Corrigendum to "Utilization of Preventive Measures for Glucocorticoid-Induced Osteoporosis among Veterans with Inflammatory Bowel Disease".

[This corrects the article DOI: 10.1155/2013/862312.].

Utilization of Preventive Measures for Glucocorticoid-Induced Osteoporosis among Veterans with Inflammatory Bowel Disease.

Purpose. We examined current osteoporosis prevention practices in patients with inflammatory bowel disease (IBD) on chronic steroid using the 2003 American Gastroenterological Association guidelines as standard of care. Methods. We identified all IBD patients followed at the Oklahoma City VA Medical Center from January 2003 to December 2010, who had been on daily oral steroids (prednisone ≥5 mg or budesonide ≥6 mg) for ≥3 consecutive months. Associations of calcium and vitamin D (vitD) prescribing and bone mineral density (BMD) testing with patient characteristics were examined by logistic regression. Results. Sixty-three of 384 consecutive patients met inclusion criteria. Among 86 steroid courses, calcium and vitD were concurrently prescribed in 46%, and BMD was tested in 30%. There was no association of demographic and clinical characteristics with calcium/vitD prescribing and BMD testing. By multivariate analysis, steroid initiation after 2006, compared to before 2006, was associated with a significant increase in calcium (OR = 3.17 and P = 0.02) and vitD (OR = 2.96 and P = 0.02) prescribing and BMD testing (OR = 4.63 and P = 0.004). Conclusions. We observed a low, yet increasing, adherence to osteoporosis prevention guidelines in IBD since 2003, which highlights the need for continued physician education to enhance guideline awareness and implementation.

Correlated electrostatic mutations provide a reservoir of stability in HIV protease.

HIV protease, an aspartyl protease crucial to the life cycle of HIV, is the target of many drug development programs. Though many protease inhibitors are on the market, protease eventually evades these drugs by mutating at a rapid pace and building drug resistance. The drug resistance mutations, called primary mutations, are often destabilizing to the enzyme and this loss of stability has to be compensated for. Using a coarse-grained biophysical energy model together with statistical inference methods, we observe that accessory mutations of charged residues increase protein stability, playing a key role in compensating for destabilizing primary drug resistance mutations. Increased stability is intimately related to correlations between electrostatic mutations - uncorrelated mutations would strongly destabilize the enzyme. Additionally, statistical modeling indicates that the network of correlated electrostatic mutations has a simple topology and has evolved to minimize frustrated interactions. The model's statistical coupling parameters reflect this lack of frustration and strongly distinguish like-charge electrostatic interactions from unlike-charge interactions for [Formula: see text] of the most significantly correlated double mutants. Finally, we demonstrate that our model has considerable predictive power and can be used to predict complex mutation patterns, that have not yet been observed due to finite sample size effects, and which are likely to exist within the larger patient population whose virus has not yet been sequenced.

Intestinal and plasma VEGF levels in cirrhosis: the role of portal pressure.

Increased levels of intestinal VEGF are thought to worsen portal hypertension. The cause of the increase in the level of intestinal VEGF found during cirrhosis is not known. The aim of this study is to demonstrate a relationship between portal pressure (PP) and intestinal/ plasma VEGF levels in different stages of fibrosis/cirrhosis. In this experiment, rats were exposed to carbon tetrachloride (CCl(4) ) for 6, 8 and 12 weeks. At the end of exposure, the three groups of rats exhibited three different stages of pathology: non-cirrhotic, early fibrotic and cirrhotic, respectively. For those rats and their age-matched controls, PP and intestinal/plasma VEGF levels were measured. Rats inhaling CCl(4) for 12 weeks developed portal hypertension (18.02 ± 1.07 mmHg), while those exposed for 6 weeks (7.26 ± 0.58 mmHg) and for 8 weeks (8.55 ± 0.53 mmHg) did not. The rats exposed for 12 weeks also showed a 40% increase in the level of intestinal VEGF compared to the controls (P < 0.05), while those rats exposed to CCl(4) inhalation for 6 and 8 weeks did not. There was a significant positive correlation between PP and intestinal VEGF levels (r(2) = 0.4, P < 0.005). Plasma VEGF levels were significantly elevated in those rats exposed to 12 weeks of CCl(4) inhalation (63.7 pg/ml, P < 0.01), compared to the controls (8.5 pg/ml). However, no correlation was observed between PP and plasma VEGF levels. It is concluded that portal pressure modulates intestinal VEGF levels during the development of cirrhosis.

Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures.

