Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols.

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semiempirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the prereaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behavior of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were reasonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that molecular dynamics (MD) simulations using this functional were only stable if a fine integration grid was used. The low-cost semiempirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics is not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to methylvinyl ketone was calculated using quantum mechanical/molecular mechanical MD in an explicit polarizable aqueous solvent. © 2019 Wiley Periodicals, Inc.

Prediction of (19)F NMR Chemical Shifts in Labeled Proteins: Computational Protocol and Case Study.

The structural analysis of ligand complexation in biomolecular systems is important in the design of new medicinal therapeutic agents; however, monitoring subtle structural changes in a protein's microenvironment is a challenging and complex problem. In this regard, the use of protein-based (19)F NMR for screening low-molecular-weight molecules (i.e., fragments) can be an especially powerful tool to aid in drug design. Resonance assignment of the protein's (19)F NMR spectrum is necessary for structural analysis. Here, a quantum chemical method has been developed as an initial approach to facilitate the assignment of a fluorinated protein's (19)F NMR spectrum. The epigenetic "reader" domain of protein Brd4 was taken as a case study to assess the strengths and limitations of the method. The overall modeling protocol predicts chemical shifts for residues in rigid proteins with good accuracy; proper accounting for explicit solvation of fluorinated residues by water is critical.

Destruction of chemical warfare agents using metal-organic frameworks.

Chemical warfare agents containing phosphonate ester bonds are among the most toxic chemicals known to mankind. Recent global military events, such as the conflict and disarmament in Syria, have brought into focus the need to find effective strategies for the rapid destruction of these banned chemicals. Solutions are needed for immediate personal protection (for example, the filtration and catalytic destruction of airborne versions of agents), bulk destruction of chemical weapon stockpiles, protection (via coating) of clothing, equipment and buildings, and containment of agent spills. Solid heterogeneous materials such as modified activated carbon or metal oxides exhibit many desirable characteristics for the destruction of chemical warfare agents. However, low sorptive capacities, low effective active site loadings, deactivation of the active site, slow degradation kinetics, and/or a lack of tailorability offer significant room for improvement in these materials. Here, we report a carefully chosen metal-organic framework (MOF) material featuring high porosity and exceptional chemical stability that is extraordinarily effective for the degradation of nerve agents and their simulants. Experimental and computational evidence points to Lewis-acidic Zr(IV) ions as the active sites and to their superb accessibility as a defining element of their efficacy.

Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems.

The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation.

Empirical and theoretical insights into the structural features and host-guest chemistry of M8L4 tube architectures.

We demonstrate a general method for the construction of M8L4 tubular complexes via subcomponent self-assembly, starting from Cu(I) or Ag(I) precursors together with suitable elongated tetraamine and 2-formylpyridine subcomponents. The tubular architectures were often observed as equilibrium mixtures of diastereomers having two different point symmetries (D2d or D2 ⇄ D4) in solution. The equilibria between diastereomers were influenced through variation in ligand length, substituents, metal ion identity, counteranion, and temperature. In the presence of dicyanoaurate(I) and Au(I), the D4-symmetric hosts were able to bind linear Au(Au(CN)2)2(-) (with two different configurations) as the best-fitting guest. Substitution of dicyanoargentate(I) for dicyanoaurate(I) resulted in the formation of Ag(Au(CN)2)2(-) as the optimal guest through transmetalation. Density functional theory was employed to elucidate the host-guest chemistries of the tubes.

Design of a metal-organic framework with enhanced back bonding for separation of N2 and CH4.

Gas separations with porous materials are economically important and provide a unique challenge to fundamental materials design, as adsorbent properties can be altered to achieve selective gas adsorption. Metal-organic frameworks represent a rapidly expanding new class of porous adsorbents with a large range of possibilities for designing materials with desired functionalities. Given the large number of possible framework structures, quantum mechanical computations can provide useful guidance in prioritizing the synthesis of the most useful materials for a given application. Here, we show that such calculations can predict a new metal-organic framework of potential utility for separation of dinitrogen from methane, a particularly challenging separation of critical value for utilizing natural gas. An open V(II) site incorporated into a metal-organic framework can provide a material with a considerably higher enthalpy of adsorption for dinitrogen than for methane, based on strong selective back bonding with the former but not the latter.

Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe(2.).

