EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature

Abstract Addition of chemical structural information in enzymatic reactions has proven to be significant for accurate enzyme function prediction. However, such chemical data lack systematic feature mining and hardly exist in enzyme-related databases. Therefore, global mining of enzymatic reactions will offer a unique landscape for researchers to understand the basic functional mechanisms of natural bioprocesses and facilitate enzyme function annotation. Here, we established a new knowledge base called EnzyMine, through which we propose to elucidate enzymatic reaction features and then link them with sequence and structural annotations. EnzyMine represents an advanced database that extends enzyme knowledge by incorporating reaction chemical feature strategies, strengthening the connectivity between enzyme and metabolic reactions. Therefore, it has the potential to reveal many new metabolic pathways involved with given enzymes, as well as expand enzyme function annotation. Database URL: http://www.rxnfinder.org/enzymine/

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Ultrasound promotes enzymatic reactions by acting on different targets: Enzymes, substrates and enzymatic reaction systems

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2018.07.133 ◽

2018 ◽

Vol 119 ◽

pp. 453-461 ◽

Cited By ~ 26

Author(s):

Danli Wang ◽

Lufeng Yan ◽

Xiaobin Ma ◽

Wenjun Wang ◽

Mingming Zou ◽

...

Keyword(s):

Enzymatic Reaction ◽

Enzymatic Reactions ◽

Reaction Systems

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Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555218759267 ◽

2018 ◽

Vol 23 (6) ◽

pp. 561-573 ◽

Cited By ~ 7

Author(s):

Martin Winter ◽

Tom Bretschneider ◽

Carola Kleiner ◽

Robert Ries ◽

Jörg P. Hehn ◽

...

Keyword(s):

Drug Discovery ◽

High Throughput Screening ◽

Tyrosine Phosphatase ◽

Enzymatic Reaction ◽

Enzymatic Reactions ◽

Label Free ◽

Ionization Time ◽

Maldi Tof ◽

Ptp1b Inhibitors ◽

Promising Perspective

Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.

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Cross-diffusion induced patterns for a single-step enzymatic reaction

Communications Physics ◽

10.1038/s42005-020-00427-w ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Giovanni Giunta ◽

Hamid Seyed-Allaei ◽

Ulrich Gerland

Keyword(s):

Enzymatic Reaction ◽

Single Step ◽

Enzymatic Reactions ◽

Transport Models ◽

Transport Dynamics ◽

Cross Diffusion ◽

Enzyme Transport ◽

Apparent Diffusion ◽

Enzyme Distribution ◽

Competing Models

Abstract Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for these transport dynamics. Here, we use mathematical modeling and numerical simulations to analyze whether the enzymatic reactions can generate a significant feedback from enzyme transport onto the substrate profile. We find that this feedback can generate spontaneous spatial patterns in the enzyme distribution, with just a single-step catalytic reaction. However, patterns are formed only for a subclass of transport models. For such models, nonspecific repulsive interactions between the enzyme and the substrate, or attractive interactions between the enzyme and the product, cause the enzyme to accumulate in regions of low substrate concentration. Reactions then amplify local substrate and product fluctuations, causing enzymes to further accumulate where substrate is low. Experimental analysis of this pattern formation process could discriminate between different transport models.

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A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution

IUCrJ ◽

10.1107/s2052252516016304 ◽

2016 ◽

Vol 3 (6) ◽

pp. 393-401 ◽

Cited By ~ 11

Author(s):

Robin Schubert ◽

Svetlana Kapis ◽

Yannig Gicquel ◽

Gleb Bourenkov ◽

Thomas R. Schneider ◽

...

Keyword(s):

Data Collection ◽

Radiation Damage ◽

Temporal Resolution ◽

Diffraction Data ◽

Structural Changes ◽

Structural Information ◽

Data Sets ◽

Enzymatic Reactions ◽

Time Resolved ◽

Site Specific

Many biochemical processes take place on timescales ranging from femtoseconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach forin situcrystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.

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PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720014420013 ◽

2014 ◽

Vol 12 (06) ◽

pp. 1442001 ◽

Cited By ~ 5

Author(s):

Masaaki Kotera ◽

Yosuke Nishimura ◽

Zen-Ichi Nakagawa ◽

Ai Muto ◽

Yuki Moriya ◽

...

Keyword(s):

Enzyme Commission ◽

Enzymatic Reaction ◽

Enzymatic Reactions ◽

Orthologous Genes ◽

Actual Usage ◽

Effective Implementation ◽

Reaction Characteristics ◽

The Given ◽

Encoding Genes ◽

Reaction Equations

Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

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EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

10.33774/chemrxiv-2021-jxxbh-v2 ◽

2021 ◽

Author(s):

Esther Heid ◽

Samuel Goldman ◽

Karthik Sankaranarayanan ◽

Connor W. Coley ◽

Christoph Flamm ◽

...

