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William H Miller

Publications and source records attributed to William H Miller.

At least 37 records · Page 2Linked to original sources
PubMed2004

On the efficient path integral evaluation of thermal rate constants within the quantum instanton approximation.

We present an efficient path integral approach for evaluating thermal rate constants within the quantum instanton (QI) approximation that was recently introduced to overcome the quantitative deficiencies of the earlier semiclassical instanton approach [Miller, Zhao, Ceotto, and Yang, J. Chem. Phys. 119, 1329 (2003)]. Since the QI rate constant is determined solely by properties of the (quantum) Boltzmann operator (specifically, by the zero time properties of the flux-flux and delta-delta correlation functions), it can be evaluated by well-established techniques of imaginary time path integrals even for quite complex chemical reactions. Here we present a series of statistical estimators for relevant quantities which can be evaluated straightforwardly with any nonlinear reaction coordinates and general Hamiltonians in Cartesian space. To facilitate the search for the optimal dividing surfaces required by the QI approximation, we introduce a two-dimensional quantum free energy surface associated with the delta-delta correlation function and describe how an adaptive umbrella sampling can be used effectively to construct such a free energy surface. The overall computational procedure is illustrated by the application to a hydrogen exchange reaction in gas phase, which shows excellent agreement of the QI rates with those obtained from quantum scattering calculations.

Journal Article↗
PubMed2004

Path integral calculation of thermal rate constants within the quantum instanton approximation: application to the H + CH4 --> H2 + CH3 hydrogen abstraction reaction in full Cartesian space.

The quantum instanton approximation for thermal rate constants of chemical reactions [Miller, Zhao, Ceotto, and Yang, J. Chem. Phys. 119, 1329 (2003)], which is modeled after the earlier semiclassical instanton approach, is applied to the hydrogen abstraction reaction from methane by a hydrogen atom, H + CH4 --> H2 + CH3, using a modified and recalibrated version of the Jordan-Gilbert potential surface. The quantum instanton rate is evaluated using path integral Monte Carlo approaches based on the recently proposed implementation schemes [Yamamoto and Miller, J. Chem. Phys. 120, 3086 (2004)]. The calculations were carried out using the Cartesian coordinates of all the atoms (thus involving 18 degrees of freedom), thereby taking explicit account of rotational effects of the whole system and also allowing the equivalent treatment of the four methane hydrogens. To achieve such a treatment, we present extended forms of the path integral estimators for relevant quantities that may be used for general N-atom systems with any generalized reaction coordinates. The quantum instanton rates thus obtained for the temperature range T = 200-2000 K show good agreement with available experimental data, which gives support to the accuracy of the underlying potential surface used.

Journal Article↗
PubMed2004

Functional genomics in rodent models of hypertension.

Inbred strains of rodents have been used to study mammalian physiology and pathophysiology in an attempt to understand the contribution of genes in the pathogenesis of the disease process. In this review we focus on experimental animal models to identify quantitative trait loci (QTL) and possible strategies for identifying underlying genetic determinants responsible for hypertension. Confirmation of the existence of the QTL and dissection of the implicated region can be undertaken by production of either recombinant inbred, consomic or congenic strains. Despite complex interactions and the relatively few confirmed causative genes underlying QTL, recent developments in rat genome resources and advancement in statistical and bioinformatic methods will facilitate the identification of major gene(s) responsible for complex, polygenic traits.

Animals↗
PubMed2004

Effect of adenovirus serotype 5 fiber and penton modifications on in vivo tropism in rats.

Sequestration of adenovirus serotype 5 (Ad5) in liver restricts its use for gene delivery to other target sites in vivo. To date, no studies have systematically assessed the impact of genetic capsid modifications on in vivo tropism in rats, an important preclinical model for many disease types. We evaluated a panel of Ad5 vectors with capsid mutations or pseudotyped with the short fiber from serotype 41 (Ad41s) for infectivity in Wistar Kyoto rats in vitro and systemically in vivo. In vitro studies demonstrated that both coxsackie and adenovirus receptor (CAR) and heparan sulfate proteoglycan (HSPG) binding were predominant predictors of Ad5 tropism. In vivo, neither CAR nor integrin mutations alone affected liver transduction. The HSPG-binding mutation alone moderately reduced rat liver transgene levels by 2-fold (P < 0.05). This was further substantially decreased by additional mutation of CAR binding (95-fold). Combining CAR and integrin mutations reduced transgene levels by >99% (509-fold, P < 0.01), an effect not observed in parallel experiments in mice and highly variable when studied further in an additional two strains of rat. Ad41s mediated very low liver transduction (58-fold lower than AdCTL). Moreover, CAR-binding mutants (KO1-containing) or pseudotyping 41s eliminated hemagglutination of rat and human red blood cells in vitro. This highlights some important potential species and strain differences dictating Ad5 tropism in vivo and identifies vectors that are substantially detargeted from rat liver in vivo.

