Evaluation of enzyme inhibitors in drug discovery. A guide for medicinal chemists and pharmacologists.
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Chemistry, Pharmaceutical↗
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Results for “Enzyme discovery”
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A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase.
High throughput screening of microbial DNA libraries was used to identify alpha-amylases with phenotypic characteristics compatible with large scale corn wet milling process conditions. Single and multiorganism DNA libraries originating from various environments were targeted for activity and sequence-based screening approaches. After initial screening, 15 clones were designated as primary hits based upon activity at pH 4.5 or 95 degrees C without addition of endogenous Ca(2+). After further characterization, three enzyme candidates were chosen each with an exceptional expression of one or more aspects of the necessary phenotype: temperature stability, pH optimum, lowered reliance on Ca(2+) and/or enzyme rate. To combine the best aspects of the three phenotypes to optimize process compatibility, the natural gene homologues were used as a parental sequence set for gene reassembly. Approximately 21,000 chimeric daughter sequences were generated and subsets screened using a process-specific, high throughput activity assay. Gene reassembly resulted in numerous improved mutants with combined optimal phenotypes of expression, temperature stability, and pH optimum. After biochemical and process-specific characterization of these gene products, one alpha-amylase with exceptional process compatibility and economics was identified. This paper describes the synergistic approach of combining environmental discovery and laboratory evolution for identification and optimization of industrially important biocatalysts.
Amino Acid Sequence↗
Impact of mechanism-based enzyme inactivation on inhibitor potency: implications for rational drug discovery.
Mechanism-based enzyme inactivators (MBEIs) have unique kinetic actions that make predictions of potency, selectivity, and potential for metabolic drug interactions more complex than for competitive antagonists. We have derived a mathematical relationship that links the influence of substrate concentration and binding constant ([S] and K(m), respectively), inhibitor concentration and binding constant ([I] and K(I), respectively), and inactivation rate constant (k(inact)) to enzyme activity (v) and maximal activity (V(max)) at any time (t). The kinetic behavior of this relationship was validated in murine-macrophage cell cultures using MBEIs of nitric oxide synthase (NOS). This initial equation was also used in the derivation of a new relationship that directly links the kinetic parameters of mechanism-based inactivation to inhibitory potency at a particular time (IC((t))(50)). Using this direct relationship, we observed that the predicted rank inhibitory potency of a series of MBEIs was improved over that predicted by the K(I) parameter alone. These relationships offer a fundamental understanding of the kinetics of MBEI action and may be useful in the evaluation of these compounds during the discovery process.
Cell Line↗
Induction of drug-metabolizing enzymes: a path to the discovery of multiple cytochromes P450.
This article provides a personal account of the discovery of the induced synthesis of drug-metabolizing enzymes and of subsequent research that led to the discovery of multiple cytochromes P450 with different catalytic activities. The manuscript also emphasizes the role of environmental factors (in addition to genetic polymorphisms) in explaining person-to-person and day-to-day differences in rates and pathways of drug metabolism that occur in the human population.
Animals↗
Discovering hidden candidate plastic-degrading enzymes: Combined multi-omics and machine learning strategy.
Plastic pollution poses a major threat to the stability of natural ecosystems as well as human health. Microbial enzymes have long been considered a potential resource for targeted biodegradation but, except for a few successful cases, the discovery of efficient enzymes has proved challenging. Aiming to accelerate the process, we propose an approach combining metagenomics, metatranscriptomics and semi-supervised learning that selects promising plastic-degrading candidate enzymes from the proteome of relevant microorganisms. Tested on a dataset of over 10,000 microbial proteins, ranking models consistently prioritize known plastic-degrading enzymes, achieving an area under the cumulative distribution function curve above 0.96, with leave-one-family-out cross-validation indicating that performance is largely retained across protein families. As a case study, this work focuses on mixed microbial cultures exposed for extended periods to polyethylene, polyethylene terephthalate, and polyurethane substrates. The prevalent species after selective enrichment were functionally characterized, finding Rhodococcus aetherivorans as the most relevant species in two of the five cultures under investigation. Among the top-ranked proteins, several have high structural similarity with known enzymes despite not being identified by sequence similarity search. Moreover, according to metatranscriptomics results, several of these enzymes were found to be expressed at the same level or above that of annotated enzymes, suggesting that they may have functional relevance. Overall, this work highlights the potential of integrating multi-omics with data-driven methods for enzyme discovery and for accelerating the development of biotechnological solutions to plastic pollution.
Biodegradation, Environmental↗
Enzyme models: design and selection.
There are two approaches to the discovery of enzyme mimics, that is identifying molecules that are able to bind substrate(s) and then catalyse reactions. The first approach, often inspired by enzymes themselves, utilises chemical knowledge and experience to design the catalyst. The other approach is to create a library and select the best host of a transition state analogue of the required reaction.
Base Sequence↗
Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase.
