled from a single cardiac surgical centre. Inclusion criteria: age 18-85, isolated severe AS referred for valve replacement. Exclusion criteria: syncope; other moderate/severe valve disease, previous valve surgery, obstructive coronary artery disease (>50% luminal stenosis on invasive angiography), chronic obstructive pulmonary disease, atrial fibrillation, estimated glomerular filtration rate <30mL/min. Investigations and primary outcome measures; cardiac magnetic resonance (CMR) - left ventricular mass index (LVMI), MPR (calculated from absolute myocardial blood flow during adenosine hyperaemia and rest determined by model-independent deconvolution of signal intensity curves with an arterial input function), late gadolinium enhancement (LGE); echocardiography - AS severity, tissue Doppler-derived diastolic function; symptom-limited bicycle ergometer cardiopulmonary exercise testing (CPEX) - peak VO$_{2}$. Linear regression investigated possible predictors of continuous outcome measures. Stepwise selection methods were used to determine the most important predictors of outcome. Results: Four patients with variable LVMI, LGE and MPR are shown, Figure 1. Univariate analyses and results from the stepwise model selection for peak VO$_{2}$ are summarised in Table 1. Only MPR was of independent significance in predicting age and sex corrected peak VO$_{2}$. The relationship between peak VO$_{2}$ and MPR is shown, Figure 2. Patients with higher NYHA Class had lower MPR (p=0.001). Examining predictors of MPR the best stepwise model contained LVMI and LGE category as independent predictors, Table 2. Conclusions: MPR is a novel independent predictor of peak VO$_{2}$ and is inversely related to NYHA functional class in severe AS. Microvascular dysfunction is determined by a combination of factors including AS severity, LVMI, diastolic perfusion time, myocardial fibrosis and LV filling pressure. Further work is required to determine the clinical significance of microvascular dysfunction in AS