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At least 1,207 records · Page 67Linked to original sources
PubMed1992

Biosynthesis of the erythromycin macrolactone and a rational approach for producing hybrid macrolides.

The three eryA genes involved in the formation of the polyketide portion of the macrolide antibiotic erythromycin in Saccharopolyspora erythraea, appear to be organized in a single transcriptional unit on the basis of the results of gene disruption experiments. An insertion sequence-like element of lower G + C content separates eryAI from eryAII. The organization of the enzymatic domains present in the eryA-encoded multifunctional polypeptides, determined by computer-assisted analysis, is presented. This has enabled the determination of a putative dehydratase domain. A rational approach for producing novel macrolides by introducing selected changes in polyketide synthase genes is outlined. The isolation of a lactone intermediate resulting from an early synthesis step in macrolactone formation is also presented.

Amino Acid Sequence↗
PubMed1991

Intervention research to promote clinically effective and economically efficient use of pharmaceuticals: the International Network for Rational Use of Drugs.

Despite acceptance of the essential drug concept by over 100 countries, current drug use patterns frequently result in unsafe use, waste of scarce resources, non-compliance, excess adverse drug reactions and disease resistance. Even in countries where resources for research are available, most efforts to improve drug prescribing have never been properly evaluated. Proposed interventions should reflect the behavioral basis for current drug use, target priority public health areas, and be feasible in developing country contexts. Most importantly, they must be critically assessed for cost and effectiveness in well-controlled field trials. The International Network for Rational Use of Drugs (INRUD) is a cooperative organization of health professionals and researchers in developing countries whose aim is to promote improved quality of care through more clinically effective and economically efficient use of pharmaceuticals. To accomplish this, INRUD will strengthen regional and national capacities to develop and scientifically evaluate programs to improve drug use and disseminate information on practical strategies shown to be cost-effective.

Developing Countries↗
PubMed1995

Ligand-protein docking and rational drug design.

Over the past year there have been some interesting and significant advances in computer-based ligand-protein docking techniques and related rational drug-design tools, including flexible ligand docking and better estimation of binding free energies and solvation energies. As a result, the successful use of computational tools to help generate interesting new guide (lead) compounds for targeted receptors is becoming more commonplace.

Algorithms↗
PubMed1992

Applications of molecular physics 'biotechnology' to the rational design of an improved phenytoin analogue.

This study exploits molecular physics, in conjunction with a large scale computing environment, as a tool for understanding the clinical phenomenology of phenytoin (PHT) toxicology at a molecular level and for employing this understanding in an attempt to design improved drugs. The application of molecular physics techniques, such as quantum mechanics and molecular force field calculations, to the process of rational anticonvulsant drug design remains virtually unexplored. A 3-step strategy for applying these techniques to the design of an improved PHT molecule is presented. Step 1 employs quantitative structure-activity relationship calculations on 80 PHT analogues to ascertain the portion of the PHT molecule necessary for bioactivity (i.e. the 'bioactive face' of PHT); the N3-C4(O)-C5-R fragment of PHT was identified as the bioactive face. Step 2 employs molecular modelling studies to determine the portion of the PHT molecule necessary for the teratogenic, mutagenic and connective tissue toxicities of PHT (i.e. the 'biotoxic face'); the C2(O)-N3 fragment of PHT was identified as the biotoxic face. Step 3 experiments design an 'improved' PHT analogue, which maintains the bioactive face while eliminating the integrity of the biotoxic face; 2-deoxy-5,5-diphenylhydantoin was designed and synthesized as the improved PHT analogue. This compound had biological activity equivalent to PHT, but was unable to bind to nucleic acids or to chelate metals involved in connective tissue metabolism.

Biotechnology↗
PubMed2005

Development of rationally designed affinity-based drug delivery systems.

Many drug delivery systems have been developed to provide sustained release of proteins in vivo. However, the ability to predict and control the rate of release from delivery systems is still a challenge. Toward this goal, we screened a random drug-binding peptide library (12 amino acids) to identify peptides of varying (i.e. low, moderate, and high) affinity for a model polysaccharide drug (heparin). Peptide domains of varying affinity for heparin identified from the library were synthesized using standard solid phase chemistry. A mathematical model of drug release from a biomaterial scaffold containing drug-binding peptide domains identified from the library was developed. This model describes the binding kinetics of drugs to the peptides, the diffusion of free drug, and the kinetics of enzymatic matrix degradation. The effect of the ratio of binding sites to drug, the effect of varying the binding kinetics and the rate of enzymatic matrix degradation on the rate of drug release was examined. The in vitro release of the model drug from scaffold containing the peptide drug-binding domains was measured. The ability of this system to deliver and modulate the biological activity of protein drugs was also assessed using nerve growth factor (NGF) in a chick dorsal root ganglia (DRG) neurite extension model. These studies demonstrate that our rational approach to drug delivery system design can be used to control drug release from tissue-engineered scaffolds and may be useful for promoting tissue regeneration in vivo.

