scholarly journals Exploration of the active site of β4GalT7: modifications of the aglycon of aromatic xylosides

2015 ◽  
Vol 13 (11) ◽  
pp. 3351-3362 ◽  
Author(s):  
Anna Siegbahn ◽  
Karin Thorsheim ◽  
Jonas Ståhle ◽  
Sophie Manner ◽  
Christoffer Hamark ◽  
...  
Keyword(s):  
Active Site ◽  
Essential Enzyme ◽  
Anomeric Center

β4GalT7 is an essential enzyme in the biosynthesis of glycosaminoglycans. Modifications at the anomeric center of aromatic xylosides change the galactosylation efficiency significantly.

scholarly journals Rules for priming and inhibition of glycosaminoglycan biosynthesis; probing the β4GalT7 active site

2014 ◽  
Vol 5 (9) ◽  
pp. 3501-3508 ◽  
Author(s):  
Anna Siegbahn ◽  
Sophie Manner ◽  
Andrea Persson ◽  
Emil Tykesson ◽  
Karin Holmqvist ◽  
...  
Keyword(s):  
Active Site ◽  
Essential Enzyme

Xylose is the optimal substrate for β4GalT7, an essential enzyme in GAG biosynthesis, but analogs act as effective inhibitors.

scholarly journals IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

2020 ◽  
Author(s):  
Heba Hashem
Keyword(s):  
Active Site ◽  
Life Cycles ◽  
High Binding Energy ◽  
Protease Inhibition ◽  
Enzyme Active Site ◽  
Therapeutic Drugs ◽  
Main Protease ◽  
The World ◽  
Essential Enzyme ◽  
The Way

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M<sup>pro</sup> ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

scholarly journals Enzymatic reconstitution of ribosomal peptide backbone thioamidation

2018 ◽  
Vol 115 (12) ◽  
pp. 3030-3035 ◽  
Author(s):  
Nilkamal Mahanta ◽  
Andi Liu ◽  
Shihui Dong ◽  
Satish K. Nair ◽  
Douglas A. Mitchell
Keyword(s):  
Posttranslational Modifications ◽  
Active Site ◽  
Methanogenic Archaea ◽  
Methanosarcina Acetivorans ◽  
Binding Studies ◽  
Peptide Backbone ◽  
Α Subunit ◽  
Essential Enzyme ◽  
Methanopyrus Kandleri

Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans. Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii. Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri. Sequence and structure-guided mutagenesis with subsequent biochemical evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O-phosphorylation. These data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.

scholarly journals Phenothiazines as dual inhibitors of SARS-CoV-2 main protease and COVID-19 inflammation

2021 ◽  
Author(s):  
Katrina L Forrestall ◽  
Darcy E Burley ◽  
Meghan Kirsten Cash ◽  
Ian Pottie ◽  
Sultan Darvesh
Keyword(s):  
Viral Replication ◽  
Active Site ◽  
Acute Infection ◽  
Binding Energies ◽  
Neurotransmitter Receptors ◽  
Main Protease ◽  
Dual Action ◽  
Inhibition Constants ◽  
Anti Inflammatory ◽  
Essential Enzyme

COVID-19, caused by the severe acute respiratory coronavirus 2 (SARS-CoV-2) currently has no treatment for acute infection. The main protease (Mpro) of SARS-CoV-2 is an essential enzyme for viral replication and an attractive target for disease intervention. The phenothiazine moiety has demonstrated drug versatility for biological systems, including inhibition of butyrylcholinesterase, a property important in the cholinesterase anti-inflammatory cascade. Nineteen phenothiazine drugs were investigated using in silico modelling techniques to predict binding energies and inhibition constants (Ki values) with SARS-CoV-2 Mpro. Since most side-effects of phenothiazines are due to interactions with various neurotransmitter receptors and transporters, phenothiazines with few such interactions were also investigated. All compounds were found to bind to the active site of SARS-CoV-2 Mpro and showed Ki values ranging from 1.30 to 52.4 µM. Nine phenothiazines showed inhibition constants <10 µM. The compounds with limited interactions with neurotransmitter receptors and transporters showed micromolar (µM) Ki values. Docking results were compared with remdesivir and showed similar interactions with key residues Glu-166 and Gln-189 in the active site. This work has identified several phenothiazines with limited neurotransmitter receptor and transporter interactions and that may provide the dual action of inhibiting SARS-CoV-2 Mpro to prevent viral replication and promote the release of anti-inflammatory cytokines to curb viral-induced inflammation. These compounds are promising candidates for further investigation against SARS-CoV-2.

