Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site
N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopo...
Gespeichert in:
Veröffentlicht in: | Protein science 2008-03, Vol.17 (3), p.577-582 |
---|---|
Hauptverfasser: | , , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 582 |
---|---|
container_issue | 3 |
container_start_page | 577 |
container_title | Protein science |
container_volume | 17 |
creator | Mochalkin, Igor Lightle, Sandra Narasimhan, Lakshmi Bornemeier, Dirk Melnick, Michael VanderRoest, Steven McDowell, Laura |
description | N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram‐negative and Gram‐positive bacteria. Here we disclose a 1.9 Å resolution crystal structure of a synthetic small‐molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high‐throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC50 ∼ 18 μM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc‐1‐P substrate‐binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure‐guided design of a new class of mechanism‐based inhibitors of GlmU. |
doi_str_mv | 10.1110/ps.073271408 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2248321</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>20930253</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4847-b1e560166b7ea97975b2b167b58b2e6ebc79dababdaa3ca630fd47d890b3add13</originalsourceid><addsrcrecordid>eNqF0c9qFTEUBvAgir1Wd64luHDl1PyZSTIboRRthUJFLbgLSeZMJ5JJxmSmteLCR_AZfRKn3EvVja6yyI_vnMOH0GNKDiil5MVUDojkTNKaqDtoQ2vRVqoVH--iDWkFrRQXag89KOUTIaSmjN9He1QxqiRlG_Tt_ZwXNy8ZcOqxwWU0Ifz8_mNMAdwSAPs4eOvnlLFL4xTgC3T4ys8DPg7jOe5zGvGJgTFNgw9LWXkfFohfDeAMl2BCwSbiNTOVGbJ32PrY-XiBi5_hIbrXrwIe7d59dP761Yejk-r07PjN0eFp5WpVy8pSaAShQlgJppWtbCyzVEjbKMtAgHWy7Yw1tjOGOyM46btadqollpuuo3wfvdzmTosdoXMQ52yCnrIfTb7WyXj990_0g75Il5qxWnF2E_B0G7Be4XVx6-5ucClGcLOmhIiGkxU9203J6fMCZdajLw5CMBHSUrQknDEu6_9CRlpOWMNX-HwLXU6lZOhvV6ZE35Svp6Jvy1_5kz_P_I13ba-Ab8GVD3D9zzD99t0ZlaSRkv8CvCq-ow</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20930253</pqid></control><display><type>article</type><title>Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site</title><source>Access via Wiley Online Library</source><source>MEDLINE</source><source>EZB-FREE-00999 freely available EZB journals</source><source>Wiley Online Library (Open Access Collection)</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Mochalkin, Igor ; Lightle, Sandra ; Narasimhan, Lakshmi ; Bornemeier, Dirk ; Melnick, Michael ; VanderRoest, Steven ; McDowell, Laura</creator><creatorcontrib>Mochalkin, Igor ; Lightle, Sandra ; Narasimhan, Lakshmi ; Bornemeier, Dirk ; Melnick, Michael ; VanderRoest, Steven ; McDowell, Laura ; Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)</creatorcontrib><description>N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram‐negative and Gram‐positive bacteria. Here we disclose a 1.9 Å resolution crystal structure of a synthetic small‐molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high‐throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC50 ∼ 18 μM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc‐1‐P substrate‐binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure‐guided design of a new class of mechanism‐based inhibitors of GlmU.</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1110/ps.073271408</identifier><identifier>PMID: 18218712</identifier><language>eng</language><publisher>Bristol: Cold Spring Harbor Laboratory Press</publisher><subject>allosteric inhibitors ; Allosteric Site ; Anti-Bacterial Agents - chemistry ; ANTIBIOTICS ; BACTERIA ; Bacterial Proteins - chemistry ; Benzamides - chemistry ; BIOSYNTHESIS ; CRYSTAL STRUCTURE ; Crystallography, X-Ray ; DESIGN ; Drug Design ; DRUGS ; Enzyme Inhibitors - chemistry ; ENZYMES ; HAEMOPHILUS ; Haemophilus influenzae ; Haemophilus influenzae - enzymology ; MATERIALS SCIENCE ; mechanism ; METABOLISM ; Models, Molecular ; Nucleotidyltransferases - chemistry ; Piperidines - chemistry ; PRECURSOR ; Protein Binding ; Protein Structure Report ; RESOLUTION ; SCREENING ; STAPHYLOCOCCUS ; Staphylococcus aureus ; TARGETS ; UDP‐N‐acetylglucosamine ; uridyltransferase</subject><ispartof>Protein science, 2008-03, Vol.17 (3), p.577-582</ispartof><rights>Copyright © 2008 The Protein Society</rights><rights>Copyright © 2008 The Protein Society 