Adenoviridae↗
PubMed2004

Strategies to reduce oxidative stress in cardiovascular disease.

A multitude of studies in experimental animals, together with clinical data, provide evidence that increased production of ROS (reactive oxygen species) are involved in the development and progression of cardiovascular disease. As ROS appear to have a critical role in atherosclerosis, there has been considerable interest in identifying the enzyme systems involved and in developing strategies to reduce oxidative stress. Prospective clinical trials with vitamins and hormone replacement therapy have not fulfilled earlier promises, although there is still interest in other dietary supplements. Superoxide dismutase mimetics, thiols, xanthine oxidase and NAD(P)H oxidase inhibitors are currently receiving much interest, while animal studies using gene therapy show promise, but are still at an early stage. Of the drugs in common clinical use, there is evidence that ACE (angiotensin-converting enzyme) inhibitors and AT1 (angiotensin II type 1) receptor blockers have beneficial effects on oxidative stress above their antihypertensive properties, whereas statins, in addition to improving lipid profiles, may also lower oxidative stress.

Angiotensin II Type 1 Receptor Blockers↗
PubMed2003

Indole naphthyridinones as inhibitors of bacterial enoyl-ACP reductases FabI and FabK.

Bacterial enoyl-ACP reductase (FabI) is responsible for catalyzing the final step of bacterial fatty acid biosynthesis and is an attractive target for the development of novel antibacterial agents. Previously we reported the development of FabI inhibitor 4 with narrow spectrum antimicrobial activity and in vivo efficacy against Staphylococcus aureus via intraperitoneal (ip) administration. Through iterative medicinal chemistry aided by X-ray crystal structure analysis, a new series of inhibitors has been developed with greatly increased potency against FabI-containing organisms. Several of these new inhibitors have potent antibacterial activity against multidrug resistant strains of S. aureus, and compound 30 demonstrates exceptional oral (po) in vivo efficacy in a S. aureus infection model in rats. While optimizing FabI inhibitory activity, compounds 29 and 30 were identified as having low micromolar FabK inhibitory activity, thereby increasing the antimicrobial spectrum of these compounds to include the FabK-containing pathogens Streptococcus pneumoniae and Enterococcus faecalis. The results described herein support the hypothesis that bacterial enoyl-ACP reductases are valid targets for antibacterial agents.

Abscess↗
PubMed2003

Concurrent follicular dysplasia and interface dermatitis in Boxer dogs.

Recurrent or persistent follicular dysplasia and interface dermatitis are described in nine Boxers. Data on age, sex, seasonality of alopecia and histopathological features of the follicular dysplasia in these nine Boxers are comparable with those described in previous reports. The interface dermatitis was characterized by multifocal annular crusted lesions confined to the areas of follicular dysplasia. The inflammatory lesions were neither pruritic nor painful and affected dogs were otherwise healthy. Histopathologically the clinically inflammatory lesions were characterized as an interface dermatitis. Immunohistochemical studies failed to demonstrate immunoglobulins or complement at the basement membrane zone or within blood vessel walls. In dogs with recurrent or persistent disease, the follicular dysplasia and interface dermatitis ran identical, concurrent courses of spontaneous remission and recurrence, or persistence, respectively. One dog with persistent disease was treated successfully with tetracycline and niacinamide for the interface dermatitis, and melatonin for the follicular dysplasia. Although the aetiopathogenesis of this newly described condition and the relationship between the two histological reaction patterns are not known, photoperiod and genetic predisposition appear to play a role.

Animals↗
PubMed2003

Hereditary nasal parakeratosis in Labrador retrievers: 11 new cases and a retrospective study on the presence of accumulations of serum ('serum lakes') in the epidermis of parakeratotic dermatoses and inflamed nasal plana of dogs.

We report 11 new cases of hereditary nasal parakeratosis in Labrador retrievers. The disease was first observed when the dogs were 6 months to 2 years of age, and affected dogs of either sex and all coat colours. Hyperkeratosis and depigmentation were confined to the nasal planum, and affected dogs were otherwise healthy. The principal histological findings in biopsy specimens were marked diffuse parakeratotic hyperkeratosis, multiple intracorneal serum lakes and superficial interstitial-to-interface lymphoplasmacytic dermatitis. Topical applications of propylene glycol in water or white petrolatum were often effective for treatment of the dermatosis. However, continued applications were required to maintain a beneficial response. A retrospective histological study of parakeratotic inflammatory diseases of canine haired skin and inflammatory diseases of the canine nasal planum was performed. The degree of parakeratotic hyperkeratosis and the number and size of intracorneal serum lakes were evaluated. The degree of parakeratotic hyperkeratosis was greater in hereditary nasal parakeratosis specimens than that seen in discoid lupus erythematosus and Malassezia dermatitis. There were more serum lakes in hereditary nasal parakeratosis specimens than in specimens from dogs with discoid lupus erythematosus, Malassezia dermatitis, primary seborrheic dermatitis or zinc-responsive dermatosis. Significant differences in sizes of serum lakes (if present) were not seen.

