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{"work":{"id":36485148,"created_at":"2018-04-23T21:34:27.787-07:00","from_world_paper_id":164866160,"updated_at":"2024-11-16T08:47:49.660-08:00","_data":{"publisher":"Springer Nature","grobid_abstract":"Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) has been identified as a drug target for the treatment of inflammatory diseases. Therefore, there is an urgent need to develop new classes of MAPKAP-K2 inhibitors. To understand the structure activity correlation of MAPKAP-K2 inhibitors, we have carried out a molecular docking study and three-dimensional quantitative structureactivity relationship (3D-QSAR) modeling. Both comparative molecular field analysis (r 2 cv = 0.602, r 2 ncv = 0.955) and comparative molecular similarity indices analysis (r 2 cv = 0.546, r 2 ncv = 0.891) models were generated using the training set on the basis of the common substructure-based alignment and gave reasonable results. The structural insights obtained from both the 3D-QSAR contour maps and molecular docking help to better interpret the structure activity relationship. The results obtained from this study will be useful in the design of potent MAPKAP-K2 inhibitors.","publication_date":"2014,,","publication_name":"Medicinal Chemistry Research","grobid_abstract_attachment_id":"56403812"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Molecular docking and 3D-QSAR studies on the MAPKAP-K2 inhibitors","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [62644927]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon'; window.userInChina = "false";</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":56403812,"attachmentType":"pdf"}"><img alt="First page of “Molecular docking and 3D-QSAR studies on the MAPKAP-K2 inhibitors”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/56403812/mini_magick20190112-17299-19wvbqd.png?1547297286" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Molecular docking and 3D-QSAR studies on the MAPKAP-K2 inhibitors</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="62644927" href="https://independent.academia.edu/EPourbasheer"><img alt="Profile image of E. Pourbasheer" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />E. Pourbasheer</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">2014, Medicinal Chemistry Research</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">12 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 36485148; const worksViewsPath = "/v0/works/views?subdomain_param=api&work_ids%5B%5D=36485148"; const getWorkViews = async (workId) => { const response = await fetch(worksViewsPath); if (!response.ok) { throw new Error('Failed to load work views'); } const data = await response.json(); return data.views[workId]; }; // Get the view count for the work - we send this immediately rather than waiting for // the DOM to load, so it can be available as soon as possible (but without holding up // the backend or other resource requests, because it's a bit expensive and not critical). const viewCount = await getWorkViews(workId); const updateViewCount = (viewCount) => { try { const viewCountNumber = parseInt(viewCount, 10); if (viewCountNumber === 0) { // Remove the whole views element if there are zero views. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); return; } const commaizedViewCount = viewCountNumber.toLocaleString(); const viewCountBody = document.getElementById('work-metadata-view-count'); if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) has been identified as a drug target for the treatment of inflammatory diseases. Therefore, there is an urgent need to develop new classes of MAPKAP-K2 inhibitors. To understand the structure activity correlation of MAPKAP-K2 inhibitors, we have carried out a molecular docking study and three-dimensional quantitative structureactivity relationship (3D-QSAR) modeling. Both comparative molecular field analysis (r 2 cv = 0.602, r 2 ncv = 0.955) and comparative molecular similarity indices analysis (r 2 cv = 0.546, r 2 ncv = 0.891) models were generated using the training set on the basis of the common substructure-based alignment and gave reasonable results. The structural insights obtained from both the 3D-QSAR contour maps and molecular docking help to better interpret the structure activity relationship. The results obtained from this study will be useful in the design of potent MAPKAP-K2 inhibitors.