Spectral CT and its specific values in the staging of patients with non-small cell lung cancer: technical possibilities and clinical impact.

AIM: To investigate how spectral computed tomography (SCT) values impact the staging of non-small cell lung cancer (NSCLC) patients. MATERIALS AND METHODS: One hundred and thirteen patients with confirmed NSCLC were included in a prospective cohort study. All patients underwent single-phase contrast-enhanced SCT (using the fast tube voltage switching technique, 80-140 kV). SCT values (iodine content [IC], spectral slope pitch, and radiodensity increase) of malignant tissue (primary and metastases) and lymph nodes (LNs) were measured. Adrenal masses were evaluated in a virtual non-contrast series (VNS). If pulmonary embolism was present, pulmonary perfusion was analysed as an additional finding. RESULTS: Fifty-two untreated primary NSCLC lesions were evaluable. Lung adenocarcinoma had significantly higher normalised IC (NIC: 19.37) than squamous cell carcinoma (NIC: 12.03; p=0.035). Pulmonary metastases were not significantly different from benign lung nodules. A total of 126 LNs were analysed and histologically proven metastatic LNs (2.08 mg/ml) had significantly lower IC than benign LNs (2.58 mg/ml; p=0.023). Among 34 adrenal masses, VNS identified adenomas with high sensitivity (91%) and specificity (100%). In two patients, a perfusion defect due to pulmonary embolism was detected in the iodine images. CONCLUSION: SCT may contribute to the differentiation of histological NSCLC subtypes and improve the identification of LN metastases. VNS differentiates adrenal adenoma from metastasis. In case of pulmonary embolism, iodine imaging can visualise associated pulmonary perfusion defects.

The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.

The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems.

Bimetallic nickel complexes for selective CO2 carbon capture and sequestration.

Herein we report a dinickel azacryptand complex that enables fast, selective, and tight CO2 binding from air. Exploiting the affinity of the cavitand towards azides, CO2 release was observed. Despite the stability of the azido complex, UV irradiation under atmospheric conditions proved to be a suitable pathway for N3(-) replacement by CO2.

Feasibility study of nonclinical safety assessments on homeopathic preparations using the example of protoanemonin in Pulsatilla pratensis L.

Homeopathy is a world-wide available form of complementary therapy, which has a tradition of 200years. Due to the long history of clinical use, i.e. reflected by the first edition of the Homeopathic Pharmacopoeia of the US of 1914, the conduct of toxicological studies is not required if the safety has been otherwise substantiated. The aim of this article is to establish a risk assessment procedure without full toxicological examination, using homeopathic preparations from Pulsatilla pratensis L. as an example. The literature review shows that protoanemonin is the most relevant constituent of these plants regarding potential toxicity. Based on structural alerts protoanemonin is classified as a Cramer class III compound with the threshold of toxicological concern (TTC) of 180µg/day in adults. Neither computer aided toxicology methods (Toxtree and Derek Nexus®) nor a literature search revealed any evidence of genotoxic, carcinogenic or teratogenic potential of protoanemonin. The protoanemonin exposure from a maximum daily dose of a typical homeopathic preparation of P. pratensis L. does not exceed the TTC. The presented method is transparent, reproducible and applicable to other homeopathic substances as a use-case scenario for computational toxicology in order to evaluate an approach for safety assessment of homeopathic medicinal products.

Morphology and hemodynamics during vascular regeneration in critically ischemic murine skin studied by intravital microscopy techniques.

BACKGROUND: With the understanding of angiogenesis and arteriogenesis, new theories about the orchestration of these processes have emerged. The aim of this study was to develop an in vivo model that enables visualization of vascular regenerating mechanisms by intravital microscopy techniques in collateral arteriolar flap vascularity. METHODS: A dorsal skin flap (15 × 30 mm) was created in mice and fixed into a skinfold chamber to allow for assessment of morphology and microhemodynamics by intravital fluorescence microscopy (IVFM). Laser scanning confocal microscopy (LSCM) was utilized for three-dimensional reconstruction of the microvascular architecture. RESULTS: Flap tpO(2) was 5.3 ± 0.9 versus 30.5 ± 1.2 mm Hg in controls (p < 0.01). The collateral arterioles in the flap tissue were dilated (29.4 ± 5.3 µm; p < 0.01 vs. controls) and lengthened in a tortuous manner (tortuosity index 1.00 on day 1 vs. 1.35± 0.05 on day 12; p < 0.01). Functional capillary density was increased from 121.00 ± 25 to 170 ± 30 cm/cm(2) (day 12; p < 0.01) as a result of angiogenesis. Morphological evidence of angiogenesis on capillary level and vascular remodeling on arteriolar level could be demonstrated by IVFM and LSCM. CONCLUSIONS: Present intravital microscopy techniques offer unique opportunities to study structural changes and hemodynamic effects of vascular regeneration in this extended axial pattern flap model.

