Protein crystallography and examples of its applications in medicinal chemistry

The field of protein crystallography inspires and enthrals, whether it be for the beauty and symmetry of a perfectly formed protein crystal, the unlocked secrets of a novel protein fold, or the precise atomic-level detail yielded from a protein-ligand complex. Since 1958, when the first protein structure was solved, there have been tremendous advances in all aspects of protein crystallography, from protein preparation and crystallisation through to diffraction data measurement and structure refinement. These advances have significantly reduced the time required to solve protein crystal structures, while at the same time substantially improving the quality and resolution of the resulting structures. Moreover, the technological developments have induced researchers to tackle ever more complex systems, including ribosomes and intact membrane-bound proteins, with a reasonable expectation of success. In this review, the steps involved in determining a protein crystal structure are described and the impact of recent methodological advances identified. Protein crystal structures have proved to be extraordinarily useful in medicinal chemistry research, particularly with respect to inhibitor design. The precise interaction between a drug and its receptor can be visualised at the molecular level using protein crystal structures, and this information then used to improve the complementarity and thus increase the potency and selectivity of an inhibitor. The use of protein crystal structures in receptor-based drug design is highlighted by (i) HIV protease, (ii) influenza virus neuraminidase and (iii) prostaglandin H-2-synthetase. These represent, respectively, examples of protein crystal structures that (i) influenced the design of drugs currently approved for use in the treatment of HIV infection, (ii) led to the design of compounds currently in clinical trials for the treatment of influenza infection and (iii) could enable the design of highly specific non-steroidal anti-inflammatory drugs that lack the common side-effects of this drug class.

Splanchnic non-hepatic hemodynamics and metabolism during liver transplantation

Background/Aims: The aim of this study is to compare the splanchnic non-hepatic hemodynamics and the metabolic changes during orthotopic liver transplantation between the conventional with bypass and the piggyback methods. Methodology: A prospective, consecutive series of 59 primary transplants were analyzed. Oxygen consumption, glucose, potassium, and lactate metabolism were quantitatively estimated from blood samples from the radial artery and portal vein, collected up to 120 minutes after graft reperfusion. Mean arterial pressure, portal venous pressure, portal venous blood flow, and splanchnic vascular resistance were also measured or calculated at postreperfusion collection times. Results: There was a greater increase in portal venous blood flow (p=0.05) and lower splanchnic vascular resistance (p=0.04) in the piggyback group. Mean arterial pressure and portal venous pressure were similar for both groups. Oxygen, glucose and potassium consumption were higher in the piggyback group, but none of the metabolic parameters differed significantly between groups. Conclusions: In conclusion, the study detected a higher portal venous blood flow and a lower and splanchnic vascular resistance associated with the piggyback technique. After graft reperfusion, no difference in the splanchnic non-hepatic metabolic parameters was observed between the conventional with bypass and the piggyback methods of orthotopic liver transplantation.

Refining specifications to logic programs

The refinement calculus provides a framework for the stepwise development of imperative programs from specifications. In this paper we study a refinement calculus for deriving logic programs. Dealing with logic programs rather than imperative programs has the dual advantages that, due to the expressive power of logic programs, the final program is closer to the original specification, and each refinement step can achieve more. Together these reduce the overall number of derivation steps. We present a logic programming language extended with specification constructs (including general predicates, assertions, and types and invariants) to form a wide-spectrum language. General predicates allow non-executable properties to be included in specifications. Assertions, types and invariants make assumptions about the intended inputs of a procedure explicit, and can be used during refinement to optimize the constructed logic program. We provide a semantics for the extended logic programming language and derive a set of refinement laws. Finally we apply these to an example derivation.

A computerized tomography scan method for calculating the hernia sac and abdominal cavity volume in complex large incisional hernia with loss of domain