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":56403812,"attachmentType":"pdf","workUrl":"https://www.academia.edu/36485148/Molecular_docking_and_3D_QSAR_studies_on_the_MAPKAP_K2_inhibitors"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":56403812,"attachmentType":"pdf","workUrl":"https://www.academia.edu/36485148/Molecular_docking_and_3D_QSAR_studies_on_the_MAPKAP_K2_inhibitors"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div><div class="ds-signup-banner-trigger-container"><div class="ds-signup-banner-trigger ds-signup-banner-trigger-control"></div></div><div class="ds-signup-banner ds-signup-banner-control"><div id="ds-signup-banner-close-button"><button class="ds2-5-button ds2-5-button--secondary ds2-5-button--inverse"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">close</span></button></div><div class="ds-signup-banner-ctas"><img src="//a.academia-assets.com/images/academia-logo-capital-white.svg" /><h4 class="ds2-5-heading-serif-sm">Sign up for access to the world's latest research</h4><button class="ds2-5-button ds2-5-button--inverse ds2-5-button--full-width js-swp-download-button" data-signup-modal="{"location":"signup-banner"}">Sign up for free<span class="material-symbols-outlined" style="font-size: 20px" translate="no">arrow_forward</span></button></div><div class="ds-signup-banner-divider"></div><div class="ds-signup-banner-reasons"><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Get notified about relevant papers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Save papers to use in your research</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Join the discussion with peers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Track your impact</span></div></div></div><script>(() => { // Set up signup banner show/hide behavior: // 1. 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Three dimensional quantitative structure- activity relationship (3D- QSAR) studies were performed on a series of 25, 2-aminothiazole analogs as inhibitors of p38α mitogen activated protein (MAP) kinase. The docking results provided a reliable conformational alignment scheme for the 3D-QSAR model. The 3D-QSAR model showed very good statistical results namely q2, r2and r2predvalues for both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The CoMFA and CoMSIA models & docking results provided the most significant correlation of steric, electrostatic, hydrophobic,H-bond donor,H-bond acceptor fields with biological activities and the provided values were in good agreement with the experimental results. The information rendered from molecular modeling studies gave valuable clue...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Docking and 3D QSAR Studies on p38α MAP Kinase Inhibitors","attachmentId":92738890,"attachmentType":"pdf","work_url":"https://www.academia.edu/88833554/Docking_and_3D_QSAR_Studies_on_p38%CE%B1_MAP_Kinase_Inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/88833554/Docking_and_3D_QSAR_Studies_on_p38%CE%B1_MAP_Kinase_Inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="98337651" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/98337651/Molecular_docking_3D_QSAR_molecular_dynamics_synthesis_and_anticancer_activity_of_tyrosine_kinase_2_TYK_2_inhibitors">Molecular docking, 3D-QSAR, molecular dynamics, synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="163906403" href="https://osmania.academia.edu/VijjulathaManga">Vijjulatha Manga</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Receptors and Signal Transduction, 2018</p><p class="ds-related-work--abstract ds2-5-body-sm">A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3 D quantitative structure-activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Molecular docking, 3D-QSAR, molecular dynamics, synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors","attachmentId":99716584,"attachmentType":"pdf","work_url":"https://www.academia.edu/98337651/Molecular_docking_3D_QSAR_molecular_dynamics_synthesis_and_anticancer_activity_of_tyrosine_kinase_2_TYK_2_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/98337651/Molecular_docking_3D_QSAR_molecular_dynamics_synthesis_and_anticancer_activity_of_tyrosine_kinase_2_TYK_2_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="10283758" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/10283758/Elucidation_of_binding_mode_and_three_dimensional_quantitative_structure_activity_relationship_studies_of_a_novel_series_of_protein_kinase_B_Akt_inhibitors">Elucidation of binding mode and three dimensional quantitative