CREB signalling regulates early survival, neuronal gene expression and morphological development in adult subventricular zone neurogenesis.

Neural stem cells in the subventricular zone (SVZ) of the lateral ventricles give rise to new interneurons of the olfactory bulb (OB) throughout life. SVZ/OB neurogenesis is influenced by olfactory network activity, which modulates the survival of new neurons during their integration into the OB network. Previous work suggested that such activity-dependent survival is regulated via the CREB signalling pathway. Curiously, CREB signalling is already active during the early developmental stages of adult SVZ/OB neurogenesis. To investigate the role of cell autonomous CREB signalling during early stages of adult SVZ/OB neurogenesis, we ablated CREB-pathway activity in the SVZ/OB neurogenic lineage using a retroviral strategy. Surprisingly, loss of CREB signalling resulted in increased cell death and loss of expression of the neurogenic transcription factor Pax 6, and of a subset of neuronal proteins in migrating neurons of the RMS. Moreover, post-migratory neurons in the OB displayed impaired dendritic development. These results demonstrate an essential role for CREB signalling in maturation of newborn neurons in the OB and uncover a novel role for CREB signalling in the survival and maintenance of neuronal gene expression during the early stages of SVZ/OB neurogenesis.

Cutaneous microcirculatory assessment of the burn wound is associated with depth of injury and predicts healing time.

RATIONALE: Current trends for the treatment of deep partial thickness and full-thickness burns include early excision and skin grafting. In this study we retrospectively evaluated the ability of Laser Doppler Flowmetry (LDF), taken within 24h of the burn to predict: (1) burn wound depth and (2) wounds which would heal in less than 21 days. METHOD: The Laser Doppler Flowmeter (O2C, LEA Medizintechnik, Germany) was employed to non-invasively measure the cutaneous microcirculation of 173 selected areas on 28 patients who suffered burns. RESULTS: A distinct association between initial flow (<24h after burn injury) and the clinical assessment of depth of burn wounds was observed. Wounds demonstrating an initial blood flow of >100 AU were, in 93.1% of cases, correctly (positively) predicted for spontaneous healing within 21 days. A blood flow of <100 AU (negatively) predicted in 88.2%, those wounds which would not go on to heal within 21 days. Sequential measurement analysis (<24h, 3 days after injury and 6 days after injury) revealed no significant decrease in skin perfusion velocity or flow rate. CONCLUSION: LDF can provide immediate results for early determination of burn wound depth and is useful in selecting patients for conservative treatment of their burn wounds.

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach.

This work examines the ability of semiempirical methods to describe the structure of liquid water. Particularly, the standard AM1 and PM3 methods together with recently developed PM3-PIF and PM3-MAIS parametrizations have been considered. We perform molecular dynamics simulations for a system consisting of 64 or 216 water molecules in a periodic cubic box. The whole system is described quantum mechanically. Calculations with 64 molecules have been carried out using standard SCF techniques whereas calculations with 216 molecules have been done using the divide and conquer approach. This method has also been used in one simulation case with 64 molecules for test purposes. Within this scope, the molecular dynamics program ROAR have been coupled with a linear scaling semiempirical code (DivCon) implemented in a parallel MPI version. The predicted liquid water structure using either AM1 or PM3 is shown to be very poor due to well-known limitations of these methods describing hydrogen bonds. In contrast, PM3-PIF and PM3-MAIS calculations lead to results in reasonably good agreement with experimental data. The best results for the heat of vaporization are obtained with the PM3-PIF method. The average induced dipole moment of the water molecule in the liquid is underestimated by all semiempirical techniques, which seems to be related to the NDDO approximation and to the use of minimal basis sets. A brief discussion on charge-transfer effects in liquid water is also presented.

One-dimensional molecular representations and similarity calculations: methodology and validation.

