Evaluation of NAD(H) analogues as selective inhibitors for Trypanosoma cruzi S-Adenosylhomocysteine hydrolase

This is an Accepted Manuscript of an article published by Taylor & Francis in Nucleosides, Nucleotides and Nucleic Acids in May 2009, available online: http://www.tandfonline.com/10.1080/15257770903044572.S-Adenosylhomocysteine (AdoHcy) hydrolases (SAHHs) from human sources (Hs-SAHHs) bind the cofactor NAD+ more tightly than several parasitic SAHHs by around 1000-fold. This property suggests the cofactor binding site of this essential enzyme as a potential anti-parasitic drug target, e.g., against SAHH from Trypansoma cruzi (Tc-SAHH). The on-rate and off-rate constants and the equilibrium dissociation constants were determined for NAD+/NADH analogues and suggested that NADH analogues were the most promising for selective inhibition of Tc-SAHH. None significantly inhibited Hs-SAHH while S-NADH and H-NADH (Fig. 1) reduced the catalytic activity of Tc-SAHH to <10% in six minutes of exposure

The Rationale for Targeting the NAD/NADH Cofactor Binding Site of Parasitic S-Adenosyl-L-homocysteine Hydrolase for the Design of Anti-parasitic Drugs

This is an Accepted Manuscript of an article published by Taylor & Francis in Nucleosides, Nucleotides and Nucleic Acids in May 2009, available online: http://www.tandfonline.com/10.1080/15257770903051031.Trypanosomal S-adenoyl-L-homocysteine hydrolase (Tc-SAHH), considered as a target for treatment of Chagas disease, has the same catalytic mechanism as human SAHH (Hs-SAHH) and both enzymes have very similar X-ray structures. Efforts toward the design of selective inhibitors against Tc-SAHH targeting the substrate binding site have not to date shown any significant promise. Systematic kinetic and thermodynamic studies on association and dissociation of cofactor NAD/H for Tc-SAHH and Hs-SAHH provide a rationale for the design of anti-parasitic drugs directed toward cofactor-binding sites. Analogues of NAD and their reduced forms show significant selective inactivation of Tc-SAHH, confirming that this design approach is rational

Comparative Kinetics of Cofactor Association and Dissociation for the Human and Trypanosomal S-Adenosylhomocysteine Hydrolases. 3. Role of Lysyl and Tyrosyl Residues of the C-Terminal Extension

Based on the available X-ray structures of S-adenosylhomocysteine hydrolases (SAHHs), free energy simulations employing the MM-GBSA approach were applied to predict residues important to the differential cofactor binding properties of human and trypanosomal SAHHs (Hs-SAHH and Tc-SAHH), within 5 Å of the cofactor NAD+/NADH binding site. Among the 38 residues in this region, only four are different between the two enzymes. Surprisingly, the four non-identical residues make no major contribution to differential cofactor binding between Hs-SAHH and Tc-SAHH. On the other hand, four pairs of identical residues are shown by free energy simulations to differentiate cofactor binding between Hs-SAHH and Tc-SAHH. Experimental mutagenesis was performed to test these predictions for a lysine residue and a tyrosine residue of the C-terminal extension that penetrates a partner subunit to form part of the cofactor binding site. The K431A mutant of Tc-SAHH (TcK431A) loses its cofactor binding affinity but retains the wild type’s tetrameric structure, while the corresponding mutant of Hs-SAHH (HsK426A) loses both cofactor affinity and tetrameric structure (Ault-Riche et al., 1994 J Biol Chem, 269, 31472–8). The tyrosine mutants HsY430A and TcY435A alter the NAD+ association and dissociation kinetics, with HsY430A increasing the cofactor equilibrium dissociation constant from approximately 10 nM (Hs-SAHH) to about 800 nM while TcY435A increases the cofactor equilibrium dissociation constant from approximately 100 nM (Tc-SAHH) to about 1 mM. Both changes result from larger increases in off-rate combined with smaller decreases in on-rate. These investigations demonstrate that computational free energy decomposition may be used to guide experimental studies by suggesting sensitive sites for mutagenesis. Our finding that identical residues in two orthologous proteins may give significantly different binding free energy contributions strongly suggests that comparative studies of homologous proteins should investigate not only different residues, but also identical residues in these proteins

Relationships between the El-Niño Southern Oscillation and spate flows in southern Africa and Australia