structure–activity relationship studies of a novel series of protein kinase B/Akt inhibitors</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="25181303" href="https://pcsirkarachi.academia.edu/YasarSaleem">Yasar Saleem</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Protein kinase B (PKB; also known as Akt kinase) is located downstream in the PI-3 kinase pathway. Overexpression and constitutive activation of PKB/Akt leads to human prostate, breast and ovarian carcinomas. A series of 69 PKB/Akt inhibitors were examined to explore their binding modes using FlexX, and three-dimensional quantitative structure–activity relationship (3D-QSAR) studies based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed to provide structural insights into these compounds. CoMFA produced statistically significant results, with cross-validated q2 and noncross validated correlation r2 coefficients of 0.53 and 0.95, respectively. For CoMSIA, steric, hydrophobic and hydrogen bond acceptor fields jointly yielded ‘leave one out’ q2=0.51 and r2=0.84. The predictive power of CoMFA and CoMSIA was determined using a test set of 13 molecules, which gave correlation coefficients, r2 predictive of 0.58 and 0.62, respectively. Molecular docking revealed that the binding modes of these molecules in the ATP binding sites of the Akt kinase domain were very similar to those of the co-crystallized ligand. The information obtained from 3D contour maps will allow the design of more potent and selective Akt kinase inhibitors.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Elucidation of binding mode and three dimensional quantitative structure–activity relationship studies of a novel series of protein kinase B/Akt inhibitors","attachmentId":36364079,"attachmentType":"pdf","work_url":"https://www.academia.edu/10283758/Elucidation_of_binding_mode_and_three_dimensional_quantitative_structure_activity_relationship_studies_of_a_novel_series_of_protein_kinase_B_Akt_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/10283758/Elucidation_of_binding_mode_and_three_dimensional_quantitative_structure_activity_relationship_studies_of_a_novel_series_of_protein_kinase_B_Akt_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="23578883" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/23578883/Application_of_3D_QSAR_on_a_Series_of_Potent_P38_MAP_Kinase_Inhibitors">Application of 3D-QSAR on a Series of Potent P38-MAP Kinase Inhibitors</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="7817864" href="https://tehran.academia.edu/JahanBGhasemi">Jahan B Ghasemi</a></div><p class="ds-related-work--abstract ds2-5-body-sm">One of the most applied methods in drug industry for development of new drugs is 3D-QSAR methodology. As p38-mitogen-activated protein kinase (p38-MAPK) plays a crucial role in regulating the production of such proinflammatory cytokines as tumor necrosis factor-α (TNF-α) and interleukin-1, emerging as an attractive target for new anti-inflammatory agents, we used a 3D-QSAR based method of Comparative Molecular Field Analysis (CoMFA) on a series of 52 potent p38-MAP kinase inhibitors with IC 50 ranging from 3.2 to 10,000 nM. An alignment rule for the compounds was defined using Distill in SYBYL 7.3. The best model was validated using a data set obtained by dividing the data set into a training set and test set using hierarchical clustering, based on the CoMFA fields and biological activities (pIC 50 ).</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Application of 3D-QSAR on a Series of Potent P38-MAP Kinase Inhibitors","attachmentId":44001768,"attachmentType":"pdf","work_url":"https://www.academia.edu/23578883/Application_of_3D_QSAR_on_a_Series_of_Potent_P38_MAP_Kinase_Inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/23578883/Application_of_3D_QSAR_on_a_Series_of_Potent_P38_MAP_Kinase_Inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="95447536" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/95447536/Evaluation_of_the_combination_mode_and_features_of_p38_MAPK_inhibitors_construction_of_different_pharmacophore_models_and_molecular_docking">Evaluation of the combination mode and features of p38 MAPK inhibitors: construction of different pharmacophore models and molecular docking</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="254304434" href="https://independent.academia.edu/liyuzhao1">liyu zhao</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Molecular Simulation, 2019</p><p class="ds-related-work--abstract