2008</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4847-b1e560166b7ea97975b2b167b58b2e6ebc79dababdaa3ca630fd47d890b3add13</citedby><cites>FETCH-LOGICAL-c4847-b1e560166b7ea97975b2b167b58b2e6ebc79dababdaa3ca630fd47d890b3add13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248321/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248321/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1417,1433,27924,27925,45574,45575,46409,46833,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18218712$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1006530$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Mochalkin, Igor</creatorcontrib><creatorcontrib>Lightle, Sandra</creatorcontrib><creatorcontrib>Narasimhan, Lakshmi</creatorcontrib><creatorcontrib>Bornemeier, Dirk</creatorcontrib><creatorcontrib>Melnick, Michael</creatorcontrib><creatorcontrib>VanderRoest, Steven</creatorcontrib><creatorcontrib>McDowell, Laura</creatorcontrib><creatorcontrib>Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)</creatorcontrib><title>Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram‐negative and Gram‐positive bacteria. Here we disclose a 1.9 Å resolution crystal structure of a synthetic small‐molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high‐throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC50 ∼ 18 μM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc‐1‐P substrate‐binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure‐guided design of a new class of mechanism‐based inhibitors of GlmU.</description><subject>allosteric inhibitors</subject><subject>Allosteric Site</subject><subject>Anti-Bacterial Agents - chemistry</subject><subject>ANTIBIOTICS</subject><subject>BACTERIA</subject><subject>Bacterial Proteins - chemistry</subject><subject>Benzamides - chemistry</subject><subject>BIOSYNTHESIS</subject><subject>CRYSTAL STRUCTURE</subject><subject>Crystallography, X-Ray</subject><subject>DESIGN</subject><subject>Drug Design</subject><subject>DRUGS</subject><subject>Enzyme Inhibitors - chemistry</subject><subject>ENZYMES</subject><subject>HAEMOPHILUS</subject><subject>Haemophilus influenzae</subject><subject>Haemophilus influenzae - enzymology</subject><subject>MATERIALS SCIENCE</subject><subject>mechanism</subject><subject>METABOLISM</subject><subject>Models, Molecular</subject><subject>Nucleotidyltransferases - chemistry</subject><subject>Piperidines - chemistry</subject><subject>PRECURSOR</subject><subject>Protein Binding</subject><subject>Protein Structure Report</subject><subject>RESOLUTION</subject><subject>SCREENING</subject><subject>STAPHYLOCOCCUS</subject><subject>Staphylococcus aureus</subject><subject>TARGETS</subject><subject>UDP‐N‐acetylglucosamine</subject><subject>uridyltransferase</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0c9qFTEUBvAgir1Wd64luHDl1PyZSTIboRRthUJFLbgLSeZMJ5JJxmSmteLCR_AZfRKn3EvVja6yyI_vnMOH0GNKDiil5MVUDojkTNKaqDtoQ2vRVqoVH--iDWkFrRQXag89KOUTIaSmjN9He1QxqiRlG_Tt_ZwXNy8ZcOqxwWU0Ifz8_mNMAdwSAPs4eOvnlLFL4xTgC3T4ys8DPg7jOe5zGvGJgTFNgw9LWXkfFohfDeAMl2BCwSbiNTOVGbJ32PrY-XiBi5_hIbrXrwIe7d59dP761Yejk-r07PjN0eFp5WpVy8pSaAShQlgJppWtbCyzVEjbKMtAgHWy7Yw1tjOGOyM46btadqollpuuo3wfvdzmTosdoXMQ52yCnrIfTb7WyXj990_0g75Il5qxWnF2E_B0G7Be4XVx6-5ucClGcLOmhIiGkxU9203J6fMCZdajLw5CMBHSUrQknDEu6_9CRlpOWMNX-HwLXU6lZOhvV6ZE35Svp6Jvy1_5kz_P_I13ba-Ab8GVD3D9zzD99t0ZlaSRkv8CvCq-ow</recordid><startdate>200803</startdate><enddate>200803</enddate><creator>Mochalkin, Igor</creator><creator>Lightle, Sandra</creator><creator>Narasimhan, Lakshmi</creator><creator>Bornemeier, Dirk</creator><creator>Melnick, Michael</creator><creator>VanderRoest, Steven</creator><creator>McDowell, Laura</creator><general>Cold Spring Harbor Laboratory Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>C1K</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>200803</creationdate><title>Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site</title><author>Mochalkin, Igor ; Lightle, Sandra ; Narasimhan, Lakshmi ; Bornemeier, Dirk ; Melnick, Michael ; VanderRoest, Steven ; McDowell, Laura</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4847-b1e560166b7ea97975b2b167b58b2e6ebc79dababdaa3ca630fd47d890b3add13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>allosteric inhibitors</topic><topic>Allosteric Site</topic><topic>Anti-Bacterial Agents - chemistry</topic><topic>ANTIBIOTICS</topic><topic>BACTERIA</topic><topic>Bacterial Proteins - chemistry</topic><topic>Benzamides - chemistry</topic><topic>BIOSYNTHESIS</topic><topic>CRYSTAL STRUCTURE</topic><topic>Crystallography, X-Ray</topic><topic>DESIGN</topic><topic>Drug Design</topic><topic>DRUGS</topic><topic>Enzyme Inhibitors - chemistry</topic><topic>ENZYMES</topic><topic>HAEMOPHILUS</topic><topic>Haemophilus influenzae</topic><topic>Haemophilus influenzae - enzymology</topic><topic>MATERIALS