scholarly journals Mutation of Tyr137 of the universalEscherichia colifimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding

IUCrJ ◽  
2017 ◽  
Vol 4 (1) ◽  
pp. 7-23 ◽  
Author(s):  
Said Rabbani ◽  
Eva-Maria Krammer ◽  
Goedele Roos ◽  
Adam Zalewski ◽  
Roland Preston ◽  
...  
Keyword(s):  
Ethylenediaminetetraacetic Acid ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Lectin Domain ◽  
E Coli ◽  
Ligand Free ◽  
Mannose Binding ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Dynamics Simulations

The most prevalent diseases manifested byEscherichia coliare acute and recurrent bladder infections and chronic inflammatory bowel diseases such as Crohn's disease.E. coliclinical isolates express the FimH adhesin, which consists of a mannose-specific lectin domain connectedviaa pilin domain to the tip of type 1 pili. Although the isolated FimH lectin domain has affinities in the nanomolar range for all high-mannosidic glycans, differentiation between these glycans is based on their capacity to form predominantly hydrophobic interactions within the tyrosine gate at the entrance to the binding pocket. In this study, novel crystal structures of tyrosine-gate mutants of FimH, ligand-free or in complex with heptyl α-D-O-mannopyranoside or 4-biphenyl α-D-O-mannopyranoside, are combined with quantum-mechanical calculations and molecular-dynamics simulations. In the Y48A FimH crystal structure, a large increase in the dynamics of the alkyl chain of heptyl α-D-O-mannopyranoside attempts to compensate for the absence of the aromatic ring; however, the highly energetic and stringent mannose-binding pocket of wild-type FimH is largely maintained. The Y137A mutation, on the other hand, is the most detrimental to FimH affinity and specificity: (i) in the absence of ligand the FimH C-terminal residue Thr158 intrudes into the mannose-binding pocket and (ii) ethylenediaminetetraacetic acid interacts strongly with Glu50, Thr53 and Asn136, in spite of multiple dialysis and purification steps. Upon mutation, pre-ligand-binding relaxation of the backbone dihedral angles at position 137 in the tyrosine gate and their coupling to Tyr48viathe interiorly located Ile52 form the basis of the loss of affinity of the FimH adhesin in the Y137A mutant.

Developing a Model to Study Commensal Translocation during IBD

2018 ◽  
Author(s):  
Kathy Yu
Keyword(s):  
Bacterial Translocation ◽  
Imaging Techniques ◽  
Coli Strain ◽  
The Body ◽  
Conjugation System ◽  
E Coli ◽  
Normal Microbiota ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Future Work

Inflammatory bowel diseases (IBD) is severe inflammation of the gastrointestinal tract. This can lead to a breakdown of mucosal barriers, causing dissemination of commensal bacteria throughout the body. To better understand bacterial translocation during IBD, aim to develop a fluorescent microbiota in mice that we can interrogate using live imaging techniques.   Our preliminary experiments depleted commensals using broad-spectrum antibiotics,  and replaced these microbiota with a fluorescent E. coli strain. The length of time that E.coli stays in the mice gut were monitored. We show that E. coli can persist in the ‘germ-free’ mouse gut for at least 21 days; control mice lose all added E. coli by 8-14 days. The establishment of the E. coli colony suggests this could be a reasonable model to study bacterial translocation.  We are currently going to treat the colonized mice with DSS to induce colitis, and then to study translocation of E. coli by intravital microscopy. Considering E. coli is only a fraction of the normal microbiota and perhaps not a relevant model, future work aims at making a fluorescent microbiota consisting of multiple endogenous murine microbes. This will entail the use of a bacterial conjugation system  capable of ubiquitously transforming many microbial species.  

scholarly journals Computational Drug Repurposing Studies on the ACE2-Spike (RBD) Interface of SARS-CoV-2

2020 ◽  
Author(s):  
Vinod Jani ◽  
Shruti Koulgi ◽  
Mallikarjunachari Uppuladinne V N ◽  
Uddhavesh Sonavane ◽  
Rajendra Joshi
Keyword(s):  
Transmembrane Protein ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Drug Binding ◽  
Tinospora Cordifolia ◽  
Strong Interactions ◽  
Angiotensin Converting Enzyme 2 ◽  
Ligand Free ◽  
Novel Coronavirus ◽  
Dynamics Simulations