ds2-5-body-sm">Abnormal expression of tumour necrosis factor-α (TNF-α) can lead to various pathological reactions, such as arthritis, psoriasis, krone disease, etc. p38 mitogen-activated protein kinase (p38 MAPK) is an important signal transduction enzyme that plays important roles in influencing the release of intracellular TNF-α factor. It is very meaningful to study the targeting kinase with specific inhibitors in the treatment of related diseases. In order to achieve a deeper insight, it is necessary to analyse the structural characteristics and the action mode of the p38 MAPK inhibitors in the active site. In the study, a ligand-based common feature pharmacophore model and the receptor structure-based pharmacophore model were constructed, respectively. Their common chemical features consisted of the hydrophobic groups (H) and the hydrogen bond acceptors (A), and kept the consistency of spatial structure distribution. Then, the molecular docking and molecular dynamics simulation were performed with the eight training set compounds. The binding characteristics of molecules binding were described in the topological region of the active site. Finally, the structure-activity relationship (SAR) was obtained by analysing docking results with the different pharmacophore models. This research leads to the proposal of an interaction model in the p38 MAPK active site and provides guidance for the screening and design of more potent and selective p38 MAPK inhibitors.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evaluation of the combination mode and features of p38 MAPK inhibitors: construction of different pharmacophore models and molecular docking","attachmentId":97628220,"attachmentType":"pdf","work_url":"https://www.academia.edu/95447536/Evaluation_of_the_combination_mode_and_features_of_p38_MAPK_inhibitors_construction_of_different_pharmacophore_models_and_molecular_docking","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/95447536/Evaluation_of_the_combination_mode_and_features_of_p38_MAPK_inhibitors_construction_of_different_pharmacophore_models_and_molecular_docking"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="71097022" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/71097022/3D_QSAR_and_HQSAR_analysis_of_protein_kinase_B_PKB_Akt_inhibitors_using_various_alignment_methods">3D QSAR and HQSAR analysis of protein kinase B (PKB/Akt) inhibitors using various alignment methods</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="80600023" href="https://iaun.academia.edu/alirezaazizi">alireza azizi</a></div><p class="ds-related-work--metadata ds2-5-body-xs">azizi, 1977</p><p class="ds-related-work--abstract ds2-5-body-sm">Protein kinase B (PKB/Akt) regulates all aspects of cell growth, differentiation, and division. PKB/Akt has recently garnered a great deal of attention as a promising molecular target for cancer therapy due to its involvement in the development of several human cancers. In this study a diverse set of 56 Akt1 inhibitors were aligned by three different methods (pharmacophore-, docking-based and rigid body alignment) for CoMFA, CoMSIA and HQSAR analysis. The best QSAR models were obtained using rigid body alignment (Distill). CoMFA and CoMSIA models were found statistically significant with leave-one-out correlation coefficient (q 2) of 0.627 and 0.598, respectively, cross validated coefficient (r 2 cv) of 0.644 and 0.563, respectively, and conventional coefficient (r 2) of 0.867 and 0.865, respectively. QSAR models were validated by a test set of 9 compounds giving satisfactory predicted correlation coefficient (r 2 pred) of 0.603 and 0.613 for CoMFA and CoMSIA models, respectively. Leave-one-out correlation value (q 2) of 0.687, r 2 pred of 0.742 and r 2 of 0.868 were obtained for HQSAR analysis and found satisfactory. This study provides valuable clues to design new compounds against PKB/Akt.