{"id":5294,"date":"2025-02-14T15:26:19","date_gmt":"2025-02-14T14:26:19","guid":{"rendered":"https:\/\/spgoo.org\/?p=5294"},"modified":"2025-03-01T15:16:56","modified_gmt":"2025-03-01T14:16:56","slug":"analyse-des-resultats-experimentaux-dans-la-chembl","status":"publish","type":"post","link":"https:\/\/spgoo.org\/?p=5294","title":{"rendered":"Analyse des r\u00e9sultats exp\u00e9rimentaux dans la Chembl"},"content":{"rendered":"\n<h2 class=\"wp-block-heading has-vivid-green-cyan-color has-text-color has-link-color wp-elements-ce0ed358ac1c93ccd291ca442139da66\">Introduction<\/h2>\n\n\n\n<p>La base de donn\u00e9e nomm\u00e9e <strong>Chembl<\/strong> est vraiment <strong>tr\u00e8s int\u00e9ressante <\/strong>pour essayer de comprendre les m\u00e9canismes en jeu lors de l&#8217;interaction entre un ligand et une prot\u00e9ine. En effet, sur le site de la Chembl, on trouve un lien vers les r\u00e9sultats exp\u00e9rimentaux li\u00e9s aux cibles biologiques. En bas \u00e0 gauche sur l&#8217;image ci-dessous.<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"581\" height=\"1024\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-113-581x1024.png\" alt=\"\" class=\"wp-image-5295\" srcset=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-113-581x1024.png 581w, https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-113-170x300.png 170w, https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-113.png 592w\" sizes=\"auto, (max-width: 581px) 100vw, 581px\" \/><\/figure>\n<\/div>\n\n\n<p>En triant les cibles par nombre de mol\u00e9cules (compounds) test\u00e9es sur une cible, on constate que certaines cibles ont \u00e9t\u00e9 vraiment tr\u00e8s \u00e9tudi\u00e9es:<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"648\" height=\"520\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-114.png\" alt=\"\" class=\"wp-image-5296\" srcset=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-114.png 648w, https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-114-300x241.png 300w\" sizes=\"auto, (max-width: 648px) 100vw, 648px\" \/><\/figure>\n<\/div>\n\n\n<p>Ce qui nous int\u00e9resse en premier lieu, ce sont les r\u00e9sultats exp\u00e9rimentaux sur des &#8220;single proteins&#8221;, des prot\u00e9ines prises seules.<\/p>\n\n\n\n<p>Pour commence une premi\u00e8re analyse, j&#8217;ai choisi une prot\u00e9ine avec quelques milliers de mol\u00e9cules test\u00e9es sur celle-ci, la CHEMBL3880, la &#8220;Heat shock protein HSP 90-alpha&#8221; avec 3019 mol\u00e9cules dont l&#8217;identifiant UniProt est <a href=\"http:\/\/www.uniprot.org\/uniprot\/?query=accession:P07900\">P07900<\/a>.<\/p>\n\n\n\n<p>Un filtre sur le nombre maximum d&#8217;atomes (naat_max=30) a \u00e9t\u00e9 appliqu\u00e9e et  seules les mol\u00e9cules avec uniquement des atomes de chimie organiques ont \u00e9t\u00e9 conserv\u00e9es soit 1855 mol\u00e9cules.<\/p>\n\n\n\n<p>Le docking de ces mol\u00e9cules sur le site d&#8217;un inhibiteur dans le pdb 2YES donne le r\u00e9sultat suivant:<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"547\" height=\"529\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-115.png\" alt=\"\" class=\"wp-image-5297\" srcset=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-115.png 547w, https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-115-300x290.png 300w\" sizes=\"auto, (max-width: 547px) 100vw, 547px\" \/><\/figure>\n<\/div>\n\n\n<p>Mol\u00e9cules ayant une valeur de &#8220;&#8216;minimizedAffinity&#8221; inf\u00e9rieure \u00e0 -9,75:<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-116.png\" alt=\"\">IC50 = 1700 nM<\/td><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-118.png\" alt=\"\">IC50 = 330 nM<\/td><\/tr><tr><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-117.png\" alt=\"\">IC50=130 nM<\/td><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-119.png\" alt=\"\">IC50 = 38 nM<\/td><\/tr><tr><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-120.png\" alt=\"\">IC50=38 nM<\/td><td><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p>La mol\u00e9cules ayant la meilleure activit\u00e9 est la suivante:<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><br><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-121.png\" alt=\"\">CHEMBL2205245 avec un IC50 de 1nM mais minimizedAffinity: -7.5 et efficiency: -0.31<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p>Diff\u00e9rence de conformation entre CHEMBL3360305 et CHEMBL2205245<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-122.png\" alt=\"\"><\/td><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-123.png\" alt=\"\"><\/td><\/tr><tr><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-125.png\" alt=\"\"><\/td><td><img decoding=\"async\" src=\"https:\/\/spgoo.org\/wp-content\/uploads\/2025\/02\/image-124.png\" alt=\"\"><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>Introduction La base de donn\u00e9e nomm\u00e9e Chembl est vraiment tr\u00e8s int\u00e9ressante pour essayer de comprendre les m\u00e9canismes en jeu lors de l&#8217;interaction entre un ligand et une prot\u00e9ine. En effet, sur le site de la Chembl, on trouve un lien vers les r\u00e9sultats exp\u00e9rimentaux li\u00e9s aux cibles biologiques. En bas \u00e0 gauche sur l&#8217;image ci-dessous. [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-5294","post","type-post","status-publish","format-standard","hentry","category-non-classe"],"_links":{"self":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/posts\/5294","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=5294"}],"version-history":[{"count":2,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/posts\/5294\/revisions"}],"predecessor-version":[{"id":5310,"href":"https:\/\/spgoo.org\/index.php?rest_route=\/wp\/v2\/posts\/5294\/revisions\/5310"}],"wp:attachment":[{"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5294"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5294"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/spgoo.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5294"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}