<p>The novel coronavirus is known to enter the cell by binding to the human transmembrane protein Angiotensin-Converting Enzyme 2 (ACE2). The S(Spike)-glycoprotein of the SARS-CoV-2 forms a complex with the ACE2. Thus, the S-glycoprotein is one of the hot targets, as it forms the first line of contact between the virus and the human cell. Drug repurposing would help in identifying drugs that are safe and have no or fewer side effects. Hence, in addition to the Food and Drug Administration (FDA) approved molecules the compounds from natural sources were also considered. The current study includes docking and simulations of the FDA approved molecules and phytochemicals from Indian medicinal plants, targeting the ACE2-Spike protein complex. Rutin DAB10 and swertiapuniside were obtained as the top-ranked drugs from these two databases, respectively. The molecular dynamics simulations of ligand-free, rutin DAB10-bound, and swertiapuniside-bound ACE2-Spike complex revealed crucial ACE2-Spike interface residues forming strong interactions with the two ligands molecules. This may infer, that they may affect the ACE2 and spike binding. The conformational flexibility in the drug-binding pocket was captured using the RMSD-based clustering of the ligand-free simulations. An ensemble docking was performed wherein the two databases were docked on each of the representatives of ACE2-Spike obtained through clustering. The potential phytochemicals identified belonged to <i>Withania somnifera, Swertia chirayita, Tinospora cordifolia, Andrographis paniculata, Piper longum, and Azadirachta indica</i>. The FDA molecules identified were rutin DAB10, fulvestrant, cefoperazone acid, escin, chlorhexidine diacetate, echinacoside, capreomycin sulfate, and elbasvir.</p>

scholarly journals Age-Dependent Fecal Bacterial Correlation to Inflammatory Bowel Disease for Newly Diagnosed Untreated Children

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Felix Chinweije Nwosu ◽  
Lill-Therse Thorkildsen ◽  
Ekaterina Avershina ◽  
Petr Ricanek ◽  
Gøri Perminow ◽  
...  
Keyword(s):  
Small Subunit ◽  
Fecal Microbiota ◽  
Newly Diagnosed ◽  
E Coli ◽  
Age Related ◽  
Age Dependent ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
The Impact ◽  
Selection Of

The knowledge about correlation patterns between the fecal microbiota and inflammatory bowel diseases (IBD)—comprising the two subforms Crohn's disease (CD) and ulcerative colitis (UC)—for newly diagnosed untreated children is limited. To address this knowledge gap, a selection of faecal specimens (CD,n=27and UC,n=16) and non-IBD controls (n=30) children (age < 18 years) was analysed utilising bacterial small subunit (SSU) rRNA. We found, surprising age dependence for the fecal microbiota correlating to IBD. The most pronounced patterns were thatE. coliwas positively (R2=0.16,P=0.05) and Bacteroidetes, negatively (R2=0.15,P=0.05) correlated to age for CD patients. For UC, we found an apparent opposite age-related disease correlation for bothBacteroidesandEscherichia. In addition, there was an overrepresentation ofHaemophilusfor the UC children. From our, results we propose a model where the aetiology of IBD is related to an on-going immunological development in children requiring different age-dependent bacterial stimuli. The impact of our findings could be a better age stratification for understanding and treating IBD in children.

scholarly journals Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4

2020 ◽  
Author(s):  
Vito F. Palmisano ◽  
Carlos Gómez-Rodellar ◽  
Hannah Pollak ◽  
Gustavo Cárdenas ◽  
Ben Corry ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Internal Cavity ◽  
Amino Groups ◽  
Voltage Gated ◽  
Accelerated Molecular Dynamics ◽  
Binding Pockets ◽  
Voltage Gated Ion Channels ◽  
Dynamics Simulations

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Na<sub>V</sub>1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel.

scholarly journals Development of the first low nanomolar Liver Receptor Homolog-1 agonist through structure-guided design

2019 ◽  
Author(s):  
Suzanne G. Mays ◽  
Autumn R. Flynn ◽  
Jeffery L. Cornelison ◽  
C. Denise Okafor ◽  
Hongtao Wang ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Nuclear Hormone Receptor ◽  
Inflammatory Gene Expression ◽  
Nonalcoholic Fatty Liver ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Potential Clinical Utility ◽  
Polar Interactions ◽  
Major Progress ◽  
Steroidogenic Genes