Affinity Labels↗
PubMed2005

Rational antibiotic treatment of outpatient genitourinary infections in a changing environment.

In the outpatient setting, genitourinary infections (GUIs) remain costly to treat and are a significant cause of morbidity. Recent evidence supports more substantial roles for pathogens other than Escherichia coli, particularly gram-positive pathogens, in the pathogenesis of GUIs. Broad-spectrum agents should be considered in order to address this etiologic change appropriately. Criteria for antimicrobial selection set forth by the Council for Appropriate and Rational Antibiotic Therapy (CARAT) recommend using antibiotics that are supported by strong clinical evidence, have good susceptibility profiles, are safe, are cost-effective, and are used for the optimal duration. Evidence-based guidelines recommend considering local E coli resistance rates to trimethoprim-sulfamethoxazole and using fluoroquinolones as second-line therapy when resistance is high. Fluoroquinolones are recommended for the treatment of pyelonephritis and prostatitis. Among the fluoroquinolones, levofloxacin and gatifloxacin offer coverage for the gram-negative and gram-positive pathogens, which may make them preferable in treating urinary tract infections empirically in such patient groups. For the treatment of bacterial prostatitis, only trimethoprim and the fluoroquinolones possess both the appropriate bactericidal activity and the ability to diffuse into the prostate. Levofloxacin shows particularly good penetration into prostatic tissue. Safety issues to consider include imbalances in intestinal microflora caused by antimicrobial agents that may lead to overgrowth of vancomycin-resistant enterococci and Clostridium difficile-associated diarrhea. Once the optimal agent is identified, the optimal duration of treatment should be determined to maximize treatment success while minimizing the potential for resistance. Finally, cost considerations include the costs of treatment failure due to inappropriate therapy or nonadherence to the therapeutic regimen.

Ambulatory Care↗
PubMed2005

A rational approach to evidence gaps in the management of osteoporosis.

Major advancements in the treatment of osteoporosis have occurred over the last decade. Therapies including the anti-resorptive drugs such as alendronate and risedronate have been shown in randomized placebo-controlled trials to increase bone mineral density and reduce fracture risk. Anabolic therapy in the form of parathyroid hormone has been introduced as the first treatment to build bone mass. However, gaps in our knowledge about specific management issues that arise frequently among primary care providers persist. In this paper, three common clinical scenarios are discussed: a postmenopausal woman with only slightly reduced bone mineral density; an osteoporotic woman on anti-resorptive therapy for more than 5 years; and a woman who continues to fracture despite treatment. Evidence gaps in each treatment scenario are presented, and rational approaches to management are suggested.

Age Factors↗
PubMed2004

Rational polynomial equation as an unbiased approach for the kinetic studies of Drosophila melanogaster acetylcholinesterase reaction mechanism.

The hydrolysis of substrates by cholinesterases does not follow the Michaelis-Menten reaction mechanism. The well-known inhibition by excess substrate is often accompanied by an unexpectedly high activity at low substrate concentrations. It appears that these peculiarities are the consequence of an unusual architecture of the active site, which conducts the substrate molecule over many stages before it is cleaved and released. Structural and kinetic data also suggest that two substrate molecules can attach at the same time to the free, as well as to the acetylated, enzyme. We present a procedure which provides an unbiased framework for mathematical modelling of such complex reaction mechanisms. It is based on regression analysis of a rational polynomial using classical initial rate data. The determination of polynomial degree reveals the number of independent parameters that can be evaluated from the available information. Once determined, these parameters can substantially facilitate the construction and evaluation of a kinetic model reflecting the expected molecular events in an enzymic reaction. We also present practical suggestions for testing the postulated kinetic model, using an original thermodynamic approach and an isolated effect in a specifically mutated enzyme.

Acetylcholinesterase↗
PubMed2005

Rational design of highly potent HIV-1 fusion inhibitory proteins: implication for developing antiviral therapeutics.

Recombinant protein containing one heptad-repeat 1 (HR1) segment and one HR2 segment of the HIV-1 gp41 (HR1-HR2) has been shown to fold into thermally stable six-helix bundle, representing the fusogenic core of gp41. In this study, we have used the fusogenic core as a scaffold to design HIV-1 fusion inhibitory proteins by linking another HR1 to the C terminus of HR1-HR2 (HR121) or additional HR2 to the N terminus of HR1-HR2 (HR212). Both recombinant proteins could be abundantly and solubly expressed and easily purified, exhibiting high stability and potent inhibitory activity on HIV-1 fusion with IC50 values of 16.2+/-2.8 and 2.8+/-0.63 nM, respectively. These suggest that these rationally designed proteins can be further developed as novel anti-HIV-1 therapeutics.

