Ultimate Guide to Power Efficiency
The respiration-coupled energy conservation in form of ATP is usually the most important mitochondrial function. In the aerobic cell, phosphorylating respiration is responsible, as a rule, for production of 90-95 of the total ATP amount, the rest being synthesized by glycolytic phosphorylation. All the ATP synthesized from ADP and inorganic phosphate is hydrolyzed back to ADP and phosphate to support the energy-consuming processes in the same cell. The adult human forms and decomposes as much as about 40 kg ATP per day 1 .
An energy usage assessment was performed on the classical resolution route versus the enzymatic route to pregabalin. The software package chosen to perform the analysis was Batch Plus . 2) Table 8.4 shows the energy usage breakdown for each process based on the three main stages (i) hydrolysis and decarboxylation, (ii) nitrile reduction, and (iii) isolation and purification. Energy values are based on MJ (1 x 106J) per kg pregabalin. The enzymatic route resulted in an energy usage reduction of 82 versus the classical resolution process. This energy usage was based on two main factors (i) 174 8 The Developmentofa Green, Energy Efficient, Chemoenzymatic ManufacturingProcessforPregabalin Table 8.5 Energy usage metrics for classical resolution and enzymatic routes.
A stranger in paradise Stefan first came to my lab on a fellowship provided by the International Atomic Energy Agency. They made all the arrangements, and I did not know when he was due to arrive. Stefan sent me this information in a telegram that was delivered two weeks after his arrival. We never found out who was responsible for holding up this telegram. In any case, Stefan arrived at the Raleigh Durham Airport. I was not there to meet him, and he did not try to reach me by telephone due to unfamiliarity with our excellent telephone system. He waited for a long while and then wandered around the airport and finally encountered some Duke students who gave him a ride to the Medical Center. He had been allowed only 28 when he left Bulgaria and had neither a credit card nor a driver's license. Hence, the hotel adjacent to the medical center would not rent him a room. The desk clerk directed him to another cheaper motel to which Stefan dragged his heavy suitcase. It was, by then, very...
Boron neutron capture therapy is a binary form of treatment of cancer in which a compound containing 10B is selectively delivered to tumor tissues prior to irradiation by neutrons.16 Upon irradiation with thermal neutrons, interaction of a 10B atom with a thermal neutron produces an a-particle, a high-energy Li-7 ion and a low-energy 7-ray Figure 2.1. The linear energy transfer (LET) of these heavily charged particles have a range of about one-cell diameter, which confines
Energy Conservation In Thylakoid As in many other fields of biological research, expansion of the research literature in the field of photosynthesis has been extremely rapid. This can be overwhelming for both the seasoned researcher and the beginner who is just entering the field. The last comprehensive reviews of photosynthetic electron transfer reactions and energy conservation in intact thylakoid membranes were by Ort (1986) and Andreasson and Vanngard (1988). In this prefatory chapter, we will provide a brief, updated overview of thylakoid membrane activities as a means of guiding the reader to appropriate chapters in this book where more detailed information on a given topic may be found.
Abstract Mitochondria are known to be multifuctional intracellular organelles. They carry out (i) energy conservation in forms of protonic potential (A iH+) and ATP, (ii) thermoregulatory energy dissipation as heat, (iii) production of useful substances, (iv) decomposition of harmful substances, and (v) regulation of intracellular processes. It is suggested that mitochondria are equipped by a mechanism of self-elimination ( mitoptosis ) responsible for purification of mitochondrial population from unwanted organelles (e.g., ROS-overproducing mitochondria). Massive mitoptosis is assumed to induce apoptosis due to release of the cell death proteins normally hidden in the intermembrane space of mitochondria. In this way tissues are purified from ROS-overproducing and other unwanted cells.
The reaction is very energy efficient nearly all of the energy input into the reaction is transformed into light. A reduction in ATP results in a reduction in the production of photons. This type of assay has the advantage of not needing specialized antibodies and is applicable to all kinases. It is also easy to run the assays with high ATP concentrations as a way of selecting against ATP-competitive
For example, the use and development of life cycle assessment (LCA) tools have shown that solvents tend to account for the majority of energy costs and greenhouse gas emissions in a process. The energy use and greenhouse gases result not only from the use of solvents but also from their manufacture, transportation, and disposal 8, 9 . This has led to the consideration of the following aspects when selecting solvents, as reported by Jim nez-Gonz lez for GSK processes 9
A method proposed by Capello 34 involves scoring solvents based on both EHS and LCI energy. In the first step a solvent index is calculated between zero and one for nine EHS impact categories that are summed to yield a final score. Next, the cumulative energy demand (CED) is calculated for each solvent based on the energy used in manufacture, transportation, and disposal. The EHS and CED scores are then combined to determine solvent greenness. The Capello methodology typically favors volatile solvents such as pentane and diethyl ether because of their low energy requirements. However, solvents such as pentane and diethyl ether, which score well with the Capello methodology, are not favored by the pharmaceutical industry as they have very low flashpoints, and their high volatility gives greater possibility of air emissions.
The infrared region of the electromagnetic spectrum includes radiation at wavelengths between 0.7 and 500 im, or, in wavenumbers (the number of waves in a length of 1 cm), between 14,000 and 20 cm1. Infrared radiation is absorbed by the bending, stretching, and more complex motions of various functional groups in molecules. The large number of vibrations occurring simultaneously in even a simple molecule results in a complex absorption spectrum, which is characteristic of the functional groups present. The low energy of the absorbed photons in the infrared region is ideal for the detection of low-energy interactions, predicted to be of importance for anesthetic binding to macromolecules.