Animals↗
PubMed2003

Medullary trichomalacia in 6 German shepherd dogs.

Medullary trichomalacia is the name proposed for a hair shaft abnormality that was recognized in 6 German shepherd dogs. Affected dogs had multifocal areas of broken hairs, especially on the dorsolateral trunk. Microscopic examination of hair shafts revealed focal areas of loss of architecture, swelling, and apparent softening of the medulla, followed by longitudinal (length-wise) splitting and breakage of the hair shaft. No cause could be found. Affected dogs were otherwise healthy, and apparent spontaneous recovery was the usual outcome. Relapses may occur.

Animals↗
PubMed2002

Discovery of aminopyridine-based inhibitors of bacterial enoyl-ACP reductase (FabI).

Bacterial enoyl-ACP reductase (FabI) catalyzes the final step in each cycle of bacterial fatty acid biosynthesis and is an attractive target for the development of new antibacterial agents. Our efforts to identify potent, selective FabI inhibitors began with screening of the GlaxoSmithKline proprietary compound collection, which identified several small-molecule inhibitors of Staphylococcus aureus FabI. Through a combination of iterative medicinal chemistry and X-ray crystal structure based design, one of these leads was developed into the novel aminopyridine derivative 9, a low micromolar inhibitor of FabI from S. aureus (IC(50) = 2.4 microM) and Haemophilus influenzae (IC(50) = 4.2 microM). Compound 9 has good in vitro antibacterial activity against several organisms, including S. aureus (MIC = 0.5 microg/mL), and is effective in vivo in a S. aureus groin abscess infection model in rats. Through FabI overexpressor and macromolecular synthesis studies, the mode of action of 9 has been confirmed to be inhibition of fatty acid biosynthesis via inhibition of FabI. Taken together, these results support FabI as a valid antibacterial target and demonstrate the potential of small-molecule FabI inhibitors for the treatment of bacterial infections.

Acrylamides↗
PubMed2002

Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase.

Semiclassical molecular dynamics simulations have been combined with quantum chemistry calculations to provide detailed modeling of the methane and ethane hydroxylation reactions catalyzed by the hydroxylase enzymes of the soluble methane monooxygenase system. The experimental distribution of enantiomeric alcohols in the reaction of ethanes made chiral by the use of hydrogen isotopes is quantitatively reproduced and explained. The reaction dynamics involve a mixture of concerted and bound radical trajectories, and we characterize each of these reactive channels in detail. Diffusion of the bound radical intermediate at the active site core determines the global rate constant. The results also provide a qualitative rationale for the lack of ring-opened products derived from certain radical clock substrate probes and for the relative rate constants and kinetic isotope effects exhibited by a variety of substrates.

Binding Sites↗
PubMed2002

Proton-transfer dynamics in the activation of cytochrome P450eryF.

Molecular dynamics simulations are combined with quantum chemistry calculations of instantaneous proton-transfer energy profiles to investigate proton-transfer events in the transient pathway of cytochrome P450eryF (6-deoxyerythronolide B hydroxylase; CYP107A1), from the oxyferrous species to the catalytically active ferryl oxygen species (compound I). This reaction is one of the most fundamental unresolved aspects in the mechanism of oxidation that is common to all cytochrome P450s. We find that this process involves an ultrafast proton transfer from the crystallographic water molecule W519 to the distal oxygen bound to the heme group, and a subsequent proton-transfer event from W564 to W519. Both proton-transfer events are found to be endothermic in the oxyferrous state, suggesting that the oxyferrous reduction is mechanistically linked to the proton-transfer dynamics. These findings indicate that the hydrogen bond network, proximate to the O(2)-binding cleft, plays a crucial functional role in the enzymatic activation of P450s. Our results are consistent with the effect of mutations on the enzymatic efficacy.

Bacterial Proteins↗
PubMed2002

Intracorneal vacuoles in skin diseases with parakeratotic hyperkeratosis in the dog: a retrospective light-microscopy study of 111 cases (1973-2000).