Drug discovery research is increasingly dedicated to biological screening on a massive scale, which seems to imply a basic rejection of many computer-assisted techniques originally designed to add rationality to the early stages of discovery. While ever-faster and more clever 3D methodologies continue to be developed and rejected as alternatives to indiscriminant screening, simpler tools based on 2D structure have carved a stable niche in the high-throughput paradigm of drug discovery. Their staying power is due in no small part to simplicity, ease of use, and demonstrated ability to explain structure-activity data. This observation led us to wonder whether an even simpler view of structure might offer an advantage over existing 2D and 3D methods. Accordingly, we introduce 1D representations of chemical structure, which are generated by collapsing a 3D molecular model or a 2D chemical graph onto a single coordinate of atomic positions. Atoms along this coordinate are differentiated according to elemental type, hybridization, and connectivity. By aligning 1D representations to match up identical atom types, a measure of overall structural similarity is afforded. In extensive structure-activity validation tests, 1D similarities consistently outperform both Daylight 2D fingerprints and Cerius(2) pharmacophore fingerprints, suggesting that this new, simple means of representing and comparing structures may offer a significant advantage over existing tried-and-true methods.

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.

A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: consequences for immunochemistry of penicillins.

Herein, we present results of a computational study on benzylpenicillin attachment to Lys199 of human serum albumin via an aminolysis reaction. The internal geometry of the reactive part of the system was taken from previous work at the B3LYP/6-31+G* level on the water-assisted aminolysis reaction of a penicillin model compound (Díaz, N.; Suárez, D.; Sordo, T. L. J. Am. Chem. Soc. 2000, 122, 6710--6719). The protein environment around Lys199, the 6-acylamino side chain, and the 2-methyl groups of benzylpenicillin were relaxed by carrying out geometry optimizations with a hybrid QM/MM method (PM3/AMBER). Two different mechanistic routes were explored: a one-step water-assisted process and a carboxylate and water-assisted route in which the beta-lactam carboxylate and the ancillary water molecule mediate the proton transfer from the epsilon-amino group of Lys199 to the beta-lactam leaving N atom. The corresponding energy profiles in the protein combine the B3LYP/6-31+G* and PM3 energies of the reactive subsystem (benzylpenicillin + Lys199 side chain + the ancillary water molecule) and semiempirical PM3 energies of the entire system evaluated with a "divide and conquer" linear-scaling method. It is observed that penicillin haptenation to HSA can proceed through the water-assisted concerted mechanism which is calculated to have a high energy barrier of approximately 38 kcal/mol, in agreement with the experimentally observed slow reaction kinetics.

Quantum chemical study of ester aminolysis catalyzed by a single adenine: a reference reaction for the ribosomal peptide synthesis.

Herein we report the results of a HF/6-31+G** and B3LYP/6-31+G** computational investigation of the title reaction for the peptide bond synthesis catalyzed by a single adenine. This system constitutes a reference reaction to study the basic chemical events that have been proposed to occur at the peptidyl transferase active site of ribosomes on the basis of structural determinations (Science 2000, 239, 920--931). Thus, the analysis of the geometry, charge distribution, and energetics of the critical structures involved in this title reaction yields insight into the catalytic mode of action of RNA molecules. Our computational results give further support to the hypotheses that the activated nucleotide A2451 in the ribosome acts as a base catalyst and that this role is similar to that of the His residue in the catalytic triad of serine proteases.

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.

Herein, we report molecular dynamics simulations of the mononuclear form of the Bacillus cereuszinc-beta-lactamase. We studied two different configurations which differ in the presence of a zinc-bound hydroxide or a zinc-bound water and in the protonation state of the essential His210 residue. Contacts of the catalytically important residues (Asp90, His210, Cys168, etc.) with the zinc center are characterized by the MD analyses. The nature of the Zn-OH(2) --> His210 proton transfer pathway connecting the two configurations was studied by means of QM calculations on cluster models while the relative stability of the two configurations was estimated from QM/MM calculations in the enzyme. From these results, a theoretical model for the kinetically active form of the B. cereus metalloenzyme is proposed. Some mechanistic implications and the influence of mutating the Cys168 residue are also discussed.

Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations.