Many papers compare the performances of EAs with other search methods such as simulated annealing, direct search methods and random search (see, e.g., 26, 37, 66, 67 ). The general conclusion is that EAs are consistently among the best performing general search algorithms, in many cases performing as well as or only slightly worse than optimization methods specifically designed for the problem at hand. As noted by several other authors, Judson states that GAs are particularly useful for quickly producing a family of low-energy conformers, but are less successful in fine-tuning these towards the exact global optimum 66 . The post-EA steepest descent optimization that is performed in most applications is the result of this realization. Because of the limited accuracy of energy calculations this disadvantage is not too important.
The main distillation types include atmospheric, vacuum, steam, azeotropic, extractive, and pressure distillation 45 . All of these distillation methods can be carried out in a batch or continuous manner with the exception of extractive distillation, which is solely continuous by nature. Complex solvent systems often require the use of multiple distillation columns in series to purify certain solvents that are not easily separated. The energy consumption in distillation columns can therefore be quite large because of the continuous operation of condensers and reboilers over extended periods of time. In order to cut down on these costs, both vacuum and steam distillation can be employed 45 .
This mechanism is highly energy-efficient because it depends on Dj receptor diffusion and NMDAR allosterism not on activation of transduction systems and intracellular signaling.53 One interesting caveat to these studies is that glutamate is the endogenous agonist for NMDARs and these experiments did not examine all the outcomes in the presence of glutamate rather than NMDA, bringing into question the natural relevance of some of these findings.
The aim of the GERM (Genetically Evolved Receptor Models) program 58, 59 is to build an atomic-level model of a receptor site based on a small set of known structure-activity relationships. First, a set of compounds with experimentally determined activities are superimposed in low-energy conformations. An initial model of the receptor site is then constructed by placing 40-60 atoms on a grid around the surface of the superimposed active compounds. The atom types consist of 14 typical protein atoms and a null atom type to correspond to no atom at all at a given position. A GA is used to alter and optimize the atom types of the receptor site in order to maximize the correlation between drug-receptor binding calculated using molecular mechanics and measured drug activity. The chromosomes of the GA encode potential receptor models as bit strings each bit corresponds to a grid point placed around the superimposed ligands together with pseudoreceptor atom assignments. The genetic operators...
The biological effect of radiation on living cells tends to vary and depends on dose. It is well known that radiation is known to cause cancer, but in clinical practice, radiotherapy is an accepted form of cancer treatment. Injured or damaged cells may self-repair, die, or be involved in a misrepair process (see discussion later). High-radiation doses tend to kill cells, while low doses tend to damage or alter the genetic code (DNA) of irradiated cells. High-radiation doses can kill so many cells that tissues and organs are damaged immediately and tend to initiate a rapid body response, often called acute radiation syndrome. High-radiation dose manifests itself early. This was evident in many of the atomic bomb survivors in 1945 and in the emergency workers who responded to the 1986 Chernobyl nuclear power plant accident (Sali et al., 1996). Low doses of radiation over long periods may not cause immediate problems in body organs, but effects may occur at the cellular level. Genetic...
Chronic pain patients also report low mood and depression, anger, and frustration.10,1112 13 IV In general medical practice, there is a longstanding concern about the underdiagnosis of depression associated with illness or disability, a situation that is also relevant to chronic pain. There is a less well-recognized risk of overdiagnosis when almost all the widely used diagnostic criteria and self-report questionnaires include somatic symptoms, such as low energy, fatigue, sleep disturbance, and poor libido, which may also be attributable to pain.14 The dominant psychological model is the diathesis and
Low-energy conformer of a xanthine derivative showing the hydrophobic fit between the N3-isobutyl and (4-benzhydrylpyperazin-l-yl)propyl groups. Such a compound is less lipophilic than expected by c. 1.5 log P units 20 , Figure 7. Low-energy conformer of a xanthine derivative showing the hydrophobic fit between the N3-isobutyl and (4-benzhydrylpyperazin-l-yl)propyl groups. Such a compound is less lipophilic than expected by c. 1.5 log P units 20 ,
A database of low-energy conformers of a subset of compounds in Wyeth's corporate database was searched using molecular shape comparison with 4 21 . A detailed computational study of the protein-ligand interactions of 380 best matches led to the selection of 29 molecules for experimental
Proposed models of the receptor-bound conformation of TIP(P)-related 5-opioid antagonists were described in detail in a recent review article 37 . These models were based on molecular mechanics studies of TIP(P)-related antagonists and comparison of the resulting low energy conformers with the structurally rigid nonpeptide 5-antagonist naltrindole. One model was obtained through identification of a low-energy conformer of TIP showing good spatial overlap of the centroids of its Tyr1 and Tic2 aromatic rings and its N-terminal amino group with the corresponding aromatic rings and the nitrogen atom in naltrindole 55 . This model is characterized by a trans peptide bond between Tyr1 and Tic2 (Fig. 1). An alternative model resulted from theoretical conformational analysis of the weak 5-opioid dipeptide antagonist H-Tyr-Tic-NH2 and was also based on spatial overlap of the Tyr1 and Tic2 aromatic rings and N-terminal amino group with the corresponding moieties in naltrindole 56 (Fig. 1). In...