International audienceThe flow records of arid zone rivers are characterised by a high degree of seasonal variability, being dominated by long periods of very low or zero flow. Discrete flow events in these rivers are influenced by aseasonal factors such as global climate forcings. The atmospheric circulations of the El-Niño Southern Oscillation (ENSO) have been shown to influence climate regimes across many parts of the world. Strong teleconnections between changing ENSO regimes and discharges are likely to be observed in highly variable arid zones. In this paper, the influence of ENSO mechanisms on the flow records of two arid zone rivers in each of Australia and Southern Africa are identified. ENSO signals, together with multi-decadal variability in their impact as identified through seasonal values of the Interdecadal Pacific Oscillation (IPO) index, are shown to influence both the rate of occurrence and the size of discrete flow episodes in these rivers. Keywords: arid zones, streamflow, spates, climate variability, ENSO, Interdecadal Pacific Oscillation, IP

The importance of spatiotemporal variability in irrigation inputs for hydrological modelling of irrigated catchments

Irrigation contributes substantially to the water balance and environmental condition of many agriculturally productive catchments. This study focuses on the representation of spatio‐temporal variability of irrigation depths in irrigation schedule models. Irrigation variability arises due to differences in farmers' irrigation practices, yet its effects on distributed hydrological predictions used to inform management decisions are currently poorly understood. Using a case study of the Barr Creek catchment in the Murray Darling Basin, Australia, we systematically compare four irrigation schedule models, including uniform vs variable in space, and continuous‐time vs event‐based representations. We evaluate simulated irrigation at hydrological response unit and catchment scales, and demonstrate the impact of irrigation schedules on the simulations of streamflow, evapotranspiration and potential recharge obtained using the Soil and Water Assessment Tool (SWAT). A new spatially‐variable event‐based irrigation schedule model is developed. When used to provide irrigation inputs to SWAT, this new model: (i) reduces the over‐estimation of actual evapotranspiration that occurs with spatially‐uniform continuous‐time irrigation assumptions (biases reduced from ∼40% to ∼2%) and (ii) better reproduces the fast streamflow response to rainfall events compared to spatially‐uniform event‐based irrigation assumptions (seasonally‐adjusted Nash‐Sutcliffe Efficiency improves from 0.15 to 0.56). The stochastic nature of the new model allows representing irrigation schedule uncertainty, which improves the characterization of uncertainty in simulated catchment streamflow and can be used for uncertainty decomposition. More generally, this study highlights the importance of spatio‐temporal variability of inputs to distributed hydrological models and the importance of using multi‐variate response data to test and refine environmental models.David McInerney, Mark Thyer, Dmitri Kavetski, Faith Githui, Thabo Thayalakumaran, Min Liu, George Kuczer

Usefulness of the Reversible Jump Markov Chain Monte Carlo Model in Regional Flood Frequency Analysis

Regional flood frequency analysis is a convenient way to reduce estimation uncertainty when few data are available at the gauging site. In this work, a model that allows a non-null probability to a regional fixed shape parameter is presented. This methodology is integrated within a Bayesian framework and uses reversible jump techniques. The performance on stochastic data of this new estimator is compared to two other models: a conventional Bayesian analysis and the index flood approach. Results show that the proposed estimator is absolutely suited to regional estimation when only a few data are available at the target site. Moreover, unlike the index flood estimator, target site index flood error estimation seems to have less impact on Bayesian estimators. Some suggestions about configurations of the pooling groups are also presented to increase the performance of each estimator

Quantifying simulator discrepancy in discrete-time dynamical simulators

When making predictions with complex simulators it can be important to quantify the various sources of uncertainty. Errors in the structural specification of the simulator, for example due to missing processes or incorrect mathematical specification, can be a major source of uncertainty, but are often ignored. We introduce a methodology for inferring the discrepancy between the simulator and the system in discrete-time dynamical simulators. We assume a structural form for the discrepancy function, and show how to infer the maximum-likelihood parameter estimates using a particle filter embedded within a Monte Carlo expectation maximization (MCEM) algorithm. We illustrate the method on a conceptual rainfall-runoff simulator (logSPM) used to model the Abercrombie catchment in Australia. We assess the simulator and discrepancy model on the basis of their predictive performance using proper scoring rules. This article has supplementary material online

Experimental evaluation of the dynamic seasonal streamflow forecasting approach

The primary focus of this experimental evaluation project is to answer the key question: is it possible to provide accurate and reliable seasonal streamflow forecasts using the dynamic hydrologic modelling approach? To address this issue, this experimental project evaluated the performance of the dynamic modelling approach to key catchments in the Murray-Darling Basin, where statistical seasonal streamflow forecasts are currently available.Tuteja NK, Shin D, Laugesen R, Khan U, Shao Q, Wang E, Li M, Zheng H, Kuczera G, Kavetski D, Evin G, Thyer M, MacDonald A, Chia T & Le