The catalytic mechanism of 5-aminoimidazole-4-carboxamide ribonucleotide transformylase (AICAR Tfase) is evaluated with pH dependent kinetics, site-directed mutagenesis, and quantum chemical calculations. The chemistry step, represented by the burst rates, was not pH-dependent, which is consistent with our proposed mechanism that the 4-carboxamide of AICAR assists proton shuttling. Quantum chemical calculations on a model system of 5-amino-4-carboxamide imidazole (AICA) and formamide using the B3LYP/6-31G level of theory confirmed that the 4-carboxamide participated in the proton-shuttling mechanism. The result also indicated that the amide-assisted mechanism is concerted such that the proton transfers from the 5-amino group to the formamide are simultaneous with nucleophilic attack by the 5-amino group. Because the process does not lead to a kinetically stable intermediate, the intramolecular proton transfer from the 5-amino group through the 4-carboxamide to the formamide proceeds in the same transition state. Interestingly, the calculations predicted that protonation of the N3 of the imidazole of AICA would reduce the energy barrier significantly. However, the pK(a) of the imidazole of AICAR was determined to be 3.23 +/- 0.01 by NMR titration, and AICAR is likely to bind to the enzyme with its imidazole in the free base form. An alternative pathway was suggested by modeling Lys266 to have a hydrogen-bonding interaction with the N3 of the imidazole of AICAR. Lys266 has been implicated in catalysis based on mutagenesis studies and the recent X-ray structure of AICAR Tfase. The quantum chemical calculations on a model system that contains AICA complexed with CH3NH3+ as a mimic of the Lys residue confirmed that such an interaction lowered the activation energy of the reaction and likewise implicated the 4-carboxamide. To experimentally verify this hypothesis, we prepared the K266R mutant and found that its kcat is reduced by 150-fold from that of the wild type without changes in substrate and cofactor Km values. The kcat-pH profile indicated virtually no pH-dependence in the pH range 6-10.5. The results suggest that the ammonium moiety of Lys or Arg is important in catalysis, most likely acting as a general acid catalyst with a pK(a) value greater than 10.5. The H267A mutant was also prepared since His267 has been found in the active site and implicated in catalysis. The mutant enzyme showed no detectable activity while retaining its binding affinity for substrate, indicating that it plays a critical role in catalysis. We propose that His267 interacts with Lys266 to aid in the precise positioning of the general acid catalyst to the N3 of the imidazole of AICAR.

New developments in applying quantum mechanics to proteins.

Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.

High throughput docking for library design and library prioritization.

The prioritization of the screening of combinatorial libraries is an extremely important task for the rapid identification of tight binding ligands and ultimately pharmaceutical compounds. When structural information for the target is available, molecular docking is an approach that can be used for prioritization. Here, we present the initial validation of a new rapid approach to molecular docking developed for prioritizing combinatorial libraries. The algorithm is tested on 103 individual cases from the protein data bank and in nearly 90% of these cases docks the ligand to within 2.0 A of the observed binding mode. Because the mean CPU time is <5 s/mol, this approach can process hundreds of thousands of compounds per week. Furthermore, if a somewhat less thorough search is performed, the search time drops to 1 s/mol, thus allowing millions of compounds to be docked per week and tested for potential activity. Proteins 2001;43:113-124.

Molecular dynamics study of the IIA binding site in human serum albumin: influence of the protonation state of Lys195 and Lys199.

The IIA binding site of human serum albumin (HSA) preferentially binds hydrophobic organic anions of medium size (e.g., aspirin, benzylpenicillin, warfarin, etc.) and bilirubin. This binding ability is particularly important for the distribution, metabolism, and efficacy of drugs. In addition, HSA can also covalently link to different IIA substrates owing to the presence of a highly reactive residue, Lys199, which is strategically located in the IIA site. Herein, we present results of three restrained molecular dynamics (MD) simulations of the IIA binding site on the HSA protein. From these simulations, we have determined the influence that the ionization state of the key residue, Lys199, and the nearby Lys195 has on the structure and dynamics of the IIA binding site. When Lys199 is neutral the computed average distances for the most significant interresidue contacts are in good agreement with those estimated from the X-ray coordinates. The analysis of the solvent structure and dynamics indicates that the basic form of Lys199 is likely connected to the acid form of Lys195 through a network of H-bonding water molecules with a donor --> acceptor character. The presence of these water bridges can be important for stabilizing the configuration of the IIA binding site and/or promoting a potential Lys195 --> Lys199 proton-transfer process. These results suggest that both lysine residues located in the IIA binding site of HSA, Lys195 and Lys199, could play a combined and comparable chemical role. Our simulations also give insight into the binding of bilirubin to HSA.