Historically, the Concord 7 program has been the most popular 3-D conversion software. It combines a knowledge base of rules with energy minimization to generate a low energy 3-D conformation for each structure. Cyclic and acyclic portions are constructed separately, with the resulting substructures fused to form the complete molecule. Optimum acyclic bond lengths, angles and torsions are extracted from a table of published values. Similarly, bond lengths and torsion angles of single cyclic portions are built using precalculated topological rules. Ring systems are constructed through the assignment of gross conformations of each ring. Each constituent ring is then fused into the system in order, with a strain minimization function employed to create an acceptable geometry. Once constructed, the structure can be further optimized through energy. Concord is able to produce reasonable low energy conformations for most small organic structures, though large rings and peptides are not...
The utility of such screens is illustrated below by the work of Marriott et al. 41 (see Figure 7.2). An additional prerequisite for these searches, over those described in the previous section is the need for a technique to elucidate the crucial pharmacophore from within a set of active molecules. In this study, 3-D conformer models of known muscarinic m3 antagonists were used in conjunction with the DISCO program 50 to determine such pharmacophore models. DISCO takes as its input a series of low energy conformations for each active molecule, and potential pharmacophore site points are generated automatically for each conformer. A useful feature of DISCO is its ability to define the locations of potential protein hydrogen bond donors and acceptors. This can be important if ligands are found to approach the same polar site point from different directions, something not easily accounted for when purely atomic superimposition is used. The program then utilizes clique detection 51 to...
A spin glass is a disordered magnetic material in which the magnetic dipoles composing the material are oriented in different directions. A dipole's preferred orientation, determined by which orientation has the lowest energy, depends on the orientations of nearby dipoles. Models of spin glasses consist of a lattice of 'Ising spins' with each spin pointing either up or down. When one spin switches to its preferred orientation, it generally will cause many other spins to switch their preferences. The system exhibits frustration in that many of the orientation preferences are mutually incompatible (Fig. 14a). If it were possible to satisfy all the preferences simultaneously, the material would have a low energy. Since frustration prevents this, the material has many possible configurations with higher energies that cannot be brought to lower energies by any spin changes. This frustration is responsible for multiple local peaks and local minima in landscapes 4,34,62,87 .
Since there are more than 20 distinct Ga subunit proteins, Ga enzymatic activity can be a major determinant of the specificity and variability of GPCR signaling in health and disease. By definition, the characteristics of variant GPCR signaling will vary depending on the G protein subunits coexpressed in tissues or cells. The rate of GTP hydrolysis varies, depending on the type of Ga subunit (78,79). The persistence of the signal depends on which Ga subunit is involved since it is the guanosine triphosphatase (GTPase) activity inherent in the Ga subunit that determines the rate of GTP hydrolysis. This process inactivates G protein signaling and restores the low-energy Ga-GDP conformation, which can then respond to the binding of another ligand (78,79).
The screening and subgraph isomorphism procedures that are used for 2-D and for rigid 3-D substructure searching can be further extended to encompass, in part at least, the representation and searching of flexible 3-D structures, where a molecule can adopt some, or many, different conformations by rotating around one or more of the rotatable bonds present in a molecule. One approach is simply to generate a number of low-energy conformations and then to search each of these as if it was a distinct rigid structure 16 . An alternative approach, and the one discussed here (and in more detail by Clark et al. 4, 27 ), adopts a graph representation in which the nodes are again the atoms of a molecule however, rather than representing just a fixed distance, each edge describes a range of distances, specifically the range spanned by the maximum and the minimum interatomic separations that are possible for a given pair of atoms, these separations typically being calculated using techniques...
With both procedures meeting the quality and cost criteria, an extensive evaluation of the environmental aspects of both routes was undertaken. In addition to the standard data obtained from mass balance analysis (that is comparing the input and output of reagents, products, by-products and process waste streams), a range of different measures and metrics were determined including energy consumption data, environmental impacts (such as generation of greenhouse gases and effect on ozone layer), plus data from several in-house programmes.
AOX is a mitochondrial inner membrane protein which functions as a component of the plant ETC (see Vanlerberghe and Mcintosh, 1997 Simons and Lambers, 1999 for recent reviews). It catalyzes the -dependent oxidation of reduced ubiquinone (Qr, ubiquinol), producing ubiquinone (Q) and water (Fig. 1). Plant-like AOX's are found in some algae (Weger et al., 1990), fungi (Yukioka et al., 1998), yeast (Minagawa et al., 1992) and protists (Clarkson et al., 1989) but it is amongst higher plants that this ETC component appears to be ubiquitous. Importantly, electron flow from Qr to AOX is not coupled to the generation ofproton motive force and hence is a non-phosphorylating branch of the ETC, bypassing the last two sites of energy conservation associated with the Cyt pathway (Fig. 1). Central questions regarding the branched nature of electron transport in plant metabolism are 1) What factors determine the partitioning of electrons in the Q pool between the energy-coupled Cyt pathway and the...
Optically transparent electrodes, modified with monolayers of photosynthetic pigments using the Langmuir-Blodgett technique, are suitable for the investigation of chemical models of photosynthesis (Gugeshashvili et al., 1995 Leblanc etal., 1991 Munger et al., 1992a,b Volkov et al., 1992a,b, 1993,1994,1995a,b Zelent et al., 1993). The phenomenon of photorespiration by a hydrated chlorophyll a monolayer deposited on an optically transparent electrode was studied by Volkov et al. (1993). A Sn02 optically transparent electrode (OTE) doped with antimony is a quasi-metallic conductor. The Sn02 electrode is transparent in the visible region of the optical spectrum. The Sn02 OTE is often used as a working electrode in photoelectrochemistry due to its large potential window and its optical transparency in the visible region. By using such an electrode, the electronic absorption spectrum of a wet chlorophyll a monolayer on Sn02 OTE was measured (Fig. 14.8). The oligomer possesses a Soret band...