Preoperative progressive pneumoperitoneum (PPP) is a safe and effective procedure in the treatment of large incisional hernia (size > 10 cm in width or length) with loss of domain (LIHLD). There is no consensus in the literature on the amount of gas that must be insufflated in a PPP program or even how long it should be maintained. We describe a technique for calculating the hernia sac volume (HSV) and abdominal cavity volume (ACV) based on abdominal computerized tomography (ACT) scanning that eliminates the need for subjective criteria for inclusion in a PPP program and shows the amount of gas that must be insufflated into the abdominal cavity in the PPP program. Our technique is indicated for all patients with large or recurrent incisional hernias evaluated by a senior surgeon with suspected LIHLD. We reviewed our experience from 2001 to 2008 of 23 consecutive hernia surgical procedures of LIHLD undergoing preoperative evaluation with CT scanning and PPP. An ACT was required in all patients with suspected LIHLD in order to determine HSV and ACV. The PPP was performed only if the volume ratio HSV/ACV (VR = HSV/ACV) was a parts per thousand yen25% (VR a parts per thousand yen 25%). We have performed this procedure on 23 patients, with a mean age of 55.6 years (range 31-83). There were 16 women and 7 men with an average age of 55.6 years (range 31-83), and a mean BMI of 38.5 kg/m(2) (range 23-55.2). Almost all patients (21 of 23 patients-91.30%) were overweight; 43.5% (10 patients) were severely obese (obese class III). The mean calculated volumes for ACV and HSV were 9,410 ml (range 6,060-19,230 ml) and 4,500 ml (range 1,850-6,600 ml), respectively. The PPP is performed by permanent catheter placed in a minor surgical procedure. The total amount of CO(2) insufflated ranged from 2,000 to 7,000 ml (mean 4,000 ml). Patients required a mean of 10 PPP sessions (range 4-18) to achieve the desired volume of gas (that is the same volume that was calculated for the hernia sac). Since PPP sessions were performed once a day, 4-18 days were needed for preoperative preparation with PPP. The mean VR was 36% (ranged from 26 to 73%). We conclude that ACT provides objective data for volume calculation of both hernia sac and abdominal cavity and also for estimation of the volume of gas that should be insufflated into the abdominal cavity in PPP.

Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae

The efficient and correct folding of bacterial disulfide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. In the pathogenic bacterium Vibrio cholerae, the DsbA homolog (TcpG) is responsible for the folding, maturation and secretion of virulence factors. Mutants in which the tcpg gene has been inactivated are avirulent; they no longer produce functional colonisation pill and they no longer secrete cholera toxin. TcpG is thus a suitable target for inhibitors that could counteract the virulence of this organism, thereby preventing the symptoms of cholera. The crystal structure of oxidized TcpG (refined at a resolution of 2.1 Angstrom) serves as a starting point for the rational design of such inhibitors. As expected, TcpG has the same fold as E. coli DsbA, with which it shares similar to 40% sequence identity. Ln addition, the characteristic surface features of DsbA are present in TcpG, supporting the notion that these features play a functional role. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA. The identification of the structural and surface features that are retained or are divergent in TcpG provides a useful assessment of their functional importance in these protein folding catalysts and is an important prerequisite for the design of TcpG inhibitors. (C) 1997 Academic Press Limited.

Local dispersion of the Eucalyptus leaf beetle Chrysophtharta bimaculata (Coleoptera: Chrysomelidae), and implications for forest protection

1. Chrysophtharta bimaculata is a native chrysomelid species that can cause chronic defoliation of plantation and regrowth Eucalyptus forests in Tasmania, Australia. Knowledge of the dispersion pattern of C. bimaculata was needed in order to assess the efficiency of an integrated pest management (IPM) programme currently used for its control. 2. Using data from yellow flight traps, local populations of C. bimaculata adults were monitored over a season at spatial scales relevant to commercial forestry: within a 50-ha operational management unit (a forestry 'coupe') and between coupes. In addition, oviposition was monitored over a season at a subset of the between-coupe sites. 3. Dispersion indices (Taylor's Power Law and Iwao's Mean Crowding regression method) demonstrated that C. bimaculata adults were spatially aggregated within and between coupes, although the number of egg-batches laid at the between-coupe scale was uniform. Spatial autocorrelation analysis showed that trap-catches at the within-coupe level were similar (positively autocorrelated) to a radius distance of approximately 110 m, and then dissimilar (negatively autocorrelated) at approximately 250 m. At the between-coupe scale, no repeatable spatial autocorrelation patterns were observed. 4. For any individual site, rapid changes in beetle density were observed to be associated with loosely aggregated flights of beetles into and out of that site. Peak adult catches (> the weekly mean plus standard deviation trap-catch) for a site occurred for a period of 2.0 +/- 0.22 weeks at a time (n = 37), with normally only one or two peaks per site per season. Peak oviposition events for a site occurred on average 1.4 +/- 0.11 times per season and lasted 1.5 +/- 0.12 weeks. 5. Analysis of an extensive data set (n = 417) demonstrated that adult abundance at a site was positively correlated with egg density, but negatively correlated with tree damage (caused by conspecifics) and the presence of conspecific larvae. There was no relationship between adult abundance and a visual estimate of the amount of young foliage on trees. 6. Adults of C. bimaculata are show n to occur in relatively small, mobile aggregations. This means that pest surveys must be both regular (less than 2 weeks apart) and intensive (with sampling points no more than 150 m apart) if beetle populations are to be monitored with confidence. Further refinement of the current IPM strategy must recognize the problems posed by this temporal and spatial patchiness, particularly with regard to the use of biological insecticides, such as Bacillus thuringiensis, for which only a very short operational window exists.

