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0-26.741-21.543-14.142-34.142l128.662-128.662c7.81-7.81 20.474-7.81 28.284 0l128.662 128.662c12.6 12.599 3.676 34.142-14.142 34.142z"></path></svg></button></li></ul></li></ul></div> <script src="//a.academia-assets.com/assets/webpack_bundles/fast_loswp-bundle-86832e264efa375cdd3fa5979579c95643bf6a5c1b20c95ec7a98005fcb4b9a4.js" defer="defer"></script><script>window.loswp = {}; window.loswp.author = 3893510; window.loswp.bulkDownloadFilterCounts = {}; window.loswp.hasDownloadableAttachment = true; window.loswp.hasViewableAttachments = true; // TODO: just use routes for this window.loswp.loginUrl = "https://www.academia.edu/login?post_login_redirect_url=https%3A%2F%2Fwww.academia.edu%2F3356166%2FNew_antitrichomonal_drug_like_chemicals_selected_by_bond_edge_based_TOMOCOMD_CARDD_descriptors%3Fauto%3Ddownload"; window.loswp.translateUrl = "https://www.academia.edu/login?post_login_redirect_url=https%3A%2F%2Fwww.academia.edu%2F3356166%2FNew_antitrichomonal_drug_like_chemicals_selected_by_bond_edge_based_TOMOCOMD_CARDD_descriptors%3Fshow_translation%3Dtrue"; window.loswp.previewableAttachments = [{"id":50317924,"identifier":"Attachment_50317924","shouldShowBulkDownload":false}]; window.loswp.shouldDetectTimezone = true; window.loswp.shouldShowBulkDownload = true; window.loswp.showSignupCaptcha = false window.loswp.willEdgeCache = false; window.loswp.work = {"work":{"id":3356166,"created_at":"2013-04-22T04:05:16.144-07:00","from_world_paper_id":117782713,"updated_at":"2024-11-14T06:11:05.803-08:00","_data":{"publisher":"jbx.sagepub.com","grobid_abstract":"Bond-based quadratic indices, new TOMOCOMD-CARDD molecular descriptors, and linear discriminant analysis (LDA) were used to discover novel lead trichomonacidals. The obtained LDA-based quantitative structure-activity relationships (QSAR) models, using nonstochastic and stochastic indices, were able to classify correctly 87.91% (87.50%) and 89.01% (84.38%) of the chemicals in training (test) sets, respectively. They showed large Matthews correlation coefficients of 0.75 (0.71) and 0.78 (0.65) for the training (test) sets, correspondingly. Later, both models were applied to the virtual screening of 21 chemicals to find new lead antitrichomonal agents. Predictions agreed with experimental results to a great extent because a correct classification for both models of 95.24% (20 of 21) of the chemicals was obtained. Of the 21 compounds that were screened and synthesized, 2 molecules (chemicals G-1, UC-245) showed high to moderate cytocidal activity at the concentration of 10 mg/ml, another 2 compounds (G-0 and CRIS-148) showed high cytocidal activity only at the concentration of 100 mg/ml, and the remaining chemicals (from CRIS-105 to were inactive at these assayed concentrations. Finally, the best candidate, G-1 (cytocidal activity of 100% at 10 mg/ml) was in vivo assayed in ovariectomized Wistar rats achieving promising results as a trichomonacidal drug-like compound. (Journal of Biomolecular Screening 2008:785-794).","publication_date":"2008,,","publication_name":"Journal of …","grobid_abstract_attachment_id":"50317924"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"New antitrichomonal drug-like chemicals selected by bond (edge)-based TOMOCOMD-CARDD descriptors","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [3893510]; 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.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div 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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">New antitrichomonal drug-like chemicals selected by bond (edge)-based TOMOCOMD-CARDD descriptors</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="3893510" href="https://independent.academia.edu/Jos%C3%A9MtzMtz"><img alt="Profile image of José Mtz Mtz" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/3893510/1441707/1765081/s65_jos_.mtz_mtz.jpg" />José Mtz Mtz</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">2008, Journal of …</p></div><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" 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Ligand-Based Virtual Screening Models</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="32430225" href="https://uio-ec.academia.edu/ORiveraborroto">O. Rivera-borroto</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="32165320" href="https://uea-ec.academia.edu/OscarMiguelRiveraBorroto">Oscar Miguel Rivera Borroto</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="11902051" href="https://independent.academia.edu/yovanmimarrero">yovani