However, in 1995 a landmark study based on alanine scanning mutagenesis of human growth hormone and its receptor demonstrated that the main contribution to the binding energy derives from contacts with a small fraction of amino acids (hotspots) constituting the protein-protein interface (Clackson and Wells 1995). For the first time it seemed feasible for small molecules to access such hotspots, and it was subsequently shown that small-molecule inhibition of protein-protein interactions is possible (Fischer and Lane 2004 He et al. 2005 Oltersdorf et al. 2005). Another strategy is exemplified by binding of a small molecule to the cytokine IL-2 which induces changes in the protein surface via low-energy rearrangement of some hotspot side chains, thereby interfering with receptor binding of the cytokine (Arkin et al. 2003). In these cases, the discovery of small-molecule inhibitors of PPIs has depended on applied screening methods rather than on in silico approaches based on the target...
Autoradiographic techniques normally require P emittors such as 14C, 3H or 35S. However, autoradiography can also be performed by using a radionuclide (such as 99mTC), which emit many low energy electrons (gammas, x-ray, and monoenergetic) while decaying 102 . The detector is gas chamber, which allows direct quantification of images and provides a clear advantage of autoradiographic film by improving image resolution, efficiency, linearity, high dynamic range and low noise levels 102 . Collectively, by using autoradiography technique, one can detect presence of radioactive isotope in tissues by covering tissue sections with photographic emulsion, followed by subsequent development and fixation, and finally the radiated silver resulting into black grains 100 . Autoradiography technique is suitable for studying sites for octopamine metabolism. It can also be used to visualize and quantitate radiolabeled octopamine binding proteins in tissue homogenate (not discussed in this review).
Gives rise to stereo-electronic control of catalysis. We usually think of nucleophiles as a species with high-lying lowest occupied molecular orbitals (e.g., lone-pair orbitals or the p-orbitals in alkenes or aromatic compounds) and electro-philes as a species with low-energy lowest unoccupied molecularorbitals (e.g., p*-orbitals of carbonyl groups and s* orbitals of C-X bonds). On-the-fly environmental reorganization of the enzyme active site during catalysis is likely to include protein motions that constrain, if not steer, reactant motions toward productive outcomes. In any event, one may confidently anticipate that isotopes will play an ever-increasing role in the elucidation of enzyme catalysis.
The effect of chronic stress on individuals caring for parients with Alzheimer's disease has also been the subject of several studies. It has been shown, for example, that such individuals show a high risk of depression (Crook and Miller, 1985 Fiore, Becker, and Cooppel, 1983). In addition to the greater physical and emotional distress shown by the carers, there is also evidence of impaired immune function (Kiecolt-Glaser, Dura, Speicher, Trask, and Glaser, 1991). Other studies of those individuals subject to chronic environmental stress (for example, living in the vicinity of Three Mile Island in the USA, the site of a nuclear power plant accident some years ago) showed that the residents had fewer T-suppressor cells, B-lymphocytes, and natural killer cells than a comparable group living in a normal environment (Davidson and Baum, 1986). The conclusions of these studies is that chronic stress in man does not necessarily lead to immunological adaptation.
An important point to take into account when the relationship between mitochondria, aging, and longevity is considered is the cross-talk between the nucleus and mitochondria. We surmise that not only the energy requirement of the cell, but also many other stimuli are conveyed to mitochondria, which in turn can adjust their metabolism and functions in response to this information flow. Accordingly, nuclear gene expression must be regulated on the basis of the status of the cell, including energy availability. Thus, mitochondria are likely involved in the control of the aging process not only because they are the ''power plant'' of the cell and the major source of ROS,
Low millimolar levels 47 , possibly as a result of the high energy consumption of the cells), the expected drop-off in potency from enzyme to cell based on ATP competition (for a typical ATP-competitive inhibitor) would be approximately 40-100-fold, in the absence of unusual kinetics, non-selectivity or alternative mechanisms of inhibition.
Taking into account the typical heterogeneity of variance associated with classical dyes, the vol spot normalization of Image Master, and the limited sample size, a non-parametric statistical test seems to be the best choice in this case. We opted here for the non-parametric univariate Kolmogorov-Smirnov test. The test is one among the options offered by Image Master. It is a two-sample test with high power efficiency for small sample sizes. The reduced power of a non-parametric test was anticipated by including a
Synthetic highlights Neoglycoconjugate 1 is a representative of a GDP-triazole screening library produced by the Cu(I)-catalyzed 2 + 3 cycloaddition reaction between azide and acetylene reactants. It is an example of click chemistry, a modular approach using low-energy chemical transformations to generate collections of test compounds. A more recent extension of click chemistry is target-guided synthesis (TGS) or freeze-frame click chemistry in which a biological target itself is used to assemble inhibitors at the binding site. This represents an exciting new strategy for the generation of compound libraries and the effective selection of hits and leads.
The pharmaceutical industry is making a conscientious effort to develop cleaner and more efficient processes for manufacturing small-molecule drugs. This development has been guided by the principles of green chemistry and engineering, which stress prevention, for example by atom economy, less hazardous chemical synthesis, use of safer chemicals, design for energy efficiency, and use of renewable feedstocks 1, 2 . The work has been spearheaded by the American Chemical Society Pharmaceutical Roundtable (ACS GCIPR), a coalition between the ACS Green Chemistry Institute (ACS GCI) and a number of major pharmaceutical corporations (Merck, Pfizer, Eli Lilly, AstraZeneca, Schering-Plough, GlaxoSmith-Kline, Wyeth, Boehringer Ingelheim, and Johnson and Johnson) with the aim of integrating the principles of green chemistry and engineering into the business of drug discovery and production.
