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A pharmacophore hypothesis contained five features such as one hydrogen bond acceptors, two hydrogen bond donors and two aromatic rings gives a best atom-based 3D-QSAR model. The obtained 3D-QSAR model had good statistical predictive values, cross validated correlation coefficient, Fisher ratio and Pearson's value. Further the predictability of the pharmacophore model was validated using test set prediction such as 2 pred R and rm 2 metrics. Moreover, this validated pharmacophore model was used as a 3D query to screen the compounds from NCI and ZINC database. The resultant hit compounds were filtered by Lipinski's rule of five as well as the ADME properties. The molecular docking study was carried out to explore the suitable binding capabilities of compounds in the AKT1 active site. Further to confirm the inhibitor potencies, we have calculated the highest occupied molecular orbital, lowest unoccupied molecular orbital and energy gap values for hit compounds. Finally, two hit molecules were selected as novel hit molecules based on good molecular interactions, docking score and electronic properties.","publication_name":"7TH NATIONAL CONFERENCE ON HIERARCHICALLY STRUCTURED MATERIALS (NCHSM-2019)","grobid_abstract_attachment_id":"67940153"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"3D-QSAR modeling, molecular docking and quantum mechanical approaches to identify pleckstrin homology domain of new AKT1 inhibitors","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [164354921]; 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":67940152,"attachmentType":"pdf"}"><img alt="First page of “3D-QSAR modeling, molecular docking and quantum mechanical approaches to identify pleckstrin homology domain of new AKT1 inhibitors”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/67940152/mini_magick20210709-28776-g9lauk.png?1625827632" /><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">3D-QSAR modeling, molecular docking and quantum mechanical approaches to identify pleckstrin homology domain of new AKT1 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="164354921" href="https://independent.academia.edu/CMeganathan"><img alt="Profile image of Chandrasekaran Meganathan" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />Chandrasekaran Meganathan</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">7TH NATIONAL CONFERENCE ON HIERARCHICALLY STRUCTURED MATERIALS (NCHSM-2019)</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">8 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 = 49638776; 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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">The Atom-based 3D-QSAR models have been generated, to identify the essential structural features required for these AKT1 inhibitors using the PHASE module of Schrodinger. A pharmacophore hypothesis contained five features such as one hydrogen bond acceptors, two hydrogen bond donors and two aromatic rings gives a best atom-based 3D-QSAR model. The obtained 3D-QSAR model had good statistical predictive values, cross validated correlation coefficient, Fisher ratio and Pearson's value. Further the predictability of the pharmacophore model was validated using test set prediction such as 2 pred R and rm 2 metrics. Moreover, this validated pharmacophore model was used as a 3D query to screen the compounds from NCI and ZINC database. The resultant hit compounds were filtered by Lipinski's rule of five as well as the ADME properties. The molecular docking study was carried out to explore the suitable binding capabilities of compounds in the AKT1 active site. Further to confirm the inhibitor potencies, we have calculated the highest occupied molecular orbital, lowest unoccupied molecular orbital and energy gap values for hit compounds. Finally, two hit molecules were selected as novel hit molecules based on good molecular interactions, docking score and electronic properties.</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":67940152,"attachmentType":"pdf","workUrl":"https://www.academia.edu/49638776/3D_QSAR_modeling_molecular_docking_and_quantum_mechanical_approaches_to_identify_pleckstrin_homology_domain_of_new_AKT1_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":67940152,"attachmentType":"pdf","workUrl":"https://www.academia.edu/49638776/3D_QSAR_modeling_molecular_docking_and_quantum_mechanical_approaches_to_identify_pleckstrin_homology_domain_of_new_AKT1_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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In this study, we have investigated the use of in silico approaches to develop inhibitors of the pleckstrin homology (PH) domain of AKT (protein kinase B). Various docking/scoring schemes have been evaluated, and the best combination was selected to study the system. Using this strategy, two hits were identified and their binding behaviors were investigated. Robust and predictive QSAR models were built using the k nearest neighbor (kNN) method to study their cellular permeability. Based on our in silico results, long flexible aliphatic tails were proposed to improve the Caco-2 penetration without affecting the binding mode. The modifications enhanced the AKT inhibitory activity of the compounds in cellbased assays, and increased their activity as in vivo antitumor testing.