Marrero-Ponce</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="46646280" href="https://ucm.academia.edu/JoseEscario">Jose A Escario</a></div><p class="ds-related-work--metadata ds2-5-body-xs">… Organic Chemistry X</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":"Quick Access to Potential Trichomonacidals Through Bond Linear Indices-Trained Ligand-Based Virtual Screening Models","attachmentId":45816961,"attachmentType":"pdf","work_url":"https://www.academia.edu/12968247/Quick_Access_to_Potential_Trichomonacidals_Through_Bond_Linear_Indices_Trained_Ligand_Based_Virtual_Screening_Models","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/12968247/Quick_Access_to_Potential_Trichomonacidals_Through_Bond_Linear_Indices_Trained_Ligand_Based_Virtual_Screening_Models"><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="11028432" 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/11028432/Discovery_of_Novel_Trichomonacidals_Using_LDA_Driven_QSAR_Models_and_Bond_Based_Bilinear_Indices_as_Molecular_Descriptors">Discovery of Novel Trichomonacidals Using LDA-Driven QSAR Models and Bond-Based Bilinear Indices as Molecular Descriptors</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="26686316" href="https://independent.academia.edu/NormaRivera4">Norma Rivera</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Qsar & Combinatorial Science, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">Few years ago, the World Health Organization estimated the number of adults with trichomoniasis at 170 million worldwide, more than the combined numbers for gonorrhea, syphilis, and chlamydia. To combat this sexually transmitted disease, Metronidazole (MTZ) has emerged, since 1959, as a powerful drug for the systematic treatment of infected patients. However, increasing resistance to MTZ, adverse effects associated to high-dose MTZ therapies and very expensive conventional technologies related to the development of new trichomonacidals necessitate novel computational methods that shorten the drug discovery pipeline. Therefore, bond-based bilinear indices, new 2-D bond-based TOMOCOMD-CARDD Molecular Descriptors (MDs), and Linear Discriminant Analysis (LDA) are combined to discover novel antitrichomonal agents. Generated models, using non-stochastic and stochastic indices, are able to classify correctly the 90.11% (93.75%) and the 87.92% (87.50%) of chemicals in the training (test) sets, respectively. In addition, they show large Matthews' correlation coefficients (C) of 0.80 (0.86) and 0.76 (0.71) for the training (test) sets, respectively. The result of predictions on the 10% full-out cross-validation test also evidences the quality of both models. In order to test the models' predictive power, 12 compounds, already proved against Trichomonas vaginalis (Tv), are screened in a simulated virtual screening experiment. As a result, they correctly classified 9 out of 12 (75.00%) and 10 out of 12 (83.33%) of the chemicals, respectively, which were the most important criteria to validate the models. Finally, in order to prove the reach of TOMOCOMD-CARDD approach and to discover new trichomonacidals, these classification functions were applied to a set of eight chemicals which, in turn, were synthesized and tested toward in vitro activity against Tv. As a result, experimental observations confirm theoretical predictions to a great extent, since it is gained a correct classification of 87.50% (7/8) of chemicals. Biological tests also show several candidates as antitrichomonals, since almost all the compounds [VAM2-(3–8)] exhibit pronounced cytocidal activities of 100% at the concentration of 100 μg/mL and at 24 h (48 h) but VAM2–2: 99.37% (100%), and it is remarkable that these compounds do not show toxic activity in macrophage assays at this concentration. The Quantitative Structure–Activity Relationship (QSAR) models presented here could significantly reduce the number of synthesized and tested compounds as well as could act as virtual shortcuts to new chemical entities with trichomonacidal 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":"Discovery of Novel Trichomonacidals Using LDA-Driven QSAR Models and Bond-Based Bilinear Indices as Molecular Descriptors","attachmentId":46959618,"attachmentType":"pdf","work_url":"https://www.academia.edu/11028432/Discovery_of_Novel_Trichomonacidals_Using_LDA_Driven_QSAR_Models_and_Bond_Based_Bilinear_Indices_as_Molecular_Descriptors","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/11028432/Discovery_of_Novel_Trichomonacidals_Using_LDA_Driven_QSAR_Models_and_Bond_Based_Bilinear_Indices_as_Molecular_Descriptors"><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="4896564" 