The development of soft (low energy) ionization techniques, in particular, MALDI1718 and electro-spray14 dramatically enhanced the feasibility of proteomic analysis by MS. In MALDI, the sample to be analyzed is incorporated into a chemical matrix containing crystallized molecules of compounds such as 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid), a-cyano-4 hydroxyninnamic acid (alpha-cyano or alpha-matrix) and 2,5-dihydroxybenzoic acid (DHB). Ionization is achieved by laser activation of a target, leading to the release of peptide and protein ions into a gas phase (Figure 15.2).
They also concluded that there is moderate evidence that low energy extracorporeal shock-wave therapy is not effective for treating chronic non-calcific rotator cuff tendonitis, although that conclusion was based on only one high-quality study which was underpowered.
An important difference between molecular motors and the macro-scale motors is that molecular motors are optimized to operate in a thermal bath, a microscopic environment wherein thermal noise is significant relative to the motor s energy consumption (Gabry, Pesz and Bartkiewicz, 2004). Although operating at only a modest distance from thermal equilibrium, molecular motors successfully manage noise and space-time asymmetry to generate the forces
Marshall'102' has criticized the conformational approach based on crystal structure, nmr solute studies, and theoretical calculations and pointed out that it is not very successful in correlating biological activity with minimum-energy geometry. He believes this is due to the fact that the procedures listed ignore the perturbation caused by interaction between the drug molecule and the asymmetric force field represented by the receptor, when it follows that there is no reason to assume that a receptor binds the low-energy conformer of a ligand. His own approach is to seek out (by computational methods) the presence of common pharmacophore candidates in orientation space within a group of active analogs and, if found, to base the active conformations on these pharmacophores. To date this procedure has not been reported for opioids.
Why are Ugi's MCRs so efficient The answer lies in the low activation energies of all the elementary steps, which are either equilibrium processes or irreversible steps. This concept of energetically preferred reactions is discussed in Chap. 15, in relation to click-reactions of azides and alkynes. Low-energy elementary reactions either occur in concert and are pericyclic or involve two reacting groups with highly matching electron distribution.
The PSA is defined as the sum of the surfaces of the polar atoms in a molecule. Because this value can vary significantly with conformation, different approaches have been devised in order to use it practically. One approach has been to calculate the PSA of the molecule in a single energy minimised conformation. Another has been to calculate a topological PSA (tPSA), which is based on average contributions that the polar functional groups make in a variety of molecules. The calculation of tPSA is much faster, since energy minimization and or a search for a low-energy conformation is not required. Of course, these different approaches do not all yield the same results, so PSA values, even for a given conformation, can vary widely
Work simplification and energy conservation strategies focus on promoting independence and safety and preventing additional stress or trauma to the individual while engaging in purposeful activity occupations. Key principles include using both hands to complete a task whenever possible, working within normal reach (not over extending or reaching), gathering supplies needed for the task prior to beginning, sliding heavy objects rather than carrying, and using gravity to decrease energy expenditure. Work simplification also addresses the storage and organization of work spaces, placing commonly used items in a place where they are easy to reach and use, sitting whenever possible, and determining the appropriate height of the work surface for the individual and the actual tasks being performed (Grangaard 2006, Sabata et al. 2008).
The x-ray crystal structures of the steroid hormones themselves have also provided important information. Although the conformations of rigid molecules in crystals and their preferred conformations in solution with receptors can differ, it is now clear from x-ray crystallography studies of steroids, prostaglandins, thyroid compounds, and many other drug classes that this technique can be a powerful tool in understanding drug action and in designing new drugs.27-29 The relationship is straightforward steroid drugs usually do not have a charge and, as a result, are held to their receptors by relatively weak forces of attraction. The same is true for steroid molecules as they pack into crystals. In both events, the binding energy is too small to hold any but low-energy conformations. In short, the steroid conformation observed in steroid crystals is often the same or very similar to that at the receptor.
The calculation of ligand strain energy also traditionally lies in the realm of molecular mechanics force fields. Usually, ligand strain is calculated during the construction of poses, but not added to the final binding free energy, because it is assumed that strained conformations can be weeded out before the final score is calculated and because better correlation with experimental binding data is observed. Effects of strain energy have rarely been determined experimentally 2 , but it is generally accepted that high-affinity ligands bind in low-energy conformations 79,80 . Estimation of ligand strain energy based on force fields can be time-consuming and therefore alternatives are often employed, such as empirical rules derived from small-molecule crystal structure data 81 . Poses generated by such programs are, however, often not strain-free, because only one torsional angle is regarded at a time.
In the context of small soluble proteins, ab initio loop modeling methods can be quite accurate (RMSD 1.0A) for short loop lengths of four to six residues 74 . This indicates that several of the smaller GPCR loops may be well approximated using loop prediction methods. However, for loops of longer length, the accuracy rapidly diminishes. In a recent loop prediction benchmark, over 50 of medium length loops (seven to nine residues) had RMSDs of worse than 2 A even when the lowest RMSD conformation was selected for comparison .74 . For membrane proteins, further inaccuracies arise, as interactions among the receptor loops, receptor termini, transmembrane helical bundle, and phospholipid membrane may affect loop conformation and are frequently not considered during the modeling procedure. These errors may be greater for GPCR homology models, as the end-to-end distances of the helices are uncertain, and may even be inappropriate for the target loop length. Recently, Mehler et al....