</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":"Computational modeling of novel inhibitors targeting the Akt pleckstrin homology domain","attachmentId":43230901,"attachmentType":"pdf","work_url":"https://www.academia.edu/15392714/Computational_modeling_of_novel_inhibitors_targeting_the_Akt_pleckstrin_homology_domain","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/15392714/Computational_modeling_of_novel_inhibitors_targeting_the_Akt_pleckstrin_homology_domain"><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="20904873" 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/20904873/Novel_chemical_scaffolds_of_the_tumor_marker_AKR1B10_inhibitors_discovered_by_3D_QSAR_pharmacophore_modeling">Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling</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="42037756" href="https://independent.academia.edu/JungKeunSuh">Jung-Keun Suh</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Acta pharmacologica Sinica, 2015</p><p class="ds-related-work--abstract ds2-5-body-sm">Recent evidence suggests that aldo-keto reductase family 1 B10 (AKR1B10) may be a potential diagnostic or prognostic marker of human tumors, and that AKR1B10 inhibitors offer a promising choice for treatment of many types of human cancers. The aim of this study was to identify novel chemical scaffolds of AKR1B10 inhibitors using in silico approaches. The 3D QSAR pharmacophore models were generated using HypoGen. A validated pharmacophore model was selected for virtual screening of 4 chemical databases. The best mapped compounds were assessed for their drug-like properties. The binding orientations of the resulting compounds were predicted by molecular docking. Density functional theory calculations were carried out using B3LYP. The stability of the protein-ligand complexes and the final binding modes of the hit compounds were analyzed using 10 ns molecular dynamics (MD) simulations. The best pharmacophore model (Hypo 1) showed the highest correlation coefficient (0.979), lowest tota...</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":"Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling","attachmentId":41623772,"attachmentType":"pdf","work_url":"https://www.academia.edu/20904873/Novel_chemical_scaffolds_of_the_tumor_marker_AKR1B10_inhibitors_discovered_by_3D_QSAR_pharmacophore_modeling","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/20904873/Novel_chemical_scaffolds_of_the_tumor_marker_AKR1B10_inhibitors_discovered_by_3D_QSAR_pharmacophore_modeling"><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="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="3" data-entity-id="103181885" 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/103181885/3D_QSAR_Studies_Molecular_Docking_Molecular_Dynamic_Simulation_and_ADMET_Proprieties_of_Novel_Pteridinone_Derivatives_as_PLK1_Inhibitors_for_the_Treatment_of_Prostate_Cancer">3D-QSAR Studies, Molecular Docking, Molecular Dynamic Simulation, and ADMET Proprieties of Novel Pteridinone Derivatives as PLK1 Inhibitors for the Treatment of Prostate Cancer</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="273277128" href="https://independent.academia.edu/MohamedElfadili3">Mohamed El fadili</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Life</p><p class="ds-related-work--abstract ds2-5-body-sm">Overexpression of polo-like kinase 1 (PLK1) has been found in many different types of cancers. With its essential role in cell proliferation, PLK1 has been determined to be a broad-spectrum anti-cancer target. In this study, 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations were applied on a series of novel pteridinone derivatives as PLK1 inhibitors to discover anti-cancer drug candidates. In this work, three models—CoMFA (Q² = 0.67, R² = 0.992), CoMSIA/SHE (Q² = 0.69, R² = 0.974), and CoMSIA/SEAH (Q² = 0.66, R² = 0.975)—of pteridinone derivatives were established. The three models that were established gave Rpred2 = 0.683, Rpred 2= 0.758, and Rpred 2= 0.767, respectively. Thus, the predictive abilities of the three proposed models were successfully evaluated. The relations between the different champs and activities were well-demonstrated by the contour chart of the CoMFA and CoMSIA/SEAH models. The results of molecular docking indicated that residues R136, R57, Y...