We extend the AMOEBA polarizable molecular mechanics force field to the Fe(2+) cation in its singlet, triplet, and quintet spin states. Required parameters are obtained either directly from first principles calculations or optimized so as to reproduce corresponding interaction energy components in a hexaaquo environment derived from quantum mechanical energy decomposition analyses. We assess the importance of the damping of point-dipole polarization at short distance as well as the influence of charge-transfer for metal-water interactions in hydrated Fe(2+); this analysis informs the selection of model systems employed for parametrization. We validate our final Fe(2+) model through comparison of molecular dynamics (MD) simulations to available experimental data for aqueous ferrous ion in its quintet electronic ground state.

Proof for the concerted inversion mechanism in the trans-->cis isomerization of azobenzene using hydrogen bonding to induce isomer locking.

Azobenzene undergoes reversible cis<-->trans photoisomerization upon irradiation. Substituents often change the isomerization behavior of azobenzene, but not always in a predictive manner. The synthesis and properties of three azobenzene derivatives, AzoAMP-1, -2, and -3, are reported. AzoAMP-1 (2,2'-bis[N-(2-pyridyl)methyl]diaminoazobenzene), which possesses two aminomethylpyridine groups ortho to the azo group, exhibits minimal trans-->cis photoisomerization and extremely rapid cis-->trans thermal recovery. AzoAMP-1 adopts a planar conformation in the solid state and is much more emissive (Phi(fl) = 0.003) than azobenzene when frozen in a matrix of 1:1 diethylether/ethanol at 77 K. Two strong intramolecular hydrogen bonds between anilino protons and pyridyl and azo nitrogen atoms are responsible for these unusual properties. Computational data predict AzoAMP-1 should not isomerize following S(2)<--S(0) excitation because of the presence of an energy barrier in the S(1) state. When potential energy curves are recalculated with methyl groups in place of anilino protons, the barrier to isomerization disappears. The dimethylated analogue AzoAMP-2 was independently synthesized, and the photoisomerization predicted by calculations was confirmed experimentally. AzoAMP-2, when irradiated at 460 nm, photoisomerizes with a quantum yield of 0.19 and has a much slower rate of thermal isomerization back to the trans form compared to that of AzoAMP-1. Its emission intensity at 77 K is comparable to that of azobenzene. Confirmation that the AzoAMP-1 and -2 retain excited state photochemistry analogous to azobenzene was provided by ultrafast transient absorption spectroscopy of both compounds in the visible spectral region. The isomerization of azobenzene occurs via a concerted inversion mechanism where both aryl rings must adopt a collinear arrangement prior to inversion. The hydrogen bonding in AzoAMP-1 prevents both aryl rings from adopting this conformation. To further probe the mechanism of isomerization, AzoAMP-3, which has only one anilinomethylpyridine substituent for hydrogen bonding, was prepared and characterized. AzoAMP-3 does not isomerize and exhibits emission (Phi(fl) = 0.0008) at 77 K. The hydrogen bonding motif in AzoAMP-1 and AzoAMP-3 provides the first example where inhibiting the concerted inversion pathway in an azobenzene prevents isomerization. These molecules provide important supporting evidence for the spectroscopic and computational studies aimed at elucidating the isomerization mechanism in azobenzene.

LDLR promoter variant and exon 14 mutation on the same chromosome are associated with an unusually severe FH phenotype and treatment resistance.

Familial hypercholesterolemia (FH) is the most common form of autosomal-dominant hypercholesterolemia, and is caused by mutations in the low-density lipoprotein receptor (LDLR) gene. Heterozygous FH is characterized by elevated low-density lipoprotein (LDL) cholesterol and early-onset cardiovascular disease, whereas homozygous FH results in more severe LDL cholesterol elevation with death by 20 years of age. We present here the case of an African-American female FH patient presenting with a myocardial infarction at the age of 48, recurrent angina pectoris and numerous coronary artery stents. Her pretreated LDL cholesterol levels were more typical of a homozygous FH pattern and she was resistant to conventional lipid-lowering treatment, yet her other clinical parameters were not necessarily consistent with homozygous FH. Genetic testing revealed two LDLR variants on the same chromosome: one a novel missense mutation in exon 14 (Cys681Gly) and the other a promoter variant (IVS1-217C>T) previously shown to result in increased LDLR transcription. Disease-associated PCSK9 or APOB mutations were not identified in this individual. Overall, her genetic and clinical profile suggests that enhanced expression of the mutant LDLR allele resulted in a severe phenotype with characteristics of both heterozygous and homozygous FH.