A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway

2014 ◽  
Vol 70 (12) ◽  
pp. 3244-3252 ◽  
Author(s):  
Alexander G. Pavlovsky ◽  
Bharani Thangavelu ◽  
Pravin Bhansali ◽  
Ronald E. Viola
Keyword(s):  
Active Site ◽  
Enzyme Inhibitor ◽  
Bacterial Survival ◽  
Cautionary Tale ◽  
Lead Compounds ◽  
Semialdehyde Dehydrogenase ◽  
Fragment Library ◽  
Aspartate Pathway ◽  
Essential Enzyme

The aspartate pathway is essential for the production of the amino acids required for protein synthesis and of the metabolites needed in bacterial development. This pathway also leads to the production of several classes of quorum-sensing molecules that can trigger virulence in certain microorganisms. The second enzyme in this pathway, aspartate β-semialdehyde dehydrogenase (ASADH), is absolutely required for bacterial survival and has been targeted for the design of selective inhibitors. Fragment-library screening has identified a new set of inhibitors that, while they do not resemble the substrates for this reaction, have been shown to bind at the active site of ASADH. Structure-guided development of these lead compounds has produced moderate inhibitors of the target enzyme, with some selectivity observed between the Gram-negative and Gram-positive orthologs of ASADH. However, many of these inhibitor analogs and derivatives have not yet achieved the expected enhanced affinity. Structural characterization of these enzyme–inhibitor complexes has provided detailed explanations for the barriers that interfere with optimal binding. Despite binding in the same active-site region, significant changes are observed in the orientation of these bound inhibitors that are caused by relatively modest structural alterations. Taken together, these studies present a cautionary tale for issues that can arise in the systematic approach to the modification of lead compounds that are being used to develop potent inhibitors.

scholarly journals Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography

2020 ◽  
Vol 295 (50) ◽  
pp. 17365-17373 ◽  
Author(s):  
Daniel W. Kneller ◽  
Gwyndalyn Phillips ◽  
Kevin L. Weiss ◽  
Swati Pant ◽  
Qiu Zhang ◽  
...  
Keyword(s):  
Active Site ◽  
Direct Determination ◽  
Catalytic Site ◽  
Amino Acid Residues ◽  
Critical Question ◽  
Main Protease ◽  
Neutron Structure ◽  
Active Site Cavity ◽  
Ionizable Residues ◽  
Essential Enzyme

The main protease (3CL Mpro) from SARS–CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease. We observe that the catalytic site natively adopts a zwitterionic reactive form in which Cys145 is in the negatively charged thiolate state and His41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged. The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen-bonding networks in the active-site cavity and at the dimer interface. The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature. Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

scholarly journals Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance

2020 ◽  
Vol 295 (51) ◽  
pp. 17514-17534
Author(s):  
Jūrate˙ Fahrig-Kamarauskait≑ ◽  
Kathrin Würth-Roderer ◽  
Helen V. Thorbjørnsrud ◽  
Susanne Mailand ◽  
Ute Krengel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
High Activity ◽  
Active Site ◽  
Shikimate Pathway ◽  
Catalytic Efficiency ◽  
Chorismate Mutase ◽  
Full Potential ◽  
Evolutionary Trajectories ◽  
Essential Enzyme