</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 Studies, Molecular Docking, Molecular Dynamic Simulation, and ADMET Proprieties of Novel Pteridinone Derivatives as PLK1 Inhibitors for the Treatment of Prostate Cancer","attachmentId":103256199,"attachmentType":"pdf","work_url":"https://www.academia.edu/103181885/3D_QSAR_Studies_Molecular_Docking_Molecular_Dynamic_Simulation_and_ADMET_Proprieties_of_Novel_Pteridinone_Derivatives_as_PLK1_Inhibitors_for_the_Treatment_of_Prostate_Cancer","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/103181885/3D_QSAR_Studies_Molecular_Docking_Molecular_Dynamic_Simulation_and_ADMET_Proprieties_of_Novel_Pteridinone_Derivatives_as_PLK1_Inhibitors_for_the_Treatment_of_Prostate_Cancer"><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="100480463" 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/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-wsj-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><p class="ds-related-work--abstract ds2-5-body-sm">Phosphoinositide-dependent kinase-1 plays a vital role in the PI3-kinase signaling pathway that regulates gene expression, cell cycle growth and proliferation. The common human cancers include lung, breast, blood and prostate possess over stimulation of the phosphoinositide-dependent kinase-1 signaling and making phosphoinositidedependent kinase-1 an interesting therapeutic target in oncology. A ligand-based pharmacophore and atom-based 3D-QSAR studies were carried out on a set of 82 inhibitors of PDK1. A six point pharmacophore with two hydrogen bond acceptors (A), three hydrogen bond donors (D) and one hydrophobic group (H) was obtained. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least square statistics results. The training set correlation is characterized by partial least square factors (R 2 = 0.9557, SD = 0.2334, F = 215.5, P = 1.407e-32). The test set correlation is characterized by partial least square factors (Q 2 ext = 0.7510, RMSE = 0.5225, Pearson-R =0.8676). The external validation indicated that our QSAR model possess high predictive power with good value of 0.99 and value of 0.88. The docking results show the binding orientations of these inhibitors at active site amino acid residues (Ala162, Thr222, Glu209 and Glu166) of phosphoinositide-dependent kinase-1 protein. The binding free energy interactions of protein-ligand complex have been calculated, which plays an important role in molecular recognition and drug design approach.</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-wsj-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-wsj-grid-card" data-collection-position="5" 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="6" 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="7" data-entity-id="3469740" 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/3469740/Extracting_the_significant_descriptors_by_2D_QSAR_and_docking_efficiency_of_NRTI_drugs_A_Molecular_Modeling_Approach">Extracting the significant descriptors by 2D QSAR and docking efficiency of NRTI drugs:A Molecular Modeling Approach</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="768335" href="https://iictindia.academia.edu/AmitBanerjee">Amit K U M A R Banerjee</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Acquired immunodeficiency syndrome (AIDS) is the most devastating pandemic in recent history of the mankind. It takes a heavy toll of life and is a major deterrent to the economic development of many countries. Human Immunodeficiency Virus type 1 (HIV-1) reverse transcriptase is an important target for chemotherapeutic agents against this devastating disease.</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":"Extracting the significant descriptors by 2D QSAR and docking efficiency of NRTI drugs:A Molecular Modeling Approach","attachmentId":31450415,"attachmentType":"pdf","work_url":"https://www.academia.edu/3469740/Extracting_the_significant_descriptors_by_2D_QSAR_and_docking_efficiency_of_NRTI_drugs_A_Molecular_Modeling_Approach","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/3469740/Extracting_the_significant_descriptors_by_2D_QSAR_and_docking_efficiency_of_NRTI_drugs_A_Molecular_Modeling_Approach"><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="85076402" 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/85076402/Combined_3D_QSAR_Based_Virtual_Screening_and_Molecular_Docking_Study_of_Some_Selected_PDK_1_Kinase_Inhibitors">Combined 3D QSAR Based Virtual Screening and Molecular Docking Study of Some Selected PDK-1 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="4965828" href="https://iitbhu.academia.edu/PradeepSrivastava">Pradeep Srivastava</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Computational Medicine, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">Phosphoinositide-dependent kinase-1 (PDK-1) is an important therapeutic target for the treatment of cancer. In order to identify the important chemical