Two recent case reports described a congenital keratinization defect (congenital follicular parakeratosis; CFP) in Rottweiler and Siberian Husky dogs. Skin biopsy specimens revealed marked parakeratosis targeting the hair follicle and numerous intracorneal vacuoles. A retrospective histopathological study was conducted on skin biopsy specimens from 111 dogs with diseases associated with parakeratotic hyperkeratosis to determine whether intracorneal vacuoles were present. Additional criteria evaluated were the size and location of the vacuoles and the degree of parakeratosis. Cases examined included dogs with primary idiopathic seborrhoea, necrolytic migratory erythema (NME), Malassezia dermatitis, zinc-responsive dermatosis, hereditary nasal hyperkeratosis of Labrador Retriever dogs, thallotoxicosis and CFP. Thirty-seven cases (37/111, 33%) had intracorneal vacuoles, including nine cases of primary idiopathic seborrhoea (9/29, 31%), 10 cases of NME (10/18, 56%), five cases of Malassezia dermatitis (5/19, 26%), five cases of zinc-responsive dermatosis (5/36, 14%), five cases of hereditary nasal hyperkeratosis (5/5, 100%) and three cases of CFP (3/3, 100%). If present, intracorneal vacuoles were found throughout all layers of the parakeratin. The sizes of intracorneal vacuoles varied among diseases, but large (> 5 microm) vacuoles only were present in CFP. Biopsies with a larger degree of parakeratosis were significantly more likely to have intracorneal vacuoles (P = < 0.001). Based on this study, intracorneal vacuoles are a common finding in many parakeratotic skin diseases of the dog, but large (> 5 microm) vacuoles are found only in CFP.

Animals↗
PubMed2002

Rapid inhibition of thyroxine-induced bone resorption in the rat by an orally active vitronectin receptor antagonist.

An excess of thyroid hormone results in increased bone turnover and loss of bone mass in humans. Exogenous administration of thyroid hormone to rats has served as a model of human hyperthyroidism in which antiresorptive therapies have been tested. We have further refined this model of thyroxine (T4)-induced turnover in the rat. Daily administration of T4 to aged rats for as short as 1 week resulted in elevated bone resorption determined by significantly higher urinary deoxypyridinoline (Dpd) compared with vehicle controls or animals receiving T4 plus estradiol. Three weeks of daily administration of T4 led to significantly lower bone mineral density compared with untreated controls or animals receiving T4 plus estradiol. In a follow-up study, a depot formulation of T4 caused an increase in Dpd identical to that achieved with a bolus dose. SB-273005 [(4S)-2,3,4,5-tetrahydro-8-[2-[6-(methylamino)-2-pyridinyl] ethoxy]-3-oxo-2-(2,2,2-trifluoroethyl)-1H-2-benzazepine-4- acetic acid] a potent antagonist of the integrins alpha(v)beta(3) and alpha(v)beta(5), has been shown previously to inhibit bone resorption in cultures of human osteoclasts and to protect bone in ovariectomized rats. The effect of SB-273005 by oral administration was evaluated in this thyroxine-induced turnover model. Dose-dependent inhibition of resorption was seen with SB-273005 after 7 days of dosing using Dpd as a measure of bone resorption. In summary, it has been demonstrated that the antiresorptive activity of a vitronectin receptor antagonist can be measured after only 7 days of treatment in this refined rat model of thyroxine-induced bone turnover. These data suggest that SB-273005 may be useful for the treatment of metabolic bone diseases, including those resulting from hyperthyroidism.

Amino Acids↗
PubMed2002

Discovery of a novel and potent class of FabI-directed antibacterial agents.

Bacterial enoyl-acyl carrier protein (ACP) reductase (FabI) catalyzes the final step in each elongation cycle of bacterial fatty acid biosynthesis and is an attractive target for the development of new antibacterial agents. High-throughput screening of the Staphylococcus aureus FabI enzyme identified a novel, weak inhibitor with no detectable antibacterial activity against S. aureus. Iterative medicinal chemistry and X-ray crystal structure-based design led to the identification of compound 4 [(E)-N-methyl-N-(2-methyl-1H-indol-3-ylmethyl)-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)acrylamide], which is 350-fold more potent than the original lead compound obtained by high-throughput screening in the FabI inhibition assay. Compound 4 has exquisite antistaphylococci activity, achieving MICs at which 90% of isolates are inhibited more than 500 times lower than those of nine currently available antibiotics against a panel of multidrug-resistant strains of S. aureus and Staphylococcus epidermidis. Furthermore, compound 4 exhibits excellent in vivo efficacy in an S. aureus infection model in rats. Biochemical and genetic approaches have confirmed that the mode of antibacterial action of compound 4 and related compounds is via inhibition of FabI. Compound 4 also exhibits weak FabK inhibitory activity, which may explain its antibacterial activity against Streptococcus pneumoniae and Enterococcus faecalis, which depend on FabK and both FabK and FabI, respectively, for their enoyl-ACP reductase function. These results show that compound 4 is representative of a new, totally synthetic series of antibacterial agents that has the potential to provide novel alternatives for the treatment of S. aureus infections that are resistant to our present armory of antibiotics.

Animals↗