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PubMedDate not supplied

A novel search engine for virtual screening of very large databases.

Virtual screening of large chemical databases using the structure of the receptor can be computationally very demanding. We present a novel strategy that combines exhaustive similarity searches directly in SMILES format with the docking of flexible ligands, whose 3D structure is generated on the fly from the SMILES representation. Our strategy makes use of the recently developed LINGO tools to extract implicit chemical information from SMILES strings and integrates LINGO similarities into a pseudo-evolutionary algorithm. The algorithm represents a combination of a fast target-independent similarity method with a slower but information richer target-focused method. A virtual search of FactorXa ligands provided 62% of the potential hits after docking only 6.5% of a database of nearly 1 million molecules. The set of solutions showed good diversity, indicating that the method shows good scaffold hopping capabilities.

Algorithms↗
PubMed2001

Immobilized RNA switches for the analysis of complex chemical and biological mixtures.

A prototype biosensor array has been assembled from engineered RNA molecular switches that undergo ribozyme-mediated self-cleavage when triggered by specific effectors. Each type of switch is prepared with a 5'-thiotriphosphate moiety that permits immobilization on gold to form individually addressable pixels. The ribozymes comprising each pixel become active only when presented with their corresponding effector, such that each type of switch serves as a specific analyte sensor. An addressed array created with seven different RNA switches was used to report the status of targets in complex mixtures containing metal ion, enzyme cofactor, metabolite, and drug analytes. The RNA switch array also was used to determine the phenotypes of Escherichia coli strains for adenylate cyclase function by detecting naturally produced 3',5'- cyclic adenosine monophosphate (cAMP) in bacterial culture media.

Adenylyl Cyclases↗
PubMed2003

Regulation of gene expression by synthetic dimerizers with novel specificity.

New synthetic chemical inducers of dimerization, comprising homodimeric FKBP ligands with engineered specificity for the designed point mutant F36V, have been evaluated for inducing targeted gene expression in mammalian cells. Structure-activity studies indicated that high-affinity dimerizers such as AP1903 are ineffective, perhaps due to kinetic trapping of non-productive dimers, whereas lower-affinity molecules, exemplified by AP1889 and AP1966, potently activate transcription.

Cross-Linking Reagents↗
PubMed1998

Physico-chemical modification of food proteins: food emulsions.

Physico-chemical protein modification involved in food processing is used for "engineering" the structure-property relationship of foods. The three main tools used for protein modification are food formulation, mechanical and thermal (heating/cooling) treatments. They correspond to the main stages of all food technologies. Food structural design is based upon incompatibility and complexing of food biopolymers as well as upon fundamental features of physico-chemical properties of biphasic aqueous systems. Some examples of functional biopolymer modification are considered in systems such as meat extenders, fat replacers, ice cream mixes and wheat flour doughs.

Chemical Phenomena↗
PubMed2003

Metabolic engineering of beta-lactam production.

Metabolic engineering has become a rational alternative to classical strain improvement in optimisation of beta-lactam production. In metabolic engineering directed genetic modification are introduced to improve the cellular properties of the production strains. This has resulted in substantial increases in the existing beta-lactam production processes. Furthermore, pathway extension, by heterologous expression of novel genes in well-characterised strains, has led to introduction of new fermentation processes that replace environmentally damaging chemical methods. This minireview discusses the recent developments in metabolic engineering and the applications of this approach for improving beta-lactam production.

Anti-Bacterial Agents↗
PubMed2002

Engineering selectivity and discrimination into ligand-receptor interfaces.

The reengineering of protein-ligand (or enzyme-substrate) interfaces using a combination of chemical and genetic methods has become an increasingly common technique to create new tools to manipulate and study biological systems. Many applications of ligand receptor engineering require that the engineered ligand and receptor function independently of endogenous ligands and receptors. Engineered ligands must selectively interact with modified receptors, and modified receptors must effectively discriminate against endogenous ligands. A variety of chemical design strategies have been used to reengineer ligand-receptor interfaces. The advantages and limitations of various strategies, which involve the manipulation of hydrophobic, polar, and charged residues, are compared. New design strategies and potential applications of ligand-receptor engineering are also discussed.

Binding Sites↗
PubMed1970

Mechanochemical turbine: a new power cycle.

A basic thermodynamic cycle for the production of mechanical power from materials that may be made to contract forcibly and reversibly is described. The cycle differs from existing mechanical power cycles which generally employ expanding fluid as working substances. A "contraction turbine" operating on this cycle has been devised, which has collagen fiber as its working substance and salt solution as fuel and produces mechanical work directly from chemical free energy. Direct conversion of chemical to mechanical energy is routinely effected in muscle but not in usual man-made engines.

Bromides↗
PubMed2005

Model-driven designs of an oscillating gene network.