Patient-important outcomes in registered diabetes trials.

CONTEXT: Concerns about the safety and efficacy of diabetes interventions persist, in part because randomized clinical trials (RCTs) have not measured their effect on patient-important outcomes, ie, death and quality of life (morbidity, pain, function). OBJECTIVE: To systematically determine the extent to which ongoing and future RCTs in diabetes will ascertain patient-important outcomes. DATA SOURCES: On November 10, 2007, we searched primary RCT registries ClinicalTrials.gov (http://www.clinicaltrials.gov), International Standard Randomized Controlled Trial Number Register (http://isrctn.org), and Australian New Zealand Clinical Trials Registry (http://www.anzctr.org.au). STUDY SELECTION: We identified phase 2 through 4 RCTs enrolling patients with diabetes. Of 2019 RCTs, 1054 proved eligible. We randomly sampled 50% of the eligible RCTs (527 of 1054) and selected 436 registered since registration became mandatory (2004). DATA EXTRACTION: Pairs of reviewers working independently collected study characteristics and determined the outcomes measured and their type (physiological outcomes, surrogate outcomes thought to reflect an increased risk for patient-important outcomes, and patient-important outcomes). RESULTS: Of the 436 registered RCTs included in this analysis, 24 (6%) had not started enrollment, 109 (25%) were actively enrolling, and 303 (69%) had completed enrollment. Primary outcomes were patient-important outcomes in only 78 of 436 RCTs (18%; 95% confidence interval [CI], 14%-22%), physiological and laboratory outcomes in 69 of 436 (16%; 95% CI, 13%-20%), and surrogate outcomes in 268 of 436 (61%; 95% CI, 57%-66%). Patient-important outcomes were reported as primary or secondary outcomes in 201 of 436 (46%; 95% CI, 41%-51%). In multivariate analysis, large trials (odds ratio [OR], 1.10; 95% CI, 1.02-1.19 for every additional 100 patients) and trials of longer duration (OR, 1.03; 95% CI, 1.01-1.06 for every additional 30 days) were more likely while parallel design RCTs (OR, 0.15; 95% CI, 0.05-0.44) and type 2 diabetes trials (OR, 0.23; 95% CI, 0.09-0.61) were less likely to assess patient-important outcomes as a primary outcome. CONCLUSION: In this sample of registered ongoing RCTs in diabetes, only 18% included patient-important outcomes as primary outcomes.

Hyperglycemia and acute coronary syndrome: a scientific statement from the American Heart Association Diabetes Committee of the Council on Nutrition, Physical Activity, and Metabolism.

Hyperglycemia is common and associated with markedly increased mortality rates in patients hospitalized with acute coronary syndromes (ACS). Despite the fact that several studies have documented this association, hyperglycemia remains underappreciated as a risk factor, and it is frequently untreated in ACS patients. This is in large part due to limitations of prior studies, and the remaining critical gaps in our understanding of the relationship between hyperglycemia and poor outcomes. The main objective of the present statement is to summarize the current state of knowledge regarding the association between elevated glucose and patient outcomes in ACS and to outline the most important knowledge gaps in this field. These gaps include the need to specifically define hyperglycemia, develop optimal ways of measuring and tracking glucose values during ACS hospitalization, and better understand the physiological mechanisms responsible for poor outcomes associated with hyperglycemia. The most important issue, however, is whether elevated glucose is a direct mediator of adverse outcomes in ACS patients or just a marker of greater disease severity. Given the marked increase in short- and long-term mortality associated with hyperglycemia, there is an urgent need for definitive large randomized trials to determine whether treatment strategies aimed at glucose control will improve patient outcomes and to define specific glucose treatment targets. Although firm guidelines will need to await completion of these clinical trials, the present statement also provides consensus recommendations for hyperglycemia management in patients with ACS on the basis of the available data.

Hyperglycemia and acute coronary syndrome: a scientific statement from the American Heart Association Diabetes Committee of the Council on Nutrition, Physical Activity, and Metabolism.