Effect of milling conditions on the synthesis of chromium carbides by mechanical alloying

The synthesis of chromium carbides, Cr7C3 and Cr3C2, by mechanically allowing chromium and carbon powders has been investigated. Milling conditions were found to have a strong influence on the evolution of microstructure, with high collision energies being required to form carbide phases. Milling at intermediate energy levels resulted in the formation of an amorphous phase, and with low energy conditions only grain size refinement of Cr occurred with no evidence of any reaction between Cr and C. The amorphous phase was found to be the precursor to carbide formation. (C) 1997 Elsevier Science S.A.

Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Vitamin D intoxication: a cause of hypocalcaemia and acute renal failure in a HIV patient

Hypercalcaemia in patients with HIV infection is usually associated with specific conditions such as lymphoma and granulomatous diseases. We described a case of severe hypercalcaemia consequent to vitamin D intoxication and secondary renal failure in a HIV patient under tenofovir using. Serum creatinine and calcium returned to near normal levels after vitamin D discontinuation, saline and furosemide administration. Some aspects of the drug-induced nephropathy are discussed.

Innovative psychosocial approaches in old age psychiatry

Purpose of review To identify and discuss recent research studies that propose innovative psychosocial interventions in old age psychiatry. Recent findings Studies have shown that cognitive training research for healthy elderly has advanced in several ways, particularly in the refinement of study design and methodology. Studies have included larger samples and longer training protocols. Interestingly, new research has shown changes in biological markers associated with learning and memory after cognitive training. Among mild cognitive impairment patients, results have demonstrated that they benefit from interventions displaying cognitive plasticity. Rehabilitation studies involving dementia patients have suggested the efficacy of combined treatment approaches, and light and music therapies have shown promising effects. For psychiatric disorders, innovations have included improvements in well known techniques such as cognitive behavior therapy, studies in subpopulations with comorbidities, as well as the use of new computer-aided resources. Summary Research evidence on innovative interventions in old age psychiatry suggests that this exciting field is moving forward by means of methodological refinements and testing of creative new ideas.

One-Stage Revision of Infected Total Hip Arthroplasty with Bone Graft

There are many different opinions in the literature regarding the best procedure for revision of infected hip arthroplasty and hence in achieving long-term stabilization of a new implant. Thirty-two patients with 32 loose and infected total hip arthroplasties underwent revision with a bone graft in a 1-stage procedure. The bone graft was used in the acetabulum and femure in 25 patients, in the acetabulum alone in 4 patients and in the femur alone in 3 patients. A metal mesh was necessary in 15 patients to contain the morselized bone graft. At the time of surgical revision, 9 patients had a draining sinus, 6 had a closed sinus, and 17 had never had sinuses in the surgical wound. Antibiotic therapy was administered intravenously and orally for 6 months. Mean follow-up was 103 months (range, 63-183 months), and infection recurred in 2 (6.2%) cases. Further studies are necessary, and continuation of this method is justified.

Three-dimensional mapping of hippocampal anatomy in unmedicated and lithium-treated patients with bipolar disorder