SCIENCE</topic><topic>mechanism</topic><topic>METABOLISM</topic><topic>Models, Molecular</topic><topic>Nucleotidyltransferases - chemistry</topic><topic>Piperidines - chemistry</topic><topic>PRECURSOR</topic><topic>Protein Binding</topic><topic>Protein Structure Report</topic><topic>RESOLUTION</topic><topic>SCREENING</topic><topic>STAPHYLOCOCCUS</topic><topic>Staphylococcus aureus</topic><topic>TARGETS</topic><topic>UDP‐N‐acetylglucosamine</topic><topic>uridyltransferase</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mochalkin, Igor</creatorcontrib><creatorcontrib>Lightle, Sandra</creatorcontrib><creatorcontrib>Narasimhan, Lakshmi</creatorcontrib><creatorcontrib>Bornemeier, Dirk</creatorcontrib><creatorcontrib>Melnick, Michael</creatorcontrib><creatorcontrib>VanderRoest, Steven</creatorcontrib><creatorcontrib>McDowell, Laura</creatorcontrib><creatorcontrib>Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mochalkin, Igor</au><au>Lightle, Sandra</au><au>Narasimhan, Lakshmi</au><au>Bornemeier, Dirk</au><au>Melnick, Michael</au><au>VanderRoest, Steven</au><au>McDowell, Laura</au><aucorp>Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2008-03</date><risdate>2008</risdate><volume>17</volume><issue>3</issue><spage>577</spage><epage>582</epage><pages>577-582</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><abstract>N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) is an essential enzyme in aminosugars metabolism and an attractive target for antibiotic drug discovery. GlmU catalyzes the formation of uridine‐diphospho‐N‐acetylglucosamine (UDP‐GlcNAc), an important precursor in the peptidoglycan and lipopolisaccharide biosynthesis in both Gram‐negative and Gram‐positive bacteria. Here we disclose a 1.9 Å resolution crystal structure of a synthetic small‐molecule inhibitor of GlmU from Haemophilus influenzae (hiGlmU). The compound was identified through a high‐throughput screening (HTS) configured to detect inhibitors that target the uridyltransferase active site of hiGlmU. The original HTS hit exhibited a modest micromolar potency (IC50 ∼ 18 μM in a racemic mixture) against hiGlmU and no activity against Staphylococcus aureus GlmU (saGlmU). The determined crystal structure indicated that the inhibitor occupies an allosteric site adjacent to the GlcNAc‐1‐P substrate‐binding region. Analysis of the mechanistic model of the uridyltransferase reaction suggests that the binding of this allosteric inhibitor prevents structural rearrangements that are required for the enzymatic reaction, thus providing a basis for structure‐guided design of a new class of mechanism‐based inhibitors of GlmU.</abstract><cop>Bristol</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>18218712</pmid><doi>10.1110/ps.073271408</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0961-8368 |
ispartof | Protein science, 2008-03, Vol.17 (3), p.577-582 |
issn | 0961-8368 1469-896X |
language | eng |
recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2248321 |
source | Access via Wiley Online Library; MEDLINE; EZB-FREE-00999 freely available EZB journals; Wiley Online Library (Open Access Collection); PubMed Central; Free Full-Text Journals in Chemistry |
subjects | allosteric inhibitors Allosteric Site Anti-Bacterial Agents - chemistry ANTIBIOTICS BACTERIA Bacterial Proteins - chemistry Benzamides - chemistry BIOSYNTHESIS CRYSTAL STRUCTURE Crystallography, X-Ray DESIGN Drug Design DRUGS Enzyme Inhibitors - chemistry ENZYMES HAEMOPHILUS Haemophilus influenzae Haemophilus influenzae - enzymology MATERIALS SCIENCE mechanism METABOLISM Models, Molecular Nucleotidyltransferases - chemistry Piperidines - chemistry PRECURSOR Protein Binding Protein Structure Report RESOLUTION SCREENING STAPHYLOCOCCUS Staphylococcus aureus TARGETS UDP‐N‐acetylglucosamine uridyltransferase |
title | Structure of a small‐molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T16%3A28%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Structure%20of%20a%20small%E2%80%90molecule%20inhibitor%20complexed%20with%20GlmU%20from%20Haemophilus%20influenzae%20reveals%20an%20allosteric%20binding%20site&rft.jtitle=Protein%20science&rft.au=Mochalkin,%20Igor&rft.aucorp=Argonne%20National%20Lab.%20(ANL),%20Argonne,%20IL%20(United%20States).%20Advanced%20Photon%20Source%20(APS)&rft.date=2008-03&rft.volume=17&rft.issue=3&rft.spage=577&rft.epage=582&rft.pages=577-582&rft.issn=0961-8368&rft.eissn=1469-896X&rft_id=info:doi/10.1110/ps.073271408&rft_dat=%3Cproquest_pubme%3E20930253%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=20930253&rft_id=info:pmid/18218712&rfr_iscdi=true |