Hyperglycemia is common and associated with markedly increased mortality rates in patients hospitalized with acute coronary syndromes (ACS). Despite the fact that several studies have documented this association, hyperglycemia remains underappreciated as a risk factor, and it is frequently untreated in ACS patients. This is in large part due to limitations of prior studies, and the remaining critical gaps in our understanding of the relationship between hyperglycemia and poor outcomes. The main objective of the present statement is to summarize the current state of knowledge regarding the association between elevated glucose and patient outcomes in ACS and to outline the most important knowledge gaps in this field. These gaps include the need to specifically define hyperglycemia, develop optimal ways of measuring and tracking glucose values during ACS hospitalization, and better understand the physiological mechanisms responsible for poor outcomes associated with hyperglycemia. The most important issue, however, is whether elevated glucose is a direct mediator of adverse outcomes in ACS patients or just a marker of greater disease severity. Given the marked increase in short- and long-term mortality associated with hyperglycemia, there is an urgent need for definitive large randomized trials to determine whether treatment strategies aimed at glucose control will improve patient outcomes and to define specific glucose treatment targets. Although firm guidelines will need to await completion of these clinical trials, the present statement also provides consensus recommendations for hyperglycemia management in patients with ACS on the basis of the available data.

Glycemic variation and hypoglycemia in patients with well-controlled type 1 diabetes on a multiple daily insulin injection program with use of glargine and ultralente as basal insulin.

OBJECTIVE: To evaluate glycemic variation and hypoglycemia in patients with well-controlled type 1 diabetes receiving multiple daily insulin injections during glargine and Ultralente use as basal insulin in a clinical trial. METHODS: Twenty-two patients (12 men and 10 women; median age, 43 years), with a hemoglobin A1c level <7.8%, were randomized in a crossover design to receive either insulin glargine or Ultralente insulin as basal insulin for 4 months each, with insulin aspart as prandial insulin. Continuous glucose monitoring and the Fear of Hypoglycemia questionnaire were used at baseline and at the end of each treatment period. RESULTS: Whereas the mean amplitude of glycemic excursions showed a correlation with the area under the curve of blood glucose <3.89 mmol/L per day, the number of periods during the day with hypoglycemia was significantly correlated with the M value. Measures of glycemic variation did not differ significantly between glargine and Ultralente treatment. With use of glargine therapy, the SD of blood glucose levels showed a tendency to be lower and the SD of nocturnal blood glucose concentrations was significantly lower. Glucose concentrations were significantly lower during the 1 hour before and the 3 hours after lunch with use of Ultralente. The "Worry" scale on the Fear of Hypoglycemia questionnaire was less during Ultralente therapy and correlated with the number of times blood glucose concentrations were <3.89 mmol/L daily. CONCLUSION: Measures of glycemic variability and hypoglycemia need to be studied more in clinical trials of glycemic control in patients with type 1 diabetes. Glycemic variability is less, particularly at night, with glargine as basal insulin.

Pilot study of combined therapy with ω-3 fatty acids and niacin in atherogenic dyslipidemia.

BACKGROUND: Niacin and ω-3 fatty acids (ω-3 FA) are both nutrients that reduce serum triglyceride and raise high-density lipoprotein cholesterol (HDL-C) levels when used at pharmacological doses. The possibility that these two agents, given in combination, might have additive effects on these lipid parameters has not been examined previously. In addition, the combination might prevent the rise in low-density lipoprotein (LDL)-C levels frequently seen with ω-3 FA treatment. OBJECTIVE: To determine the effect of therapy of niacin and ω-3 FA alone and in combination versus placebo on lipid parameters in subjects with atherogenic dyslipidemia. METHODS: In a pilot parallel group study, we studied 29 patients with atherogenic dyslipidemia who were assigned to either dual placebo (n = 7), ω-3 FA (3.4 g/d; n = 8), crystalline niacin (3 g/d; n = 7), or the combination (n = 7) for 12 weeks. Fasting lipid profiles were assessed before and after treatment. RESULTS: Changes in serum triglyceride levels from baseline were 10%, -2%, -17%, and -52%, respectively, while HDL-C concentrations rose by 4%, 10%, 18%, and 33%, respectively. Both of these results were statistically significantly different for combination therapy compared to changes with placebo and ω-3 FA monotherapy (analysis of variance with Tukey's post-hoc test). No statistically significant changes were seen for LDL-C. Addition of ω-FA to niacin had no effect on niacin-induced flushing. CONCLUSION: From this small pilot study, we conclude that combined therapy with niacin and ω-3 FA has beneficial effects on triglyceride and HDL-C levels, and use of these two agents in combination prevents the ω-3 FA-induced rise in LDL-C. Larger studies of this combination therapy are clearly warranted in patient populations with atherogenic dyslipidemia to assess not only lipid effects, but also potential coronary heart disease benefits.