Keyword(s):

Expert Knowledge ◽

Enzymatic Reaction ◽

Software Tool ◽

Optimal Number ◽

Data Driven ◽

Enzymatic Reactions ◽

Hasse Diagrams ◽

Large Databases ◽

Rule Sets ◽

The Given

Data-driven computer-aided synthesis planning utilizing organic or biocatalyzed reactions from large databases has gained increasing interest in the last decade, sparking the development of numerous tools to extract, apply and score general reaction templates. The generation of reaction rules for enzymatic reactions is especially challenging, since substrate promiscuity varies between enzymes, causing the optimal levels of rule specificity and optimal number of included atoms to differ between enzymes. This complicates an automated extraction from databases and has promoted the creation of manually curated reaction rule sets. Here we present EHreact, a purely data-driven open-source software tool to extract and score reaction rules from sets of reactions known to be catalyzed by an enzyme at appropriate levels of specificity without expert knowledge. EHreact extracts and groups reaction rules into tree-like structures, Hasse diagrams, based on common substructures in the imaginary transition structures. Each diagram can be utilized to output a single or a set of reaction rules, as well as calculate the probability of a new substrate to be processed by the given enzyme by inferring information about the reactive site of the enzyme from the known reactions and their grouping in the template tree. EHreact heuristically predicts the activity of a given enzyme on a new substrate, outperforming current approaches in accuracy and functionality.

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Catalytic Active Hollow Fiber Membranes with an Enzyme-embedded MOF Coating

10.31224/osf.io/xdphy ◽

2020 ◽

Author(s):

Matthias Wessling

Keyword(s):

Enzymatic Activity ◽

Hollow Fiber ◽

Enzyme Stability ◽

Hollow Fiber Membrane ◽

Continuous Process ◽

Enzymatic Reaction ◽

Convective Transport ◽

Enzymatic Reactions ◽

Active Centers ◽

Selective Coating

Enzymatic reactions have the potential to enable a greener production of chemicals and pharmaceuticals. Enzyme stability, -recycling, and the implementation into a continuous process are vital points for the commercial success of enzymatic reactions. Recent publications revealed the suitability of Metal-Organic Frameworks (MOFs) as an enzyme immobilization matrix, with increased physiochemical stability. However, the separation of these enzyme MOFs and the additional transport resistances are still challenging. We report for the first time the in-situ biomineralization of enzymes into MOF structures via interfacial crystallization. This method proves to be effective for the selective coating of porous polymeric hollow fibers in a straightforward one-step process. We produced well adhering and stable enzyme embedded MOF layers with high enzymatic activity. The fusion of the enzymatic active layer and the hollow fiber membrane enables the continuous enzymatic reaction by the combination of permeation and reaction. The results show the successful improvement of the enzymatic activity due to the convective transport of educts and products to the enzymatic active centers during permeation.

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Further Insight into Polycyclization Cascades of Acyclic Geranylfarnesol and its Acetate by Squalene-hopene Cyclase from Alicyclobacillus Acidocaldarius

Natural Product Communications ◽

10.1177/1934578x1601100207 ◽

2016 ◽

Vol 11 (2) ◽

pp. 1934578X1601100

Author(s):

Jun Cheng ◽

Chiaki Nakano ◽

Guang Lu Shi ◽

Tsutomu Hoshino

Keyword(s):

Double Bond ◽

Enzymatic Reaction ◽

High Yield ◽

Enzymatic Reactions ◽

Terminal Double Bond ◽

Tricyclic Compounds ◽

Acetyl Group ◽

Alicyclobacillus Acidocaldarius ◽

Insight Into

The enzymatic reactions of geranylfarnesol (8) and its acetate 9, classified as sesterterpenes (C25), using squalene-hopene cyclase (SHC) were investigated. The enzymatic reaction of 8 afforded 6/6-fused bicyclic 20, 6/6/6-fused tricyclic 21, and 6/6/6/6-fused tetracyclic compounds 22 and 23 as the main products (35% yield), whereas that of 9 afforded two 6/6/6-fused tricyclic compounds 24 and 25 in a high yield (76.3%) and a small amount (5.0%) of 26 (the acetate of 22). A significantly higher conversion of 9 indicates that the arrangement of the substrate in the reaction cavity changed. The lipophilic nature and/or the bulkiness of the acetyl group may have changed its binding with SHC, thus placing the terminal double bond of 9 in the vicinity of the DXDD motif of SHC, which is responsible for the proton attack on the double bond to initiate the polycyclization reaction. The results obtained for 8 are different to some extent than those reported by Shinozaki et al. The products obtained in this study were deprotonated compounds; however, the products reported by Shinozaki et al. were hydroxylated compounds.

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Implementation of an Enzyme Membrane Reactor to Intensify the α-O-Glycosylation of Resveratrol Using Cyclodextrins

Pharmaceuticals ◽

10.3390/ph14040319 ◽

2021 ◽

Vol 14 (4) ◽

pp. 319

Author(s):

Irina Ioannou ◽

Eduardo Barboza ◽

Gaëlle Willig ◽

Thomas Marié ◽

Andreïa Texeira ◽

...