The current rapid expansion of biological knowledge offers a great opportunity to rationally engineer biological systems that respond to signals such as light and chemical inducers by producing specific proteins. Turning on and off the production of proteins on demand holds great promise for creating significant biotechnological and biomedical applications. With successful stories already registered, the challenge still lies with rationally engineering gene regulatory networks which, like electronic circuits, sense inputs and generate desired outputs. From the literature, we have found kinetic and thermodynamic information describing the molecular components and interactions of the transcriptionally repressing lac, tet, and ara operons. Connecting these components in a model gene network, we determine how to change the kinetic parameters to make this normally nonperiodic system one which has well-defined oscillations. Simulating the designed lac-tet-ara gene network using a hybrid stochastic-discrete and stochastic-continuous algorithm, we seek to elucidate the relationship between the strength and type of specific connections in the gene network and the oscillatory nature of the protein product. Modeling the molecular components of the gene network allows the simulation to capture the dynamics of the real biological system. Analyzing the effect of modifications at this level provides the ability to predict how changes to experimental systems will alter the network behavior, while saving the time and expense of trial and error experimental modifications.

Animals↗
PubMed2002

The revolutionary implications of the word biotechnology.

Despite the success of the chemical industry, since the early 20th century biotechnology has been framed as a natural and revolutionary alternative. The idea has involved the interweaving of the concepts of engineering new products using living processes, and of engineering new living beings themselves. The potential of these twin themes as alternatives to chemical technologies has been debated since the revolutionary era at the end of World War I. Highpoints included the 1930s and the 1960s. The emergence of genetic engineering techniques in the 1970s enabled the realisation of long-existing aspirations. Ever since then there have been marked changes as the emphasis of biotechnology has shifted from the engineering of micro-organisms to produce proteins to the engineering of animals and even man. The sense of millenial change expressed when the human genome was first drafted is therefore both genuine and old-established.

Biotechnology↗
PubMed1989

Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.

A computer modeling procedure for assessing the stereochemical suitability of pairs of residues in proteins as potential sites for introduction of cystine disulfide crosslinks has been developed. Residue pairs with C alpha-C alpha distances of less than or equal to 6.5 A and C beta-C beta distances of less than or equal to 4.5 A are chosen for geometrical fixation of S atoms using the program MODIP. The stereochemistry of the modeled disulfides is evaluated using limits for the structural parameters of the various torsion angles and S-S bond length in the disulfide bridge. The ability of the procedure to correctly model disulfides has been checked with examples of cystine peptides of known crystal structures and 103 disulfide bridges from 25 available protein crystal structures determined at less than or equal to 2 A resolution. An analysis of results on three proteins with engineered disulfides, T4 lysozyme, dihydrofolate reductase and subtilisin, is presented. Two positions for the introduction of 'stereochemically optimal' disulfides are identified in subtilisin.

Disulfides↗
PubMed1991

Cost-effectiveness of environmental management for vector control in resource development projects.

Vector control methods are traditionally divided in chemical, biological and environmental management approaches, and this distinction also reflected in certain financial and economic aspects. This is particularly true for environmental modification, usually engineering or other structural works. It is highly capital intensive, as opposed to chemical and biological control which require recurrent expenditures, and discount rates are therefore a prominent consideration in deciding for one or the other approach. Environmental manipulation requires recurrent action, but can often be carried out with the community participation, which raises the issue of opportunity costs. The incorporation of environmental management in resource projects is generally impeded by economic considerations. The Internal Rate of Return continues to be a crucial criterion for funding agencies and development banks to support new projects; at the same time Governments of debt-riden countries in the Third World will do their best to avoid additional loans on such frills as environmental and health safeguards. Two approaches can be recommended to nevertheless ensure the incorporation of environmental management measures in resource projects in an affordable way. First, there are several examples of cases where environmental management measures either have a dual benefit (increasing both agricultural production and reducing vector-borne disease transmission) or can be implemented at zero costs. Second, the additional costs involved in structural modifications can be separated from the project development costs considered in the calculations of the Internal Rate of Return, and financial support can be sought from bilateral technical cooperation agencies particularly interested in environmental and health issues. There is a dearth of information in the cost-effectiveness of alternative vector control strategies in the developing country context. The process of integrating vector control in the general health services will make it even more difficult to gain a clear insight in the matter.

Animals↗
PubMed2002

Photocrosslinkable polyvinyl alcohol hydrogels that can be modified with cell adhesion peptides for use in tissue engineering.

Photoactive polyvinyl alcohol hydrogels (PVA) have been investigated for use as tissue engineering scaffolds. These materials allow in situ polymerization for minimally invasive implantation methods. The mechanical properties of these materials can be tailored for a variety of soft tissue applications. The Young's modulus and ultimate tensile strength of PVA hydrogels are increased with increasing polymer concentration, and highly elastic hydrogels can be formed by altering the number of crosslinkable groups per chain. Fibroblasts homogeneously seeded within 3 mm thick PVA hydrogels remained viable throughout 2 weeks in culture, with no differences in viability across the thickness of the hydrogel. Cells seeded within the PVA hydrogels also produce extracellular matrix proteins, as indicated by the production of hydroxyproline during culture. Intrinsically cell non-adhesive, these PVA hydrogels were functionalized with the cell-adhesive peptide RGDS and found to support the attachment and spreading of fibroblasts in a dose-dependent manner. These results suggest that photopolymerizable PVA hydrogels are promising for tissue engineering applications.