Comparison of apolipoprotein-B/apolipoprotein-AI in subjects with versus without the metabolic syndrome.

Recent studies have suggested that the apolipoprotein-B (apo-B)/apolipoprotein-AI (apo-AI) ratio predicts cardiovascular risk better than any of the cholesterol indexes. The aim of the present study was to assess if the apo-B/apo-AI ratio is related to the metabolic syndrome and its components. Data were analyzed from 2,964 subjects (mean age 48 years; 1,516 men, 1,448 women) from the National Health and Nutrition Examination Survey III with apolipoprotein data who were evaluated for the metabolic syndrome and its components. The metabolic syndrome was defined according to the criteria of the National Cholesterol Education Program Adult Treatment Panel III and the International Diabetes Federation. The mean values of the apo-B/apo-AI ratio in subjects with and without the metabolic syndrome were compared. Overall, the median distribution of the apo-B/apo-AI ratio was significantly greater (p <0.0001) in subjects with the Adult Treatment Panel III metabolic syndrome (0.90) than without (0.69). The apo-B/apo-AI ratio was associated significantly with each of the metabolic syndrome components, in descending order of magnitude: low high-density lipoprotein cholesterol (odds ratio [OR] 5.7), high triglycerides (OR 4.7), high waist circumference (OR 2.6), high fasting glucose (OR 1.9), and high blood pressure (OR 1.5). The apo-B/apo-AI ratio was also different between subjects with and without the metabolic syndrome. Mean values of apo-B/apo-AI increased significantly as the numbers of metabolic syndrome components increased in men (p <0.0001) and women (p <0.0001). After excluding high-density lipoprotein cholesterol and triglycerides as criteria for the metabolic syndrome, the association between means persisted (analysis of variance p <0.0001) in men and women. Apo-B/apo-AI was significantly associated with the presence of the metabolic syndrome (OR 5.1, p <0.0001). In conclusion, the apo-B/apo-AI ratio is strongly associated with the presence of individual metabolic syndrome components, with the metabolic syndrome itself, and with insulin resistance. An elevated apo-B/apo-AI ratio may constitute an important feature of the metabolic syndrome and may provide an additional mechanism to explain the increased cardiovascular risk in subjects with this syndrome.

Low-density lipoprotein cholesterol lowering in the prevention of CHD: how low should we go?

The past 12 years have seen the publication of numerous randomized placebo-controlled studies using statins to lower low-density lipoprotein cholesterol (LDLC) to assess the efficacy of cholesterol lowering on cardiovascular events. Initial studies predominantly evaluated mortality or nonfatal myocardial infarctions and coronary heart disease (CHD) death in patients with known or presumed established coronary disease and moderately elevated to very elevated serum cholesterol concentrations. Subsequent investigations studied a broader spectrum of cardiovascular events as a composite primary end point in both primary and secondary prevention strategies in subjects with lower mean entry serum LDLC concentrations. These studies have generally shown a reduction in a composite end point of cardiovascular events, although not necessarily the more restricted end points used in previous studies. Although the LDLC mantra "lower is better" has been popularized in advertising and continuing medical education and suggested as an option in "very high risk" patients by the National Cholesterol Education Program Adult Treatment Panel, the precise target level for LDLC for optimal treatment has not been rigorously defined. Serum LDLC less than 100 mg/dL seems reasonable for patients with known atherosclerosis or at high risk for atherosclerosis (diabetes or presence of multiple risk factors). Serum LDLC less than 70 mg/dL may be a reasonable goal in the setting of acute coronary syndromes, but there are many problems with the data on which this recommendation is made. Furthermore, many advocates of "lower is better" seem oblivious to the potential downsides of more aggressive lipid-lowering therapy. The LDLC target in lower risk primary prevention is less clear. What is obvious is that moderate-dose statin therapy can lower CHD risk in primary prevention and secondary prevention with minimal side effects, and with the imminent availability of several generic statins, with great cost-effectiveness.