Keyword(s):

Membrane Reactor ◽

Enzymatic Reaction ◽

Reaction Medium ◽

Polymeric Membrane ◽

Partial Hydrolysis ◽

Enzymatic Reactions ◽

Solubility In Water ◽

Recent Developments ◽

Hydrolysis Of ◽

Enzymatic Membrane

The O-glycosylation of resveratrol increases both its solubility in water and its bioavailability while preventing its oxidation, allowing a more efficient use of this molecule as a bioactive ingredient in pharmaceutical and cosmetic applications. Resveratrol O-glycosides can be obtained by enzymatic reactions. Recent developments have made it possible to selectively obtain resveratrol α-glycosides from the β-cyclodextrin–resveratrol complex in water with a yield of 35%. However, this yield is limited by the partial hydrolysis of the resveratrol glycosides produced during the reaction. In this study, we propose to intensify this enzymatic reaction by coupling the enzymatic reactor to a membrane process. Firstly, membrane screening was carried out at the laboratory scale and led to the choice of a GE polymeric membrane with a cut-off of 1 kDa. This membrane allowed the retention of 65% of the β-cyclodextrin–resveratrol complex in the reaction medium and the transfer of 70% of the resveratrol α-O-glycosides in the permeate. In a second step, this membrane was used in an enzymatic membrane reactor and improved the yield of the enzymatic glycosylation up to 50%.

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Organophosphorus pesticides stress deranged kinetic values of a few midgut carbohydrases of naiad of Trithemis aurora (burm.) (Odonata: Libellulidae)

International Journal of Agricultural Invention ◽

10.46492/ijai/2016.1.2.6 ◽

2016 ◽

Vol 1 (02) ◽

pp. 155-160

Author(s):

Shekhar Chand

Keyword(s):

Substrate Concentration ◽

Initial Velocity ◽

Ph Value ◽

Organophosphorus Pesticides ◽

Enzymatic Reaction ◽

Organophosphorus Pesticide ◽

Enzymatic Reactions ◽

Reaction Velocity ◽

Straight Line ◽

Maximum Reaction

The 40 Hrs. treatment of last instar naiad of Trithemis aurora (Burm.) in Chlorphyriphos and Quinalphos pesticides concentrations (LC50 = 5.12 ×10-7 ppm and 7.6 × 10-8 ppm) has shown significant variations in the enzyme kinetic parameters and arrested the enzymatic activity in the midgut tissue of last instar naiad of T. aurora causing deleterious effect on various carbohydrases at standard temp. and pH value. The midgut amylase ( μ and β amylase) showed the change in the velocity of enzymatic reaction under LC50 conc. of chlorpyriphos. The data of initial velocity and substrate concentration were processed to achieve their reciprocal values. These values were plotted and a characteristic Lineweaver Burke straight line was observed from the graph and values of maximum reaction velocity (Vmax) and Michaelis Menten constants (km) were assessed. The present organophosphorus pesticide showed an inhibitory impact on midgut amylase reaction velocity. The double reciprocal plot of initial velocity and substrate concentration after exposing the enzyme under LC50 conc. of chlorphyriphos resulted in varied Vmax and Km. values. These carbohydrase on treatment with LC50 conc. of chlorphyriphos showed an inhibitory change in the reaction velocity. The 1/V and 1/S values were plotted to achieve a characteristic Lineweaver – Burke pattern of Vmax and km values obtained as 5.0 × 10-2 [M] and 2.0 under LC50 chlorphyriphos stress for α amylase. The km and Vmax values were obtained from 0.625 × 10-3 [M] to 1.25 × 10-2 [M] for various other midgut carbohydrases with Vmax value obtained from 0.28 to 5.0 under chlorpyriphos stress. The Quinalphos inhibited the enzymatic efficiencies of various carbohydrases severely and changed Km and Vmax values were found under the pesticidal stress and found as potent uncompetitive inhibitor for enzymes as values compared to the controlled enzymatic reactions by deranging the kinetic values. The Km values determined as on 1/V and 1/S basis found deranged from 1.66 × 10-3 [M] to 10 × 10-2 [M]. The Vmax values were found in a range of 0.41 to 3.3 under LC50 Quinalphos stress for midgut hydrolases. The analysis of enzymec kinetic values revealed the great inhibitory and deranged activities of various carbohydrases under both the pesticide constrain. The present toxicants were found to change the enzymatic velocity negatively. The LC50 concentrations of these toxicants were sufficient to inhibit the activity of present hydrolases as α and β amylase, α glucosidase, α galactosidase, β galactosidase, β frictosidase and α trehalase obtaining a meaningful Lineweaver – Burke line of plotted reciprocals of data of reaction velocity and substrate concentration.

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