Amino Acid Sequence↗
PubMed2005

Rational design of an EGF-IL18 fusion protein: implication for developing tumor therapeutics.

Interleukin-18 (IL-18) is a proinflammatory cytokine. This protein has a role in regulating immune responses and exhibits significant anti-tumor activities. Epidermal growth factor (EGF) is an important growth factor that plays a central role in the regulation of cell cycle and differentiation. It was proposed that a targeted delivery of IL-18 by generation of IL-18-EGF fusion protein might decrease adverse effects and result in enhancing cytotoxic and antitumor activities. In the present study, a fusion protein, consisting of EGFR binding domain fused to human IL-18 mature peptide via a linker peptide of (Gly(4)Ser) 3, was constructed and expressed in the insect cell line Sf9 using Bac-to-Bac baculovirus expression system. We showed that the purified recombinant fusion protein induced similar levels of IFN-gamma to that of native IL-18 protein in human PBMC in the presence of ConA. Furthermore, EGF receptor competitive test in human epithelial cancer A431 cell line showed that EGF-IL18 fusion protein can specifically bind with EGFR by competing with native EGF protein. These suggest that this rationally designed protein can be further developed as novel tumor therapeutics.

Animals↗
PubMed2006

Natural compounds as a source of protein tyrosine phosphatase inhibitors: application to the rational design of small-molecule derivatives.

Reversible phosphorylation of tyrosine residues is a key regulatory mechanism for numerous cellular events. Protein tyrosine kinases and protein tyrosine phosphatases (PTPs) have a pivotal role in regulating both normal cell physiology and pathophysiology. Accordingly, deregulated activity of both protein tyrosine kinases and PTPs is involved in the development of numerous congenitically inherited and acquired human diseases, prompting obvious pharmaceutical and academic research interest. The development of compound libraries with higher selective PTP inhibitory activity has been bolstered by the realization that many natural products have such activity and thus are interesting biologically lead compounds, which properties are widely exploited. In addition, more rational approaches have focused on the incorporation of phosphotyrosine mimetics into specific peptide templates (peptidomimetic backbones). Additional factors furthering discovery as well as therapeutic application of new bioactive molecules are the integration of functional genomics, cell biology, structural biology, drug design, molecular screening and chemical diversity. Together, all these factors will lead to new avenues to treat clinical disease based on PTP inhibition.

Animals↗
PubMed2006

Rational design of hydrogels for tissue engineering: impact of physical factors on cell behavior.

When designing suitable biomaterials for tissue-engineering applications, biological and chemical parameters are frequently taken into account, while the equally important physical design variables have often been neglected. For a rational design of biomaterials, however, all variables influencing cell function and tissue morphogenesis have to be considered. This review will stress the development of cross-linked hydrogels and outline the impact of their physical properties on cell function and tissue morphogenesis. In the first part, the principles of cellular mechanosensitivity, as well as the influence of substrate mechanics on cell behavior, will be discussed. Afterwards, methods to characterize the mechanical properties of biomaterials will be presented. The subsequent chapters will address hydrogels that allow for the control of their physical qualities followed by a discussion of their use in tissue-engineering applications.

Biocompatible Materials↗
PubMed2005

A theoretical study of the different radical-scavenging activities of catechin, quercetin, and a rationally designed planar catechin.

To improve the radical-scavenging activity of catechin, a planar catechin analogue was designed and synthesized by Fukuhara [J. Am. Chem. Soc. 124 (2002) 5952]. Although the planar catechin is less active than quercetin, it is much more active than catechin in its ability to scavenge galvinoxyl radical, suggesting that the rational design was successful. However, an interesting question remains: what is the basis for the enhanced radical-scavenging activity of the planar catechin? By DFT calculations, we determined that the galvinoxyl radical is scavenged through an electron-transfer mechanism rather than a hydrogen-atom-transfer mechanism. Moreover, the antioxidant anion, derived from proton dissociation, plays a key role in the radical-scavenging process. Hence, the different radical-scavenging activities of the three antioxidants may result from the different ionization potentials of their anions.

Antioxidants↗
PubMed2005

Non-stochastic and stochastic linear indices of the 'molecular pseudograph's atom adjacency matrix': application to 'in silico' studies for the rational discovery of new antimalarial compounds.