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"3D QSAR and HQSAR analysis of protein kinase B (PKB/Akt) inhibitors using various alignment methods","attachmentId":80592498,"attachmentType":"pdf","work_url":"https://www.academia.edu/71097022/3D_QSAR_and_HQSAR_analysis_of_protein_kinase_B_PKB_Akt_inhibitors_using_various_alignment_methods","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/71097022/3D_QSAR_and_HQSAR_analysis_of_protein_kinase_B_PKB_Akt_inhibitors_using_various_alignment_methods"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="8243102" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/8243102/Three_dimensional_quantitative_structure_activity_relationship_3_D_QSAR_and_docking_studies_on_benzothiazole_2_yl_acetonitrile_derivatives_as_c_Jun_N_terminal_kinase_3_JNK3_inhibitors">Three-dimensional quantitative structure–activity relationship (3 D-QSAR) and docking studies on (benzothiazole-2-yl) acetonitrile derivatives as c-Jun N-terminal kinase-3 (JNK3) inhibitors</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="16280954" href="https://independent.academia.edu/MohamedIsmael1">Mohamed Ismael</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioorganic & Medicinal Chemistry Letters, 2006</p><p class="ds-related-work--abstract ds2-5-body-sm">A homology model of Helicobacter pylori urease was developed by using the crystal structure of urease from Klebsiella aerogenes (EC 3.5.1.5) as a template. The acetohydroxamic acid moiety was docked into the active pocket of the enzyme model, followed by relaxation of the complex by use of molecular dynamics. The resulting conformation was used as a template to construct 24 potential dipeptide hydroxamic acid inhibitors with which comparative molecular field analysis (CoMFA) was performed. The resulting model provided a cross-validation correlation coefficient (q 2 L00 ) of 0.610, a conventional r 2 value of 0.988, and an F (Fisher indication of statistical significance) value of 294.88. We were able to validate the CoMFA model by using the 50% inhibitory concentrations of six compounds that were not included in the construction of the model. A very good structural correlation was observed between the amino acids in the model urease's active pocket and the contour maps derived from the CoMFA model. This correlation, accompanied by the validation supplied by use of the CoMFA data, illustrates that the model can aid in the prediction and design of novel H. pylori urease inhibitors.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Three-dimensional quantitative structure–activity relationship (3 D-QSAR) and docking studies on (benzothiazole-2-yl) acetonitrile derivatives as c-Jun N-terminal kinase-3 (JNK3) inhibitors","attachmentId":48169502,"attachmentType":"pdf","work_url":"https://www.academia.edu/8243102/Three_dimensional_quantitative_structure_activity_relationship_3_D_QSAR_and_docking_studies_on_benzothiazole_2_yl_acetonitrile_derivatives_as_c_Jun_N_terminal_kinase_3_JNK3_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/8243102/Three_dimensional_quantitative_structure_activity_relationship_3_D_QSAR_and_docking_studies_on_benzothiazole_2_yl_acetonitrile_derivatives_as_c_Jun_N_terminal_kinase_3_JNK3_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="53091772" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/53091772/Molecular_modeling_studies_of_phenoxypyrimidinyl_imidazoles_as_p38_kinase_inhibitors_using_QSAR_and_docking_">Molecular modeling studies of phenoxypyrimidinyl imidazoles as p38 kinase inhibitors using QSAR and docking☆</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="61386588" href="https://independent.academia.edu/GarlapatiAchaiah">Achaiah Garlapati</a></div><p class="ds-related-work--metadata ds2-5-body-xs">European Journal of Medicinal Chemistry, 2008</p><p class="ds-related-work--abstract ds2-5-body-sm">p38 Kinase plays a vital role in inflammation mediated by tumor necrosis factor-a (TNFa) and interleukin-1b (IL-1b) pathways and inhibitors of p38 kinase provide effective approach for the treatment of inflammatory diseases. Pyridinyl and pyrimidinyl imidazoles, selectively inhibit p38a MAP kinase, are useful in the treatment of inflammatory diseases like rheumatoid arthritis. Three dimensional quantitative structureeactivity relationship studies (3D-QSAR) involving comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA) and molecular docking were performed on 44 phenoxypyrimidinyl imidazole p38 kinase inhibitors to find out the structural relationship with the activity. The best predictive CoMFA model with atom fit alignment resulted in cross-validated r 2 value of 0.553, noncross-validated r 2 value of 0.908 and standard error of estimate 0.187. Similarly the best predictive CoMSIA model was derived with q 2 of 0.508, noncross-validated r 2 of 0.894 and standard error of estimate of 0.197, comprising steric, electrostatic, hydrophobic and hydrogen bond donor fields. These models were able to predict the activity of test set molecules efficiently within an acceptable error range. GOLD and FlexX were employed to dock the inhibitors into the active site of the p38 kinase and these docking studies revealed the vital interactions and binding conformation of the inhibitors. The information rendered by 3D-QSAR models and the docking interactions may afford valuable clues to optimize the lead and design new potential inhibitors.