Clustering of 99 available X-ray crystal structures of HIV-1 reverse transcriptase (RT) at the flexible non-nucleoside inhibitor binding pocket (NNIBP) provides information about features of the conformational landscape for binding non-nucleoside inhibitors (NNRTIs), including effects of mutation and crystal forms. The ensemble of NNIBP conformations is separated into eight discrete clusters based primarily on the position of the functionally important primer grip, the displacement of which is believed to be one of the mechanisms of inhibition of RT. Two of these clusters are populated by structures in which the primer grip exhibits novel conformations that differ from the predominant cluster by over 4 A and are induced by the unique inhibitors capravirine and rilpivirine/TMC278. This work identifies a new conformation of the NNIBP that may be used to design NNRTIs. It can also be used to guide more complete exploration of the NNIBP free energy landscape using advanced sampling techniques.

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease.

BACKGROUND: The reaction of HIV protease to inhibitor therapy is characterized by the emergence of complex mutational patterns which confer drug resistance. The response of HIV protease to drugs often involves both primary mutations that directly inhibit the action of the drug, and a host of accessory resistance mutations that may occur far from the active site but may contribute to restoring the fitness or stability of the enzyme. Here we develop a probabilistic approach based on connected information that allows us to study residue, pair level and higher-order correlations within the same framework. RESULTS: We apply our methodology to a database of approximately 13,000 sequences which have been annotated by the treatment history of the patients from which the samples were obtained. We show that including pair interactions is essential for agreement with the mutational data, since neglect of these interactions results in order-of-magnitude errors in the probabilities of the simultaneous occurence of many mutations. The magnitude of these pair correlations changes dramatically between sequences obtained from patients that were or were not exposed to drugs. Higher-order effects make a contribution of as much as 10% for residues taken three at a time, but increase to more than twice that for 10 to 15-residue groups. The sequence data is insufficient to determine the higher-order effects for larger groups. We find that higher-order interactions have a significant effect on the predicted frequencies of sequences with large numbers of mutations. While relatively rare, such sequences are more prevalent after multi-drug therapy. The relative importance of these higher-order interactions increases with the number of drugs the patient had been exposed to. CONCLUSION: Correlations are critical for the understanding of mutation patterns in HIV protease. Pair interactions have substantial qualitative effects, while higher-order interactions are individually smaller but may have a collective effect. Together they lead to correlations which could have an important impact on the dynamics of the evolution of cross-resistance, by allowing the virus to pass through otherwise unlikely mutational states. These findings also indicate that pairwise and possibly higher-order effects should be included in the models of protein evolution, instead of assuming that all residues mutate independently of one another.

Torsion angle preference and energetics of small-molecule ligands bound to proteins.

Small organic molecules can assume conformations in the protein-bound state that are significantly different from those in solution. We have analyzed the conformations of 21 common torsion motifs of small molecules extracted from crystal structures of protein-ligand complexes and compared them with their torsion potentials calculated by an ab initio DFT method. We find a good correlation between the potential energy of the torsion motifs and their conformational distribution in the protein-bound state: The most probable conformations of the torsion motifs agree well with the calculated global energy minima, and the lowest torsion-energy state becomes increasingly dominant as the torsion barrier height increases. The torsion motifs can be divided into 3 groups based on torsion barrier heights: high (>4 kcal/mol), medium (2-4 kcal/mol), and low (<2 kcal/mol). The calculated torsion energy profiles are predictive for the most preferred bound conformation for the high and medium barrier groups, the latter group common in druglike molecules. In the high-barrier group of druglike ligands, >95% of conformational torsions occur in the energy region <4 kcal/mol. The conformations of the torsion motifs in the protein-bound state can be modeled by a Boltzmann distribution with a temperature factor much higher than room temperature. This high-temperature factor, derived by fitting the theoretical model to the experimentally observed conformation occurrence of torsions, can be interpreted as the perturbation that proteins inflict on the conformation of the bound ligand. Using this model, it is calculated that the average strain energy of a torsion motif in ligands bound to proteins is approximately 0.6 kcal/mol, a result which can be related to the lower binding efficiency of larger ligands with more rotatable bonds. The above results indicate that torsion potentials play an important role in dictating ligand conformations in both the free and the bound states.

Decreased intrahepatic response to alpha(1)-adrenergic agonists in lipopolysaccharide-treated rats is located in the sinusoidal area and depends on Kupffer cell function.