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/4896564/Predicting_antitrichomonal_activity_A_computational_screening_using_atom_based_bilinear_indices_and_experimental_proofs">Predicting antitrichomonal activity: A computational screening using atom-based bilinear indices and experimental proofs</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="6386912" href="https://independent.academia.edu/JoseAntonioMachadoCastillo">Jose Antonio Machado Castillo</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioorganic & Medicinal Chemistry, 2006</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":"Predicting antitrichomonal activity: A computational screening using atom-based bilinear indices and experimental proofs","attachmentId":49572846,"attachmentType":"pdf","work_url":"https://www.academia.edu/4896564/Predicting_antitrichomonal_activity_A_computational_screening_using_atom_based_bilinear_indices_and_experimental_proofs","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/4896564/Predicting_antitrichomonal_activity_A_computational_screening_using_atom_based_bilinear_indices_and_experimental_proofs"><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="3356154" 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/3356154/Bond_based_linear_indices_in_QSAR_computational_discovery_of_novel_anti_trichomonal_compounds">Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds</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="3893510" href="https://independent.academia.edu/Jos%C3%A9MtzMtz">José Mtz Mtz</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Computer-aided Molecular Design, 2008</p><p class="ds-related-work--abstract ds2-5-body-sm">Trichomonas vaginalis (Tv) is the causative agent of the most common, non-viral, sexually transmitted disease in women and men worldwide. Since 1959, metronidazole (MTZ) has been the drug of choice in the systemic treatment of trichomoniasis. However, resistance to MTZ in some patients and the great cost associated with the development of new trichomonacidals make necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, bond-based linear indices, new TOMOCOMD-CARDD molecular descriptors, and linear discriminant analysis were used to discover novel trichomonacidal chemicals. The obtained models, using non-stochastic and stochastic indices, are able to classify correctly 89.01% (87.50%) and 82.42% (84.38%) of the chemicals in the training (test) sets, respectively. These results validate the models for their use in the ligand-based virtual screening. In addition, they show large Matthews’ correlation coefficients (C) of 0.78 (0.71) and 0.65 (0.65) for the training (test) sets, correspondingly. The result of predictions on the 10% full-out cross-validation test also evidences the robustness of the obtained models. Later, both models are applied to the virtual screening of 12 compounds already proved against Tv. As a result, they correctly classify 10 out of 12 (83.33%) and 9 out of 12 (75.00%) of the chemicals, respectively; which is the most important criterion for validating the models. Besides, these classification functions are applied to a library of seven chemicals in order to find novel antitrichomonal agents. These compounds are synthesized and tested for in vitro activity against Tv. As a result, experimental observations approached to theoretical predictions, since it was obtained a correct classification of 85.71% (6 out of 7) of the chemicals. Moreover, out of the seven compounds that are screened, synthesized and biologically assayed, six compounds (VA7-34, VA7-35, VA7-37, VA7-38, VA7-68, VA7-70) show pronounced cytocidal activity at the concentration of 100 μg/ml at 24 h (48 h) within the range of 98.66%–100% (99.40%–100%), while only two molecules (chemicals VA7-37 and VA7-38) show high cytocidal activity at the concentration of 10 μg/ml at 24 h (48 h): 98.38% (94.23%) and 97.59% (98.10%), correspondingly. The LDA-assisted QSAR models presented here could significantly reduce the number of synthesized and tested compounds and could increase the chance of finding new chemical entities with anti-trichomonal 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":"Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds","attachmentId":50317933,"attachmentType":"pdf","work_url":"https://www.academia.edu/3356154/Bond_based_linear_indices_in_QSAR_computational_discovery_of_novel_anti_trichomonal_compounds","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" 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