ABSTRACTAs a key regulator of metabolism and inflammation, the orphan nuclear hormone receptor, Liver Receptor Homolog-1 (LRH-1), has potential as a therapeutic target for diabetes, nonalcoholic fatty liver disease, and inflammatory bowel diseases. Discovery of LRH-1 modulators has been difficult, in part due to the tendency for synthetic compounds to bind unpredictably within the lipophilic binding pocket. Using a structure-guided approach, we exploited a newly-discovered polar interaction to lock agonists in a consistent orientation. This enabled the discovery of the first low nanomolar LRH-1 agonist, one hundred times more potent than the best previous modulator. We elucidate a novel mechanism of action that relies upon specific polar interactions deep in the LRH-1 binding pocket. In an organoid model of inflammatory bowel disease, the new agonist increases expression of LRH-1-conrolled steroidogenic genes and promotes anti-inflammatory gene expression changes. These studies constitute major progress in developing LRH-1 modulators with potential clinical utility.

scholarly journals Computational Drug Repurposing Studies on the ACE2-Spike (RBD) Interface of SARS-CoV-2

2020 ◽  
Author(s):  
Vinod Jani ◽  
Shruti Koulgi ◽  
Mallikarjunachari Uppuladinne V N ◽  
Uddhavesh Sonavane ◽  
Rajendra Joshi
Keyword(s):  
Transmembrane Protein ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Drug Binding ◽  
Tinospora Cordifolia ◽  
Strong Interactions ◽  
Angiotensin Converting Enzyme 2 ◽  
Ligand Free ◽  
Novel Coronavirus ◽  
Dynamics Simulations

<p>The novel coronavirus is known to enter the cell by binding to the human transmembrane protein Angiotensin-Converting Enzyme 2 (ACE2). The S(Spike)-glycoprotein of the SARS-CoV-2 forms a complex with the ACE2. Thus, the S-glycoprotein is one of the hot targets, as it forms the first line of contact between the virus and the human cell. Drug repurposing would help in identifying drugs that are safe and have no or fewer side effects. Hence, in addition to the Food and Drug Administration (FDA) approved molecules the compounds from natural sources were also considered. The current study includes docking and simulations of the FDA approved molecules and phytochemicals from Indian medicinal plants, targeting the ACE2-Spike protein complex. Rutin DAB10 and swertiapuniside were obtained as the top-ranked drugs from these two databases, respectively. The molecular dynamics simulations of ligand-free, rutin DAB10-bound, and swertiapuniside-bound ACE2-Spike complex revealed crucial ACE2-Spike interface residues forming strong interactions with the two ligands molecules. This may infer, that they may affect the ACE2 and spike binding. The conformational flexibility in the drug-binding pocket was captured using the RMSD-based clustering of the ligand-free simulations. An ensemble docking was performed wherein the two databases were docked on each of the representatives of ACE2-Spike obtained through clustering. The potential phytochemicals identified belonged to <i>Withania somnifera, Swertia chirayita, Tinospora cordifolia, Andrographis paniculata, Piper longum, and Azadirachta indica</i>. The FDA molecules identified were rutin DAB10, fulvestrant, cefoperazone acid, escin, chlorhexidine diacetate, echinacoside, capreomycin sulfate, and elbasvir.</p>

scholarly journals Tackling the Threat of Cancer Due to Pathobionts Producing Colibactin: Is Mesalamine the Magic Bullet?

Toxins ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 897
Author(s):  
Min Tang-Fichaux ◽  
Priscilla Branchu ◽  
Jean-Philippe Nougayrède ◽  
Eric Oswald
Keyword(s):  
Colorectal Cancer ◽  
Intestinal Inflammation ◽  
Gene Mutations ◽  
Magic Bullet ◽  
Induced Mutations ◽  
Human Colorectal Cancer ◽  
E Coli ◽  
Bowel Diseases ◽  
Inflammatory Bowel