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Molecular modeling studies of phenoxypyrimidinyl imidazoles as p38 kinase inhibitors using QSAR and docking☆","attachmentId":70041243,"attachmentType":"pdf","work_url":"https://www.academia.edu/53091772/Molecular_modeling_studies_of_phenoxypyrimidinyl_imidazoles_as_p38_kinase_inhibitors_using_QSAR_and_docking_","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/53091772/Molecular_modeling_studies_of_phenoxypyrimidinyl_imidazoles_as_p38_kinase_inhibitors_using_QSAR_and_docking_"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="85803872" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/85803872/Identification_of_Potential_C_kit_Protein_Kinase_Inhibitors_Associated_with_Human_Liver_Cancer_Atom_based_3D_QSAR_Modeling_Pharmacophores_based_Virtual_Screening_and_Molecular_Docking_Studies">Identification of Potential C-kit Protein Kinase Inhibitors Associated with Human Liver Cancer: Atom-based 3D-QSAR Modeling, Pharmacophores-based Virtual Screening and Molecular Docking Studies</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="48372877" href="https://independent.academia.edu/WacothonKarimeCoulibaly">Wacothon-Karime Coulibaly</a></div><p class="ds-related-work--metadata ds2-5-body-xs">American Journal of Pharmacological Sciences, 2021</p><p class="ds-related-work--abstract ds2-5-body-sm">Rhodanine and its derivatives exhibit interesting biological activities as well as a wide range of biological applications. In this study, a dataset of seventy-four molecules with anticancer activities against human cancer cell line Huh-7D12, were chosen for the modeling of pharmacophores and Quantitative Structure Activity (3D-QSAR) relationship. Pharmacophoric models containing five sites were generated from three characteristics: hydrogen bond acceptor (A), hydrophobic (H) and aromatic ring (R). After the validation, eight hypotheses which presented a good power of selectivity of the active agents were selected (GH > 0.5). Internal and external validation parameters indicated that the generated 3D-QSAR model exhibits good predictive capabilities and significant statistical reliability (R 2 = 0.9606, Q 2 = 0.955, 2 pred r = 0.952). Pharmacophoric models and contour maps provided significant information on the main structural features of rhodanine derivatives. Twenty-one molecules were returned from the Enamine chemical database after molecular docking studies (HTVS, SP, XP, and IFD). These provided an estimate of ligand-protein binding interactions essential for anticancer activity. The ADMET prediction of these 21 compounds suggested that their pharmacophoric properties lie within an acceptable range. This result indicates that these new compounds provide an effective basis for the methodical development of potent inhibitors of the protein kinase C-kit.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Identification of Potential C-kit Protein Kinase Inhibitors Associated with Human Liver Cancer: Atom-based 3D-QSAR Modeling, Pharmacophores-based Virtual Screening and Molecular Docking Studies","attachmentId":90393708,"attachmentType":"pdf","work_url":"https://www.academia.edu/85803872/Identification_of_Potential_C_kit_Protein_Kinase_Inhibitors_Associated_with_Human_Liver_Cancer_Atom_based_3D_QSAR_Modeling_Pharmacophores_based_Virtual_Screening_and_Molecular_Docking_Studies","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/85803872/Identification_of_Potential_C_kit_Protein_Kinase_Inhibitors_Associated_with_Human_Liver_Cancer_Atom_based_3D_QSAR_Modeling_Pharmacophores_based_Virtual_Screening_and_Molecular_Docking_Studies"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="11539179" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/11539179/Docking_and_3D_QSAR_modeling_of_cyclin_dependent_kinase_5_p25_inhibitors">Docking and 3D-QSAR modeling of cyclin-dependent kinase 5/p25 inhibitors</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="28174458" href="https://independent.academia.edu/nordinlajis">nordin lajis</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Modeling, 2011</p><p class="ds-related-work--abstract ds2-5-body-sm">Structure-based 