Declarative memory impairments are common in patients with bipolar illness, suggesting underlying hippocampal pathology. However, hippocampal volume deficits are rarely observed in bipolar disorder. Here we used surface-based anatomic mapping to examine hippocampal anatomy in bipolar patients treated with lithium relative to matched control subjects and unmedicated patients with bipolar disorder. High-resolution brain magnetic resonance images were acquired from 33 patients with bipolar disorder ( 21 treated with lithium and 12 unmedicated), and 62 demographically matched healthy control subjects. Three-dimensional parametric mesh models were created from manual tracings of the hippocampal formation. Total hippocampal volume was significantly larger in lithium-treated bipolar patients compared with healthy controls (by 10.3%; p=0.001) and unmedicated bipolar patients ( by 13.9%; p=0.003). Statistical mapping results, confirmed by permutation testing, revealed localized deficits in the right hippocampus, in regions corresponding primarily to cornu ammonis vertical bar subfields, in unmedicated bipolar patients, as compared to both normal controls (p=0.01), and in lithium-treated bipolar patients (p=0.03). These findings demonstrate the sensitivity of these anatomic mapping methods for detecting subtle alterations in hippocampal structure in bipolar disorder. The observed reduction in subregions of the hippocampus in unmedicated bipolar patients suggests a possible neural correlate for memory deficits frequently reported in this illness. Moreover, increased hippocampal volume in lithium-treated bipolar patients may reflect postulated neurotrophic effects of this agent, a possibility warranting further study in longitudinal investigations.

A tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation

Platelet aggregation and acute inflammation are key processes in vertebrate defense to a skin injury. Recent studies uncovered the mediation of 2 serine proteases, cathepsin G and chymase, in both mechanisms. Working with a mouse model of acute inflammation, we revealed that an exogenous salivary protein of Ixodes ricinus, the vector of Lyme disease pathogens in Europe, extensively inhibits edema formation and influx of neutrophils in the inflamed tissue. We named this tick salivary gland secreted effector as I ricinus serpin-2 (IRS-2), and we show that it primarily inhibits cathepsin G and chymase, while in higher molar excess, it affects thrombin activity as well. The inhibitory specificity was explained using the crystal structure, determined at a resolution of 1.8 angstrom. Moreover, we disclosed the ability of IRS-2 to inhibit cathepsin G-induced and thrombin-induced platelet aggregation. For the first time, an ectoparasite protein is shown to exhibit such pharmacological effects and target specificity. The stringent specificity and biological activities of IRS-2 combined with the knowledge of its structure can be the basis for the development of future pharmaceutical applications. (Blood. 2011;117(2):736-744)

Helminths of Sotalia guianensis (Cetacea: Delphinidae) from the South and Southeastern Coasts of Brazil

From May 1997 to October 2000, 49 Sotalia guianensis (tucuxi dolphin) incidentally caught in fishing nets or stranded in Sao Paulo (SP) and Parana (PH) states in Brazil were necropsied. In total, 17 lungs, 35 stomachs, and 30 intestines were analyzed. Contents were washed through a sieve (mesh, 150 mm) and examined under a stereoscopic microscope for parasites. Histopathologic analyses were performed in the lungs of five infected dolphins. The nematode Halocereus brasiliensis was found in 88% of all lungs examined, inducing moderate-to-severe pneumonia. Braunina cordiformis, Anisakis sp., and acanthocephalans were found in the stomachs. The trematode Synthesium tursionis was the only parasite found in the intestines, and it was identified in 73% of the animals necropsied. No macroscopic lesions were seen due to parasites in the stomachs and intestines analyzed.

The suitability of different FEA models for studying root fractures caused by wedge effect

Finite element analysis (FEA) utilizing models with different levels of complexity are found in the literature to study the tendency to vertical root fracture caused by post intrusion (""wedge effect""). The objective of this investigation was to verify if some simplifications used in bi-dimensional FEA models are acceptable regarding the analysis of stresses caused by wedge effect. Three plane strain (PS) and two axisymmtric (Axi) models were studied. One PS model represented the apical third of the root entirely, in dentin (PS-nG). The other models included gutta-percha in the apical third, and differed regarding dentin-post relationship: bonded (PS-B and Axi-B) or nonbonded (PS-nB and Axi-nB). Mesh discretization and material properties were similar for all cases. Maximum principal stress (sigma(max)) was analyzed as a response to a 165 N longitudinal load. Stress magnitude and orientation varied widely (PS-nG: 10.3 MPa; PS-B: 0.8 MPa; PS-nB: 10.4 MPa; Axi-13: 0.2 MPa, Axi-nB: 10.8 MPa). Axi-nB was the only model where all (sigma(max) vectors at the apical third were perpendicular to the model plane. Therefore, it is adequate to demonstrate the tendency to vertical root fractures caused by wedge effect. Axi-13 showed only part of the (sigma(max) perpendicular to the model plane while PS models showed sigma(max) on the model plane. In these models, sigma(max) orientation did not represent a situation where vertical root fracture would occur due to wedge effect. Adhesion between post and dentin significantly reduced (c) 2007 Wiley Periodicals, Inc.