Chorismate mutase (CM), an essential enzyme at the branch-point of the shikimate pathway, is required for the biosynthesis of phenylalanine and tyrosine in bacteria, archaea, plants, and fungi. MtCM, the CM from Mycobacterium tuberculosis, has less than 1% of the catalytic efficiency of a typical natural CM and requires complex formation with 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase for high activity. To explore the full potential of MtCM for catalyzing its native reaction, we applied diverse iterative cycles of mutagenesis and selection, thereby raising kcat/Km 270-fold to 5 × 105m−1s−1, which is even higher than for the complex. Moreover, the evolutionarily optimized autonomous MtCM, which had 11 of its 90 amino acids exchanged, was stabilized compared with its progenitor, as indicated by a 9 °C increase in melting temperature. The 1.5 Å crystal structure of the top-evolved MtCM variant reveals the molecular underpinnings of this activity boost. Some acquired residues (e.g. Pro52 and Asp55) are conserved in naturally efficient CMs, but most of them lie beyond the active site. Our evolutionary trajectories reached a plateau at the level of the best natural enzymes, suggesting that we have exhausted the potential of MtCM. Taken together, these findings show that the scaffold of MtCM, which naturally evolved for mediocrity to enable inter-enzyme allosteric regulation of the shikimate pathway, is inherently capable of high activity.

scholarly journals IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

2020 ◽  
Author(s):  
Heba Hashem
Keyword(s):  
Active Site ◽  
Life Cycles ◽  
High Binding Energy ◽  
Protease Inhibition ◽  
Enzyme Active Site ◽  
Therapeutic Drugs ◽  
Main Protease ◽  
The World ◽  
Essential Enzyme ◽  
The Way

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M<sup>pro</sup> ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

scholarly journals IN Silico Approach of Some Selected Honey Constituents as SARS-CoV-2 Main Protease (COVID-19) Inhibitors

2020 ◽  
Author(s):  
Heba Hashem
Keyword(s):  
Active Site ◽  
Life Cycles ◽  
High Binding Energy ◽  
Protease Inhibition ◽  
Enzyme Active Site ◽  
Therapeutic Drugs ◽  
Main Protease ◽  
The World ◽  
Essential Enzyme ◽  
The Way

<p>The huge attack of coronavirus disease 2019 (COVID-19) over all the world forces the researcher around the world to study the crystal structure of the main protease M<sup>pro</sup> ( 3-chymotrypsin-like cysteine enzyme) which is the essential enzyme for coronavirus processing the polyproteins and its life cycles. And by the way, the inhibition of this enzyme active site becomes the target of all scientists of drug discovery in order to overcome this disease. In this study, we have used the molecular modeling approach to evaluate the activity of different active compounds from honeybee and propolis to inhibit the presented sars-cov-2 main protease via Schrödinger Maestro v10.1. the presented study resulted in six main compounds possess high binding energy with the receptor active site of COVID-19 main protease. we hope this study being the way for honeybee constitution as an effective ligand for sars-cov-2 main protease inhibition and be in the medicinal study of anti-COVID-19 therapeutic drugs.</p>

Structures of SAICAR synthetase (PurC) fromStreptococcus pneumoniaewith ADP, Mg2+, AIR and Asp

2014 ◽  
Vol 70 (3) ◽  
pp. 841-850 ◽  
Author(s):  
Nina M. Wolf ◽  
Celerino Abad-Zapatero ◽  
Michael E. Johnson ◽  
Leslie W.-M. Fung
Keyword(s):  
Streptococcus Pneumoniae ◽  
Active Site ◽  
De Novo ◽  
Multidrug Resistant ◽  
Metabolic Enzyme ◽  
Antibacterial Drug ◽  
Biosynthesis Pathway ◽  
Essential Enzyme ◽  
Bacterial Replication ◽  
Model Structures

Streptococcus pneumoniaeis a multidrug-resistant pathogen that is a target of considerable interest for antibacterial drug development. One strategy for drug discovery is to inhibit an essential metabolic enzyme. The seventh step of thede novopurine-biosynthesis pathway converts carboxyaminoimidazoleribonucleotide (CAIR) and L-aspartic acid (Asp) to 4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR) in the presence of adenosine 5′-triphosphate (ATP) using the enzyme PurC. PurC has been shown to be conditionally essential for bacterial replication. Two crystal structures of this essential enzyme fromStreptococcus pneumoniae(spPurC) in the presence of adenosine 5′-diphosphate (ADP), Mg2+, aminoimidazoleribonucleotide (AIR) and/or Asp have been obtained. This is the first structural study ofspPurC, as well as the first of PurC from any species with Asp in the active site. Based on these findings, two model structures are proposed for the active site with all of the essential ligands (ATP, Mg2+, Asp and CAIR) present, and a relay mechanism for the formation of the product SAICAR is suggested.

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