3D-QSAR approaches (CoMFA and CoMSIA) were applied to understand the structural requirements of the Cyclin-dependent kinase 5/p25 inhibitors. Cyclin-dependent kinase 5 (CDK5) is believed to play an important role in the development of the central nervous system during the process of mammalian embryogenesis. Genetic algorithm based docking program (GOLD) was successfully utilized to orient the compounds inside the binding pocket of the CDK5/p25 structure. The adapted alignment method with the suitable parameters resulted in a reliable model. Furthermore, the final model was robust enough to forecast the activities of test compounds, satisfactorily. The contour maps were produced around the functional groups to understand the SAR requirements. Moreover, we also investigate the structural attributes of the inhibitors which make them selective toward CDK5/ p25 over its close counterpart, i.e., CDK2. The study could be helpful to rationalize the new compounds with better inhibition and selectivity profiles against CDK5/ p25.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Docking and 3D-QSAR modeling of cyclin-dependent kinase 5/p25 inhibitors","attachmentId":46645191,"attachmentType":"pdf","work_url":"https://www.academia.edu/11539179/Docking_and_3D_QSAR_modeling_of_cyclin_dependent_kinase_5_p25_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/11539179/Docking_and_3D_QSAR_modeling_of_cyclin_dependent_kinase_5_p25_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":56403812,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":56403812,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_56403812" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="11643947" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/11643947/Combined_3D_QSAR_modeling_and_molecular_docking_study_on_multi_acting_quinazoline_derivatives_as_HER2_kinase_inhibitors">Combined 3D-QSAR modeling and molecular docking study on multi-acting quinazoline derivatives as HER2 kinase inhibitors</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="26655805" href="https://iausdj.academia.edu/SakoMirzaie">Sako Mirzaie</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Combined 3D-QSAR modeling and molecular docking study on multi-acting quinazoline derivatives as HER2 kinase inhibitors","attachmentId":46591932,"attachmentType":"pdf","work_url":"https://www.academia.edu/11643947/Combined_3D_QSAR_modeling_and_molecular_docking_study_on_multi_acting_quinazoline_derivatives_as_HER2_kinase_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/11643947/Combined_3D_QSAR_modeling_and_molecular_docking_study_on_multi_acting_quinazoline_derivatives_as_HER2_kinase_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="1" data-entity-id="100480463" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/100480463/Ligand_based_pharmacophore_modeling_atom_based_3D_QSAR_analysis_and_molecular_docking_studies_of_phosphoinositide_dependent_kinase_1_inhibitors">Ligand-based pharmacophore modeling; atom-based 3D-QSAR analysis and molecular docking studies of phosphoinositide-dependent kinase-1 inhibitors</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="251850954" href="https://independent.academia.edu/venkatareddygorla">venkata reddy gorla</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Indian Journal of Pharmaceutical Sciences, 2012</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Ligand-based pharmacophore modeling; atom-based 3D-QSAR analysis and molecular docking studies of phosphoinositide-dependent kinase-1 inhibitors","attachmentId":101293030,"attachmentType":"pdf","work_url":"https://www.academia.edu/100480463/Ligand_based_pharmacophore_modeling_atom_based_3D_QSAR_analysis_and_molecular_docking_studies_of_phosphoinositide_dependent_kinase_1_inhibitors","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/100480463/Ligand_based_pharmacophore_modeling_atom_based_3D_QSAR_analysis_and_molecular_docking_studies_of_phosphoinositide_dependent_kinase_1_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="2" data-entity-id="3236854" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/3236854/IKK_%CE%B2_inhibitors_An_analysis_of_drug_receptor_interaction_by_using_Molecular_Docking_and_Pharmacophore_3D_QSAR_approaches">IKK-β inhibitors: An analysis of drug–receptor interaction by using Molecular Docking and Pharmacophore 3D-QSAR approaches</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm 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