BACKGROUND AND AIM: Livers from lipopolysaccharide-treated rats have a decreased vascular response to alpha(1)-adrenergic agonists due to an increased production of nitric oxide. Kupffer cells play a central role in the development of intrahepatic microvascular abnormalities during endotoxemia. We investigated the role of Kupffer cells in the intrahepatic vascular tone control in normal and endotoxemic rats. METHOD: Twenty-four hours after pretreatment with gadolinium chloride (to eliminate/inactivate Kupffer cells) or saline, rats were treated with lipopolysaccharide or a second dose of saline. Six hours later, rats (under deep anesthesia) were submitted to liver perfusion with Krebs-Henseleit solution using a system that allowed the measurement of both perfusion and sinusoidal pressures. Dose-response curves to methoxamine (alpha(1)-adrenergic agonist) were obtained in the absence or the presence of the nitric oxide synthase inhibitor N-monomethyl-L-arginine. RESULTS: Pretreatment with gadolinium did not change the intrahepatic vascular response to methoxamine in normal livers. Livers from lipopolysaccharide-treated rats showed a decreased sinusoidal vascular response to methoxamine and a 10-fold increase in nitric oxide production during liver perfusion. Either pretreatment with gadolinium or the presence of N-monomethyl-L-arginine in the perfusate restored the response to methoxamine and decreased the nitric oxide overproduction by more than 50%. CONCLUSIONS: Kupffer cells neither mediate nor modulate the intrahepatic vascular response to alpha(1)-adrenergic agonists in normal livers. Reduction in intrahepatic vascular response to alpha(1)-adrenergic agonists in livers from lipopolysaccharide-treated rats is located in the sinusoidal area and depends on Kupffer cell function.

Mild increases in portal pressure upregulate vascular endothelial growth factor and endothelial nitric oxide synthase in the intestinal microcirculatory bed, leading to a hyperdynamic state.

Increased nitric oxide (NO) is the main factor leading to the hyperdynamic circulation associated with advanced portal hypertension (PHT), but the initial mechanisms and the magnitude of increase in portal pressure required to trigger NO production are not known. We addressed these issues by studying systemic and splanchnic hemodynamics and endothelial NO synthase (eNOS) and VEGF expression in rats with different degrees of portal hypertension. Portal vein ligation (PVL) performed over needles of three different calibers (16-, 18-, and 20-gauge) yielded different degrees of PHT and portosystemic shunting. Compared with sham rats, all three groups of PVL rats exhibited features of hyperdynamic circulation. Rats with minimal portal hypertension (PVL with a 16-gauge needle) showed an early increase in VEGF and eNOS expression selectively at the jejunum. Immunofluorescence showed that VEGF expression was located in highly vascularized areas of the mucosa. Inhibition of VEGF signaling markedly attenuated the increase in eNOS expression. In conclusion, mild increases in portal pressure are enough to upregulate eNOS at the intestinal microcirculation, and this occurs, at least in part, through VEGF upregulation.

Increased phosphodiesterase-5 expression is involved in the decreased vasodilator response to nitric oxide in cirrhotic rat livers.

BACKGROUND/AIMS: Cirrhotic livers have a deficient vasodilator response to nitric oxide (NO). The vasodilator effect of NO is normally limited by the degradation of its second messenger cyclic guanosine 3', 5' monophosphate by phosphodiesterases. We investigated (1) the phosphodiesterase-5 (PDE-5) expression in normal and cirrhotic rat livers, (2) the location of the deficient response to NO in cirrhotic livers, and (3) the effect of the PDE-5 inhibitor Sildenafil citrate on this deficient response. METHODS: Normal and ascitic cirrhotic rats were subjected to liver perfusion with continuous measurement of both perfusion and sinusoidal (wedge hepatic) pressures. After incubation with N-monomethyl-l-arginine and pre-constriction with Methoxamine, concentration-response curves to the spontaneous NO donor S-nitroso-N-acetylpenicillamine were obtained in the absence or presence of Sildenafil (10(-8)M). RESULTS: PDE-5 expression (Western blot) in cirrhotic livers was higher than in normal livers (P=0.042). Compared to normal livers, cirrhotic livers showed a decreased response to S-nitroso-N-acetylpenicillamine in the pre-sinusoidal area (P=0.003) but not in the sinusoidal/post-sinusoidal area (P=0.433). In the presence of Sildenafil, normal and cirrhotic livers showed similar pre-sinusoidal (P=0.419) and sinusoidal/post-sinusoidal (P=0.875) responses to S-nitroso-N-acetylpenicillamine. CONCLUSIONS: Increased PDE-5 expression is involved in the decreased vascular response to NO in cirrhotic livers.