Colibactin is a genotoxin produced primarily by Escherichia coli harboring the genomic pks island (pks+ E. coli). Pks+ E. coli cause host cell DNA damage, leading to chromosomal instability and gene mutations. The signature of colibactin-induced mutations has been described and found in human colorectal cancer (CRC) genomes. An inflamed intestinal environment drives the expansion of pks+ E. coli and promotes tumorigenesis. Mesalamine (i.e., 5-aminosalycilic acid), an effective anti-inflammatory drug, is an inhibitor of the bacterial polyphosphate kinase (PPK). This drug not only inhibits the production of intestinal inflammatory mediators and the proliferation of CRC cells, but also limits the abundance of E. coli in the gut microbiota and diminishes the production of colibactin. Here, we describe the link between intestinal inflammation and colorectal cancer induced by pks+ E. coli. We discuss the potential mechanisms of the pleiotropic role of mesalamine in treating both inflammatory bowel diseases and reducing the risk of CRC due to pks+ E. coli.

scholarly journals The Cu(II) reductase RclA protectsEscherichia coliagainst the combination of hypochlorous acid and intracellular copper

2019 ◽  
Author(s):  
Rhea M. Derke ◽  
Alexander J. Barron ◽  
Caitlin E. Billiot ◽  
Ivis F. Chaple ◽  
Suzanne E. Lapi ◽  
...  
Keyword(s):  
Redox Reactions ◽  
Hypochlorous Acid ◽  
Innate Immune ◽  
Health Concern ◽  
Antimicrobial Compounds ◽  
E Coli ◽  
Highly Sensitive ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Intracellular Copper

ABSTRACTInflammatory bowel diseases (IBDs) are a growing health concern. Enterobacteria, includingEscherichia coli, bloom to high levels in the gut during inflammation and strongly contribute to the pathology of IBDs. To survive in the inflamed gut,E. colimust tolerate high levels of antimicrobial compounds produced by the immune system, including toxic metals like copper and reactive chlorine oxidants like hypochlorous acid (HOCl). In this work, we show that the widely-conserved bacterial HOCl resistance enzyme RclA catalyzes the reduction of copper (II) to copper (I), and specifically protectsE. coliagainst the combination of HOCl and intracellular copper, probably by preventing Cu(III) accumulation.E. colilacking RclA were highly sensitive to HOCl and were defective in colonizing an animal host. Our results indicate unexpected complexity in the interactions between antimicrobial toxins produced by innate immune cells and suggest an important and previously unsuspected role for copper redox reactions during inflammation.

scholarly journals Computational Drug Repurposing Studies on the ACE2-Spike (RBD) Interface of SARS-CoV-2

2020 ◽  
Author(s):  
Vinod Jani ◽  
Shruti Koulgi ◽  
Mallikarjunachari Uppuladinne V N ◽  
Uddhavesh Sonavane ◽  
Rajendra Joshi
Keyword(s):  
Transmembrane Protein ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Drug Binding ◽  
Tinospora Cordifolia ◽  
Strong Interactions ◽  
Angiotensin Converting Enzyme 2 ◽  
Ligand Free ◽  
Novel Coronavirus ◽  
Dynamics Simulations

<p>The novel coronavirus is known to enter the cell by binding to the human transmembrane protein Angiotensin-Converting Enzyme 2 (ACE2). The S(Spike)-glycoprotein of the SARS-CoV-2 forms a complex with the ACE2. Thus, the S-glycoprotein is one of the hot targets, as it forms the first line of contact between the virus and the human cell. Drug repurposing would help in identifying drugs that are safe and have no or fewer side effects. Hence, in addition to the Food and Drug Administration (FDA) approved molecules the compounds from natural sources were also considered. The current study includes docking and simulations of the FDA approved molecules and phytochemicals from Indian medicinal plants, targeting the ACE2-Spike protein complex. Rutin DAB10 and swertiapuniside were obtained as the top-ranked drugs from these two databases, respectively. The molecular dynamics simulations of ligand-free, rutin DAB10-bound, and swertiapuniside-bound ACE2-Spike complex revealed crucial ACE2-Spike interface residues forming strong interactions with the two ligands molecules. This may infer, that they may affect the ACE2 and spike binding. The conformational flexibility in the drug-binding pocket was captured using the RMSD-based clustering of the ligand-free simulations. An ensemble docking was performed wherein the two databases were docked on each of the representatives of ACE2-Spike obtained through clustering. The potential phytochemicals identified belonged to <i>Withania somnifera, Swertia chirayita, Tinospora cordifolia, Andrographis paniculata, Piper longum, and Azadirachta indica</i>. The FDA molecules identified were rutin DAB10, fulvestrant, cefoperazone acid, escin, chlorhexidine diacetate, echinacoside, capreomycin sulfate, and elbasvir.</p>

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