Malaria is one of the most deadly diseases, affecting million of people especially in developing countries. Because of the rapidly increasing threat worldwide of malaria epidemics multidrugs resistant to therapies, there is an urgent global need to discover new classes of antimalarial compounds. In an effort to overcome this problem, we have investigated the use of structure-based classification models for the 'rational' selection/identification or design/optimization of new lead antimalarials from virtual combinatorial data sets. In this sense, TOpological MOlecular COMputer Design strategy (TOMOCOMD approach) has been introduced in order to obtain two quantitative models for the discrimination of antimalarials. A collected data set containing 597 antimalarial compounds is presented as a helpful tool not only for theoretical chemist but for other researchers in this area. The validated models (including non-stochastic and stochastic indices) classify correctly more than 90% of compounds in both training and external prediction data sets. They showed high Matthews' correlation coefficients; 0.87 and 0.82 for training and 0.86 and 0.79 for test set. The TOMOCOMD-CARDD approach implemented in this work was successfully compared with two of the most useful models for antimalarials selection reported so far. Thus we expect that these two QSAR models can be used in the identification of previously un-known antimalarials compounds.

Antimalarials↗
PubMed2005

A theoretical study on the structure-activity relationships of metabolites of folates as antioxidants and its implications for rational design of antioxidants.

To elucidate the structure-activity relationships of metabolites of folates as antioxidants, the O-H bond dissociation enthalpies (BDEs) and ionization potentials (IPs) for these compounds were calculated by density functional theory (DFT) on B3LYP/6-31+G(,3pd) level. Accordingly, the antioxidant activity difference for metabolites of folates can be elucidated by O-H BDE and IP values and can be further explained in terms of electronic effect and intramolecular hydrogen bond effect of substituents. Furthermore, the potential of the active center of metabolites of folates, 4-hydroxypyrimidine (4-HP), as lead antioxidant, was evaluated by comparing the BDEs and IPs of 4-HP with those of 5-hydroxypyrimidine (5-HP). It was revealed that 4-HP and 5-HP held identical IPs, but the O-H BDE of the former was 22.84 kcal/mol higher than that of the latter, which meant 4-HP was inert in H-atom donation. Nevertheless, the O-H BDE of 4-HP was very sensitive to the substituents, which made NH2-derivatives of 4-HP very active as antioxidants. Therefore, 4-HP is also a potential lead antioxidant and deserves attention in rational design of antioxidants.

Antioxidants↗
PubMed2003

Rational design, synthesis and structure-activity relationships of a cyclic succinate series of TNF-alpha converting enzyme inhibitors. Part 1: lead identification.

Rational design based on the broad spectrum MMP inhibitor CGS 27023A led to the identification of a novel series of cyclic succinate TACE inhibitors. As a mixture of two enantiomers, the lead compound 17b exhibited potent enzyme activity (IC(50)=8 nM) in the inhibition of porcine TNF-alpha converting enzyme (pTACE) and excellent selectivity over aggrecanase and MMP-1, -2 and -9.

ADAM Proteins↗
PubMed2004

Rational design of potent and selective NH-linked aryl/heteroaryl cathepsin K inhibitors.

Prior reports from our laboratories have identified the nonpeptidic inhibitor 2 as a potent and selective Cathepsin K (Cat K) inhibitor. Modelling studies suggested that the introduction of a NH linker between the P3 aryl and P2 leucinamide moieties would allow the formation of a H-bond with the Gly66 residue of Cat K, hopefully increasing potency. Aniline 4 was thus synthesized and showed improved potency over its predecessor 2. Further modelling concluded that a 2-substituted five membered ring could more adequately place the P3 moiety of 4 into the S3 pocket of Cat K. The synthesis of the 2-substituted thiophene 5 confirmed this hypothesis by displaying a slight increase in potency against Cat K (>10-fold increase in potency vs 2) and a good selectivity profile against Cathepsins B, L, and S. This rationally designed inhibitor 5 also displayed increased potency in a functional bone resorption assay (10nM) versus 2 (95 nM).

Binding Sites↗
PubMed2004

Rational design of 6-methylsulfonylindoles as selective cyclooxygenase-2 inhibitors.

The introduction of 3-arylmethyl, 3-aryloxy and 3-arylthio moieties into a 6-methylsulfonylindole framework using rational drug design led to potent, selective COX-2 inhibitors having efficacy in a rat carrageenan air pouch model. Incorporation of a conformationally more rigid 3-aroyloxy substituent onto the 6-methylsulfonylindole scaffold led to selective, but considerably less potent COX-2 inhibitors. Variation of the hydrophilicity and size of the indole 2-substituent of 3-arylthio-6-methylsulfonylindole inhibitors led to modulation of the COX-2 human whole blood (HWB) potency and selectivity.

Administration, Oral↗