Biocompatible Materials↗
PubMed2003

Physical activity and cancer prevention: animal-tumor models.

PURPOSE: The aims of this paper are to briefly review the types of animal and tumor models used in carcinogenesis studies and to consider their utility in studies of physical activity and cancer. METHODS: Published data from animal studies using tumor models for which corresponding human epidemiologic evidence shows a clear association between physical activity and that cancer (i.e., colon and breast) are reviewed. RESULTS: A variety of animal-tumor models have been used in cancer studies including spontaneous tumors, chemically induced tumors, orthotopic and syngeneic tumor transplantation, injected tumors, and genetically engineered (transgenic, knockout, and mutation-induced) mice with a predisposition to neoplasia. The most commonly used animal-tumor model in the study of physical activity has been the chemical carcinogenesis model. Methodological limitations of the various animal-tumor models are described including variations in dosing, route of administration, and type of carcinogen used, and forced versus voluntary exercise effects. CONCLUSIONS: Animal-tumor models are useful for understanding specific aspects of the carcinogenesis process and the interaction of this process with exercise. There is no one animal-tumor model that is ideally suited for studying physical activity interventions. However, animal-tumor models can be viewed as complementary to epidemiologic studies and human clinical trials in the area of physical activity and cancer prevention.

Animals↗
PubMed2024

Strategies in engineering sustainable biochemical synthesis through microbial systems.

Growing environmental concerns and the urgency to address climate change have increased demand for the development of sustainable alternatives to fossil-derived fuels and chemicals. Microbial systems, possessing inherent biosynthetic capabilities, present a promising approach for achieving this goal. This review discusses the coupling of systems and synthetic biology to enable the elucidation and manipulation of microbial phenotypes for the production of chemicals that can substitute for petroleum-derived counterparts and contribute to advancing green biotechnology. The integration of artificial intelligence with metabolic engineering to facilitate precise and data-driven design of biosynthetic pathways is also discussed, along with the identification of current limitations and proposition of strategies for optimizing biosystems, thereby propelling the field of chemical biology towards sustainable chemical production.

Metabolic Engineering↗
PubMed2006

Protein engineering of formate dehydrogenase.

NAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) is one of the best enzymes for the purpose of NADH regeneration in dehydrogenase-based synthesis of optically active compounds. Low operational stability and high production cost of native FDHs limit their application in commercial production of chiral compounds. The review summarizes the results on engineering of bacterial and yeast FDHs aimed at improving their chemical and thermal stability, catalytic activity, switch in coenzyme specificity from NAD+ to NADP+ and overexpression in Escherichia coli cells.

Amino Acid Sequence↗
PubMedDate not supplied

The occupational physician and chemical disasters: old problem, new threats.

Chemical disasters continue to occur, in spite of significant progress in process engineering, industrial hygiene practices, and improved enforcement of health and safety legislation. In addition to the ever-present risk of unintentional incidents, recent geopolitical events have raised the specter of chemical terrorism. Terrorists or even disgruntled employees may exploit lapses in chemical plant security and ready access to large quantities commodity chemicals, capable of causing great harm to the population if suddenly and unexpectedly released. Occupational physicians, who are uniquely equipped to understand the health hazards associated with industrial chemicals should be involved in prevention of planning for, and response to chemical disasters. Measures for improving preparedness include training and collaboration, not only with plant health and safety personnel but also with public safety and health care providers, through drills and assessment of needs and capacities. Occupational physicians should be aware that communications and other systems often fail in disasters, requiring multiple alternatives. Likewise, occupational health specialists should be prepared to deal with mass casualties, including psychological casualties which may be difficult to distinguish from those of organic etiology. Chemical disaster preparedness is an urgent and demanding responsibility for occupational physicians everywhere.

Decontamination↗
PubMed1999

Combinatorial protein engineering by incremental truncation.

We have developed a combinatorial approach, using incremental truncation libraries of overlapping N- and C-terminal gene fragments, that examines all possible bisection points within a given region of an enzyme that will allow the conversion of a monomeric enzyme into its functional heterodimer. This general method for enzyme bisection will have broad applications in the engineering of new catalytic functions through domain swapping and chemical synthesis of modified peptide fragments and in the study of enzyme evolution and protein folding. We have tested this methodology on Escherichia coli glycinamide ribonucleotide formyltransferase (PurN) and, by genetic selection, identified PurN heterodimers capable of glycinamide ribonucleotide transformylation. Two were chosen for physical characterization and were found to be comparable to the wild-type PurN monomer in terms of stability to denaturation, activity, and binding of substrate and cofactor. Sequence analysis of 18 randomly chosen, active PurN heterodimers revealed that the breakpoints primarily clustered in loops near the surface of the enzyme, that the breaks could result in the deletion of highly conserved residues and, most surprisingly, that the active site could be bisected.

Amino Acid Sequence↗