Amidohydrolytic reactions in oxidative pyrimidine metabolism were investigated in detail. Barbiturase has been reported to catalyze the amidohydrolysis of barbituric acid to urea and malonic acid. However, purification of the enzyme revealed that it catalyzes the ring-opening of barbituric acid to ureidomalonic acid. The existence of a consecutive enzyme named ureidomalonase, which hydrolyzes ureidomalonic acid to urea and malonic acid, was also discovered during the purification of barbiturase.
Amides↗
Discovery of a novel enzyme, isonitrile hydratase, involved in nitrogen-carbon triple bond cleavage.
Isonitrile containing an N triple bond C triple bond was degraded by microorganism sp. N19-2, which was isolated from soil through a 2-month acclimatization culture in the presence of this compound. The isonitrile-degrading microorganism was identified as Pseudomonas putida. The microbial degradation was found to proceed through an enzymatic reaction, the isonitrile being hydrated to the corresponding N-substituted formamide. The enzyme, named isonitrile hydratase, was purified and characterized. The native enzyme had a molecular mass of about 59 kDa and consisted of two identical subunits. The enzyme stoichiometrically catalyzed the hydration of cyclohexyl isocyanide (an isonitrile) to N-cyclohexylformamide, but no formation of other compounds was detected. The apparent K(m) value for cyclohexyl isocyanide was 16.2 mm. Although the enzyme acted on various isonitriles, no nitriles or amides were accepted as substrates.
Carbon↗
Metabolism of the Raffinose Family Oligosaccharides in Leaves of Ajuga reptans L. (Cold Acclimation, Translocation, and Sink to Source Transition: Discovery of Chain Elongation Enzyme).
Ajuga reptans is a frost-hardy, perennial labiate that is known for its high content of raffinose family oligosaccharide(s) (RFO). Seasonal variations in soluble nonstructural carbohydrate levels in above-ground parts of Ajuga showed that the RFO were by far the most predominant components throughout the whole year. RFO were lowest in summer (75 mg/g fresh weight) and highest in fall/winter (200 mg/g fresh weight), whereas sucrose and starch were only minor components. Cold treatment (14 d at 10/3[deg]C, day/night) of plants that were precultivated under warm conditions (25[deg]C) lowered the temperature optimum of net photosynthesis from 16[deg] to 8[deg]C, decreased the maximum rate, and increased the total nonstructural carbohydrate content of leaves by a factor of about 10, mainly because of an increase of RFO. The degree of polymerization of the RFO increased sequentially up to at least 15. A novel, galactinol-independent galactosyltransferase enzyme was found, forming from two molecules of RFO, the next higher and lower degree of polymerization of RFO. The enzyme had a pH optimum of 4.5 to 5.0 and may be responsible for RFO chain elongation. RFO were the main carbohydrates translocated in the phloem, with stachyose being by far the most dominant form. Studies of carbon balance during leaf development revealed a transition point between import and export at approximately 25% maximal leaf area. RFO synthesis could be detected even before the commencement of export, suggesting the existence of a nonphloem-linked RFO pool even in very young leaves. Taken together, it seems that Ajuga leaves contain two pools of RFO metabolism, a pronounced long-term storage pool in the mesophyll, possibly also involved in frost resistance, and a transport pool in the phloem.
Journal Article↗
[Nobel prize in 1931 for Otto Warburg for discovery of the respiratory enzyme].
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Enzymes↗
Microtiter plate based chemistry and in situ screening: a useful approach for rapid inhibitor discovery.
The use of libraries extracted from nature or constructed by combinatorial chemistry, have been widely appreciated in the drug discovery area. In this perspective, we present our contribution to the field of enzyme inhibitor discovery using a useful approach that allows diversification of a common core in a microtiter plate followed by in situ screening. Our method relies on an organic reaction that is highly selective, high yielding, amenable to the microscale and preferably can be performed in water. The core can be a designed molecule based on the structural and mechanistic information of the target, a compound with a weak binding affinity, or a natural product. Several reactions were found useful for this approach and were applied to the rapid discovery of potent inhibitors of representative enzymes.
Combinatorial Chemistry Techniques↗
Enzymes in the synthesis of bioactive compounds: the prodigious decades.
The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.
Animals↗
Wellcome Trust Award Lecture. Chromatin-modifying enzymes in transcription and cancer.
In recent years, our view of how gene expression is controlled has changed dramatically. The discovery of enzymes that modify histones has revealed that transcription is an enzymically driven process. Such modifications can recruit specific proteins and mediate chromatin changes that affect transcription either positively or negatively. Important biological pathways leading to cell proliferation are under the control of these enzymes, and several of them are found deregulated in cancer. The hope is that chromatin-modifying enzymes will be a rich source of targets for drug discovery.
Acetylesterase↗
Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA.