The clinical radioisotope of xenon for organ imaging is xenon-133, a noble gas used in its elemental form. Xenon-133 is produced in a nuclear reactor as a byproduct of uranium fission by the nuclear reaction 235U(n, fission)133Xe. Xenon-133 (t1 2 5.3 days) decays by 3- emission to ce-sium-133, with y-ray emission of 81 keV (37 ). Gases used in lung ventilation studies must be chemically and physiologically inert at the concentrations used for imaging studies. Xenon-133 is chemically inert and insoluble in water, which makes it insoluble in body fluids. Unfavorable physical characteristics of xenon-133 include poor image quality because of the low tissue penetration of the low-energy y-ray, increased patient dose due to 3- emission, and the low y-ray emission yield (36 y-rays 100 disintegrations).
Unnatural b-agonists interact with all or part of the epinephrine binding site and with other chemical groups in the receptor protein that are determined by the structures of the agonist and the protein. The binding site for each agonist and the nature of its active complex are, therefore, unique. These interactions involve formation of low-energy ionic and or hydrogen bonds, which contribute much to the specificity of binding, and of hydrophobic (nonpolar) binding, which contributes to the specificity
The conformational properties of valsartan have been analyzed both in solution and at the binding site of the AT1 receptor. These studies revealed two low energy conformations of valsartan in solution, cis trans around the amide bond in the ratio of approximately 40 60, while the majority of the docked molecules at the ATI receptor are bound in the trans conformation 15 . A schematic presentation of some of the important interactions of valsartan with the AT1 receptor is given in Fig. 5.1 16 .
The calculation of the energy requirement is aimed at achieving normal growth and development while maintaining ketosis during the course of ketogenic diet therapy. A calorie level that is too high will result in rapid weight gain. A calorie level that is too low may result in poor growth and insufficient ketosis. Experience has shown that children can grow on the ketogenic diet, but often growth occurs at a decelerated rate. The calorie level may need to be adjusted several times during the course of ketogenic diet therapy to support individual growth needs. The child's ideal weight for height is the main parameter for determining caloric needs. If the child is underweight, his or her actual weight should be used as the initial caloric goal. Overweight children should be calculated at or close to their ideal weight for height. Factors affecting energy expenditure, such as immobility (low energy expenditure) or muscle spasticity (increased energy expenditure), should be taken into...
Exists in an equilibrium between an inactive conformation (R) and an active conformation (R*). In absence of agonist, the inactive form R prevails, but a certain fraction of receptors spontaneously assume the R* state because of the low-energy barrier separating the two conformations. Agonists are predicted to bind with highest affinity to R* and to shift the equilibrium to a larger proportion of receptors under the active conformation. Conversely, inverse agonists that have the ability to inhibit agonist-independent activity (also called constitutive activity) stabilize the inactive conformation R, thereby shifting the equilibrium away from R*. On the other hand, neutral antagonists do not influence the equilibrium between R and R*.
This energy is provided by the electron transport chain. The oxidative phosphorylation system is localized in the inner mitochondrial membrane. Uncoupling agents allow electron transport to oxygen to continue but prevent the phosphorylation of ADP to ATP, that is, they uncouple the energy-yielding from the energy-saving process. This results in increased mitochondrial oxygen uptake and reduced ATP levels despite an increased ATP-synthase activity.
B-Particle emitters have relatively long penetration ranges (2-12 mm in the tissue) depending on the energy level. The long-range penetration is particularly important for solid tumors with high heterogeneity. The b-particle emitters yield a more homogeneous dose distribution even when they are heterogeneously distributed within the target tissue. Among various metallic radionuclides, lanthanide radiometals are of particular interest. There are several lanthanide isotopes to choose, including low-energy b-emitter 177Lu, medium-energy b-emitters 149Pm and 153Sm, and high-energy b-emitters 166Ho and 90Y. Yttrium and lanthanide metals share similar coordination chemistry. The chelator technology is well developed and well understood. For systemic cancer radiotherapy, 90Y is of particular interest because it is a high-energy pure b-particle emitter. The half-life of 2.7 days is short enough to achieve a critical dose rate and long enough to allow the radiopharmaceutical to be manufactured...
Biopharmaceutics Integration of Physical Chemical and Biological Pharmacokinetic Principles and Impact on Clinical
Solutions or dispersions in lipid-based matrices have also been extensively evaluated as means to improve oral BA. Presenting the drug to the GI tract in solution removes the dissolution step, and lipid-based or amphiphilic excipients can be used to enhance solubility and dissolution rate for a hydrophobic drug. As with amorphous high energy systems, a risk with solutions and dispersions is the potential for conversion to a less soluble polymorphic form in the dosage form over time leading to potential quality issues. Addition of nucleation inhibitors such as polymers can minimize the potential for form conversion, but the preferred approach is to formulate in a system that is thermodynamically stable. This requires an exhaustive screening for polymorphs and solvates, but even with an extensive body of knowledge on known crystalline forms, the potential may exist for new forms to appear. The potential for precipitation upon dilution in the GI tract must also be considered for these...