features of PDK-1 inhibitors, a 3D QSAR pharmacophore model was developed based on 21 available PDK-1 inhibitors. The best pharmacophore model (Hypo1) exhibits all the important chemical features required for PDK-1 inhibitors. The correlation coefficient, root mean square deviation (RMSD), and cost difference were 0.96906, 1.0719, and 168.13, respectively, suggesting a good predictive ability of the model (Hypo1) among all the ten pharmacophore models that were analyzed. The best pharmacophore model (Hypo1) was further validated by Fisher’s randomization method (95%), test set method(r=0.87), and the decoy set with the goodness of fit (0.73). Further, this validated pharmacophore model Hypo1 was used as a 3D query to screen the molecules from databases like NCI database and Maybridge. The resultant hit compounds were subsequently sub...</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":"Combined 3D QSAR Based Virtual Screening and Molecular Docking Study of Some Selected PDK-1 Kinase Inhibitors","attachmentId":89889575,"attachmentType":"pdf","work_url":"https://www.academia.edu/85076402/Combined_3D_QSAR_Based_Virtual_Screening_and_Molecular_Docking_Study_of_Some_Selected_PDK_1_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/85076402/Combined_3D_QSAR_Based_Virtual_Screening_and_Molecular_Docking_Study_of_Some_Selected_PDK_1_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></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":67940152,"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":67940152,"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_67940152" 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="92331831" 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/92331831/Alignment_independent_3D_QSAR_quantum_calculations_and_molecular_docking_of_Mer_specific_tyrosine_kinase_inhibitors_as_anticancer_drugs">Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs</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="63009631" href="https://independent.academia.edu/JahanBGhasemi">Jahan B. Ghasemi</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Saudi Pharmaceutical Journal, 2016</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":"Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs","attachmentId":95368700,"attachmentType":"pdf","work_url":"https://www.academia.edu/92331831/Alignment_independent_3D_QSAR_quantum_calculations_and_molecular_docking_of_Mer_specific_tyrosine_kinase_inhibitors_as_anticancer_drugs","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/92331831/Alignment_independent_3D_QSAR_quantum_calculations_and_molecular_docking_of_Mer_specific_tyrosine_kinase_inhibitors_as_anticancer_drugs"><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="100955386" 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/100955386/QSAR_modeling_molecular_docking_studies_and_ADMET_prediction_on_a_series_of_phenylaminopyrimidine_thio_urea_derivatives_as_CK2_inhibitors">QSAR modeling, molecular docking studies and ADMET prediction on a series of phenylaminopyrimidine-(thio) urea derivatives as CK2 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="237288915" href="https://independent.academia.edu/ELHamdaniHicham">Hicham EL Hamdani</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Materials Today: Proceedings, 2020</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":"QSAR modeling, molecular docking studies and ADMET prediction on a series of phenylaminopyrimidine-(thio) urea derivatives as CK2 inhibitors","attachmentId":101629689,"attachmentType":"pdf","work_url":"https://www.academia.edu/100955386/QSAR_modeling_molecular_docking_studies_and_ADMET_prediction_on_a_series_of_phenylaminopyrimidine_thio_urea_derivatives_as_CK2_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/100955386/QSAR_modeling_molecular_docking_studies_and_ADMET_prediction_on_a_series_of_phenylaminopyrimidine_thio_urea_derivatives_as_CK2_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="36485148" 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/36485148/Molecular_docking_and_3D_QSAR_studies_on_the_MAPKAP_K2_inhibitors">Molecular docking and 3D-QSAR studies on the MAPKAP-K2 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="62644927" href="https://independent.academia.edu/EPourbasheer">E. Pourbasheer</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Medicinal Chemistry Research, 2014</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 and 3D-QSAR studies on the MAPKAP-K2 inhibitors","attachmentId":56403812,"attachmentType":"pdf","work_url":"https://www.academia.edu/36485148/Molecular_docking_and_3D_QSAR_studies_on_the_MAPKAP_K2_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/36485148/Molecular_docking_and_3D_QSAR_studies_on_the_MAPKAP_K2_inhibitors"><span class="ds2-5-text-link__content">View PDF</span><span 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