The discovery of RNA enzymes has, for the first time, provided a single molecule that has both genetic and catalytic properties. We have devised techniques for the mutation, selection and amplification of catalytic RNA, all of which can be performed rapidly in vitro. Here we describe how these techniques can be integrated and performed repeatedly within a single reaction vessel. This allows evolution experiments to be carried out in response to artificially imposed selection constraints. We worked with the Tetrahymena ribozyme, a self-splicing group I intron derived from the large ribosomal RNA precursor of Tetrahymena thermophila that catalyses sequence-specific phosphoester transfer reactions involving RNA substrates. It consists of 413 nucleotides, and assumes a well-defined secondary and tertiary structure responsible for its catalytic activity. We selected for variant forms of the enzyme that could best react with a DNA substrate. This led to the recovery of a mutant form of the enzyme that cleaves DNA more efficiently than the wild-type enzyme. The selected molecule represents the discovery of the first RNA enzyme known to cleave single-stranded DNA specifically.
Animals↗
Recent advances in the understanding of the biological chemistry of manganese.
Developments in manganese biochemistry have centered on the discovery of new manganese enzymes, X-ray analysis of binuclear manganese enzymes, and the discovery of new spectroscopic signatures for the oxygen-evolving complex. Despite these gains, many questions regarding the structure, composition and redox state of the oxygen-evolving complex remain unanswered.
Arginase↗
A trans-acting regulatory mutation that causes overproduction of phosphatidylserine synthase in Escherichia coli.
We have isolated three mutants of Escherichia coli which have elevated levels of the phospholipid synthetic enzyme phosphatidylserine synthase. One of these strains carries a mutation, designated pssR1, which maps near minute 84 of the chromosome, distinct from the synthase structural gene (pss) at minute 56. The pssR1 mutation causes selective overproduction of phosphatidylserine synthase, since the levels of six other lipid synthetic enzymes are unaltered. The specific activity of the synthase in crude cell extracts of mutants harboring pssR1 is about five times greater than wild type. The synthase can also be overproduced 10-fold in wild type strains with hybrid ColE1 plasmids carrying the synthase structural gene (pss). A pssR1 mutant harboring such a pss plasmid overproduces the synthase about 50-fold. This multiplicative interaction of pssR1 and cloned pss demonstrates that pssR1 is trans-acting. The synthase has been purified in parallel from pssR1 and pssR+ strains. The pssR1 mutant yields more total synthase protein than pssR+, but the pure enzyme has the same specific activity in both cases. Therefore, pssR1 acts by increasing the amount of the normal protein, not by activating the enzyme. The discovery of pssR shows that there are regulatory loci which control the production of enzymes involved in membrane lipid synthesis.
CDPdiacylglycerol-Serine O-Phosphatidyltransferase↗
A long-range ordered structure in mitochondrial cristae revealed by a pathological structural modification.
An experimentally imposed 6-hr local ischemia in the anterior wall of the left ventricle in dog hearts leads to a structural modification of the mitochondria in the posterior wall with the cristae revealing a zig-zag pattern when viewed in cross sections. This pattern was found to reveal a change in the distribution of crista mass with an increase of mass at circumscribed regions in each crista membrane and a reduction of mass from the surrounding region in each crista membrane. The accumulation of mass contributed to the elevations that caused the zig-zag pattern. These elevations were distributed according to a tetragonal pattern with a periodicity of 850 A. The tetragonal pattern contributed by one crista membrane was translocated halfway along the diagonals of the tetrameric pattern of the other crista membrane within each crista. The change in mass distribution reveals differences in the strength of bonds that account for binding of the proteins to the cristae with strong bonds in the elevated regions, while enzymes less firmly bound are located in the surrounding region. The respiratory chain enzymes will then be located in the elevated regions and the soluble enzymes including the tricarboxylic acid cycle enzymes will be located in the surrounding region. The tissue in the posterior wall was functionally impaired and normal function was restored when substrate for oxidative phosphorylation was added to the blood perfusing the tissue. It is concluded that the functional impairment is a consequence of a partial breakdown of the structural organization of the tricarboxylic acid cycle enzymes. The discovery of a long-range structural order involving the entire cristae reveals that the enzymes of the multienzyme systems as well as those systems in the cristae are structurally highly organized and it excludes that the enzymes are randomly mixed and highly mobile.
Animals↗
Molecular docking studies of natural cholinesterase-inhibiting steroidal alkaloids from Sarcococca saligna.
Alkaloids isolated from Sarcococca saligna significantly inhibit acetyl- and butyrylcholinesterase enzyme, suggesting discovery of inhibitors for nervous-system disorders. Studying interactions with the active site of the AChE enzyme from Torpedo californica, we have identified hydrophobic interactions inside the aromatic gorge area as the major stabilizing factor in enzyme-inhibitor complexes of these alkaloids. Molecular Dynamics simulation of a predicted complex indicates that ligand binding does not extensively alter enzyme structure, but reduces flexibility at the gorge.
Acetylcholinesterase↗