The microphysiometer, which measures extracellular media acidification in response to perturbations of energy consumption in mammalian cells, provides a low-throughput capability. Since activation of any signal-transduction pathway results in energy usage, this approach also obviates the need to define intracellular signalling mechanistically. This assay has been used to identify the natural ligand for the orphan GPCR APJ, termed apelin (Habata et al. 1999), and the receptor for mammalian RF-amide peptides (Hinuma et al. 2000). However, in the absence of improvements for a higher throughput capacity assay, broader application of the above technologies will be limited.
The atomic partial charges onto the solvent accessible areas of the individual atoms within a molecule. All of the 30 possible Jurs descriptors 35 were calculated for each member of the dataset. The values were then normalised, and the similarity between pairs of sets of values calculated using the non-binary Tanimoto coefficient. In what follows, the inclusion of the Jurs rankings in a fusion combination is indicated by 'J'. The FBSS similarity measure has been described previously its inclusion in a fusion combination is denoted by 'F'. The ChemX 3D flexible fingerprint keys record the presence or absence of potential pharmacophoric patterns (consisting of three pharmacophore centres and the associated inter-atomic distances) in any of the low-energy conformations identified by a rule-based conformational analysis of a molecule. Two sets of similarity scores were generated from these fingerprints the Tanimoto coefficient scores and the Tversky similarity scores 5,36 , the inclusion...
Once potential drug designs have been identified by the methods described earlier, other molecular modeling techniques may then be applied. For example, geometric optimization may be used to relax the structures and to identify low-energy orientations of drugs in receptor sites. Molecular dynamics may assist in exploring the energy landscape, and free energy simulations can be used to compute the relative binding of free energies of a series of putative drugs. Many of these tools are available at the National Institutes of Health website (7).
In a hash table for the reference structure. Each such match of two triangles defines a placement of the base fragment on the reference structure. If the triangle matching procedure fails, the slower RIGFIT procedure is invoked to place the fragment. In this way a number of base fragments, each with a set of low-energy conformers, is placed in a number of plausible orientations on the reference structure. Subsequently, the test ligand is incrementally built up by adding the remaining fragments in a stepwise fashion. Each fragment contains exactly one rotatable bond or a whole ring system. Upon adding a fragment, each of its preferred torsions or ring conformers are tried in turn. Thus, in each step, a number of partial placements is extended to a larger number of partial placements of molecular entities that are larger by one fragment. In order to avoid the inherent combinatorial explosion of alternative solutions, in each step, all partial placements are scored and only the...
Pfizer has developed and commercialized a new sustainable, enzymatic synthesis of pregabalin in which every process step is performed in water. This has resulted in significant environmental savings in terms of both material and energy usage. This book chapter quantifies those savings with the hope of encouraging more process chemists to use biocatalysis in their everyday work. Batch Plus was shown to be a valuable tool for performing energy balance analysis and can be applied to other pharmaceutical processes to document process changes and easily calculate green chemistry metrics as the process evolves from laboratory-scale to full-scale production. As energy prices increase, it is hoped that more scientists will include energy assessment in their process selection methodology as part of their drive toward greener and more cost-effective processes.
Simulated annealing can be viewed as an improved variation of the Monte Carlo search. Note that there are several different formulations of simulated annealing. In all of them, the energy-accessible solution space is reduced once the calculation is far enough along to have started finding some low energy regions. This is sometimes done by reducing the temperature in a statistical mechanical simulation, which might be a Monte Carlo simulation or sometimes a molecular dynamics simulation. Another form of simulated annealing starts with a Monte Carlo search, and then gradually changes the statistical probability to make conformers near the lowest energy conformer thus found far more likely to be generated in subsequent steps. The ant colony search runs multiple chain growth runs in a single process. This search samples the surrounding low energy space efficiently. It does this by using some of the conformation angles from previous runs (analogous to ants following a pheromone trial part...
Stenberg et al. (1999) compared the utility of three different predictive models for intestinal absorption. They demonstrated that molecular surface descriptors and descriptors derived from quantum mechanics were much more useful than the simple rule of five as the predictor of intestinal absorption. These in sil-ico methods have a great potential as virtual screens in testing permeability of test drugs. The utility of polar molecular surface area (PSAd) as a predictor of intestinal absorption was demonstrated by Clark (1999). Similarly, the evaluation of the dynamic PSAd as a predictor of drug absorption was performed by Palm et al. (1998). PSAd of the compounds was calculated from all low energy
Scintillation proximity assays use resin beads (SPA beads) whose surface has been engineered so it is capable of binding to a wide variety of substances. The bead also contains a scintillant that only fluoresces when a low energy radioactive source comes within about 20 pm of the surface of the beads. The radioactive isotopes used in SPA assays emit low energy emissions that have very short pathways in aqueous media (Table 5.5).
Since the structures for potential ligands are taken from crystal structures (CSD) or rule-derived models (NCI), they begin in a low-energy conformation. To deal with cases where the binding conformation of a ligand is very different from the database conformation, the database can be enriched by a series of low-energy conformers for screening 28,59 .
A molecular orbital having a lower energy level than the atomic orbitals from which the bonding orbital is formed. Such an orbital can contain two electrons, and their presence results in a strong bond when the overlap of the atomic orbitals is large. Two overlapping atomic orbitals combine to yield one low-energy bonding orbital (designated a) and one high-energy antibonding orbital (designated a*). Two paired electrons are sufficient to fill the s orbital, and any additional electrons must occupy the high energy a* orbital where, rather than stabilizing the bond, they lead to repulsion between the atoms.
We first applied 18F FDG PET to healthy human subjects undertaking a running task in the upright posture (Fig. 3). We demonstrated a relative increase in glucose uptake in the temporo-parietal association cortex, occipital cortex, premotor cortex, primary sensorimotor cortex, and the cerebellar vermis 24 . This was probably due to the higher energy consumption necessary for integrating multimodal sensory inputs. A relative reduction in glucose uptake was detected in the prefrontal cortex, temporal cortex, cerebellar hemisphere, brain stem, and striatum. The mean value of global brain glucose uptake was relatively lower in the runners than in resting controls 24 . Kemppainen and coworkers 25 later demonstrated a significant reduction of the regional glucose metabolic rate in all cortical regions in correlation with exercise intensity. They also pointed out that exercise could be associated with adaptive metabolic changes in the frontal cortex 25 . Thus, global and regional brain...
However, the latter alignment is probably more realistic 100 , indicating that a 5 amino acid loop in the first sequence and structure is to be replaced with a 3 amino acid loop in the second sequence. The customary practice is to remove the whole segment between two conserved secondary structures units. Even with this practice, ambiguity remains, since the ends of secondary structures, especially a-helices, are not well determined. If loop building methods were accurate, then removing more of the segment would be a good idea. But long loops (longer than 6 amino acids) are difficult to rebuild accurately, and hence there is cause to preserve as much of the starting structure as possible. Once the backbone has been borrowed from the template in stepwise modeling, one has to decide the order of building the core side chains, the backbone of loops to be built, and their side chains. They may be built sequentially, or allowed to vary simultaneously. Side chains from the core may guide the...
The photochemical reactions of C4 plants are of course the same as those operating in C3 plants however, the ratios of PSI and PSII may be different in the two plant types and also among the subgroups of the C4 plants. In C4 plants, the relationship of the quantum yield of PSII electron transport to quantum yield of CO2 fixation is linear suggesting that photochemical use of energy absorbed by PSII is tightly linked to CO2 fixation in C4 plants. This is nearly identical in all the three subgroups and may allow estimates of the photosynthetic rate based on the PSII efficiency. The energy requirement for the classical PCR cycle is 3ATP and 2NADPH CO2 fixed. The real cost of oxygenase and photorespiration is much higher. The estimate of energy requirement of C4 plants is based on the specific demand for carbon metabolism. Since NADP-malic enzyme species exhibit agranal chloro-plast, the entire NADPH requirement has to be met by NADP-malic enzyme. However, the latter could provide only...
Another united-atom model is the Ca structure representation used by Bowie et al. 30 . Small fragments of proteins were constructed using a fold recognition algorithm. Nine-residue segments were selected from a library of fragment conformations on the basis of their environment codes 30 . A similar method was used for some larger fragments (15-25 residues). Homologous structures were carefully removed from the database. The method of selecting initial conformations did enhance the local structure accuracy to a value higher than that expected by chance alone. Structures were then improved by a GA procedure in which each gene represented the set of dihedral angles of a structure and mutations made changes to one angle. For recombination, segments of one gene were replaced with segments of another. Mutations had a high probability of occurring at the fragment junctions. The fitness was evaluated with a function containing contributions from the fold recognition profile fit,...
Fiber, causing cross-bridge activation and muscle contraction. Because of the excess ACh present, the depolarization is sustained and the muscle can become maximally contracted with the sarcomeres at their shortest, causing the muscle to become taut and resulting in a trigger point (see Figure 42.3). This contraction increases the energy consumption of the muscle, putting increased demand on the microcirculation and leading to local ischemia and hypoxia. As previously discussed this can initiate a pain state. MFP is also associated with enhanced pain sensitivity and wind-up, due to the persistent stimulation of the nociceptors. Similar to FMS, TMD patients have reduced pressure pain thresholds and decreased descending inhibition of nociceptive reflexes.
One item frequently neglected, when researchers report on the room light used for testing, is whether the fixture did or did not have a diffuser. This one item can affect the SPD of the radiation source very dramatically as illustrated in Figure 2, taken from a publication of Cole and associates.34 Many have probably personally experienced this same phenomena. The absorption of UV rays by the plastic sandwiched between the glass of windshields, accounts for why photochromic lenses do not work in automobiles. A similar problem might be found in using windowsill or more properly called energy-efficient window-glass filtered daylight for testing in some modern laboratory buildings.
However, pullulan hydrophobised by a modification of the backbone constituted the main type of derivative for forming gels through low-energy interactions of macromolecular structures with hydrophobic associative domains 108, 166, 167 . Without crosslinkers, these domains self-associate into stable nanocolloids with an inner hydrophobic core 168, 169 . The self-assembly method based on associating polymers is an efficient and versatile technique for the preparation of functional nanogels and hydrogels. In particular, amphiphilic pullulans obtained from cholesteryl, acetyl or chloroacetyl graftings onto the hydroxyl groups form nanogels that are able to trap hydrophobic molecules, proteins or peptides, and nucleic acids. Moreover, hydrophobised pullulan-based nanogels interact also with various molecular assemblies such as liposomes and oil-water emulsions 170 . They
An important consideration in choosing a lamp source is the lack of control one has when using mass marketed commercial lamps as opposed to specialty lamps such as the long-arc Xenon. This factor is currently much in evidence in the US where because of the putting into effect of the Energy Policy Act of 199226 and the American National Standard Institute (ANSI) and Illuminating Engineering Society of North America (IESNA) Recommended Practice for Photobiological Safety for Lamps and Lamp Systems RP-27.1-9627 and RP-27-3.96.28 The first law has already resulted in the removal from the mass market of certain lamps and substitution of SPD non-equivalents.
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