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In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics
Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes the reduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of human DHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cell proliferation. In th...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406960/ https://www.ncbi.nlm.nih.gov/pubmed/30754680 http://dx.doi.org/10.3390/jcm8020233 |
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author | Rana, Rabia Mukhtar Rampogu, Shailima Zeb, Amir Son, Minky Park, Chanin Lee, Gihwan Yoon, Sanghwa Baek, Ayoung Parameswaran, Sarvanan Park, Seok Ju Lee, Keun Woo |
author_facet | Rana, Rabia Mukhtar Rampogu, Shailima Zeb, Amir Son, Minky Park, Chanin Lee, Gihwan Yoon, Sanghwa Baek, Ayoung Parameswaran, Sarvanan Park, Seok Ju Lee, Keun Woo |
author_sort | Rana, Rabia Mukhtar |
collection | PubMed |
description | Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes the reduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of human DHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cell proliferation. In the current study, ligand-based pharmacophore modeling identified and evaluated the critical chemical features of hDHFR inhibitors. A pharmacophore model (Hypo1) was generated from known inhibitors of DHFR with a correlation coefficient (0.94), root mean square (RMS) deviation (0.99), and total cost value (125.28). Hypo1 was comprised of four chemical features, including two hydrogen bond donors (HDB), one hydrogen bond acceptor (HBA), and one hydrophobic (HYP). Hypo1 was validated using Fischer’s randomization, test set, and decoy set validations, employed as a 3D query in a virtual screening at Maybridge, Chembridge, Asinex, National Cancer Institute (NCI), and Zinc databases. Hypo1-retrieved compounds were filtered by an absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment test and Lipinski’s rule of five, where the drug-like hit compounds were identified. The hit compounds were docked in the active site of hDHFR and compounds with Goldfitness score was greater than 44.67 (docking score for the reference compound), clustering analysis, and hydrogen bond interactions were identified. Furthermore, molecular dynamics (MD) simulation identified three compounds as the best inhibitors of hDHFR with the lowest root mean square deviation (1.2 Å to 1.8 Å), hydrogen bond interactions with hDHFR, and low binding free energy (−127 kJ/mol to −178 kJ/mol). Finally, the toxicity prediction by computer (TOPKAT) affirmed the safety of the novel inhibitors of hDHFR in human body. Overall, we recommend novel hit compounds of hDHFR for cancer and rheumatoid arthritis chemotherapeutics. |
format | Online Article Text |
id | pubmed-6406960 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-64069602019-03-22 In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics Rana, Rabia Mukhtar Rampogu, Shailima Zeb, Amir Son, Minky Park, Chanin Lee, Gihwan Yoon, Sanghwa Baek, Ayoung Parameswaran, Sarvanan Park, Seok Ju Lee, Keun Woo J Clin Med Article Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes the reduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of human DHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cell proliferation. In the current study, ligand-based pharmacophore modeling identified and evaluated the critical chemical features of hDHFR inhibitors. A pharmacophore model (Hypo1) was generated from known inhibitors of DHFR with a correlation coefficient (0.94), root mean square (RMS) deviation (0.99), and total cost value (125.28). Hypo1 was comprised of four chemical features, including two hydrogen bond donors (HDB), one hydrogen bond acceptor (HBA), and one hydrophobic (HYP). Hypo1 was validated using Fischer’s randomization, test set, and decoy set validations, employed as a 3D query in a virtual screening at Maybridge, Chembridge, Asinex, National Cancer Institute (NCI), and Zinc databases. Hypo1-retrieved compounds were filtered by an absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment test and Lipinski’s rule of five, where the drug-like hit compounds were identified. The hit compounds were docked in the active site of hDHFR and compounds with Goldfitness score was greater than 44.67 (docking score for the reference compound), clustering analysis, and hydrogen bond interactions were identified. Furthermore, molecular dynamics (MD) simulation identified three compounds as the best inhibitors of hDHFR with the lowest root mean square deviation (1.2 Å to 1.8 Å), hydrogen bond interactions with hDHFR, and low binding free energy (−127 kJ/mol to −178 kJ/mol). Finally, the toxicity prediction by computer (TOPKAT) affirmed the safety of the novel inhibitors of hDHFR in human body. Overall, we recommend novel hit compounds of hDHFR for cancer and rheumatoid arthritis chemotherapeutics. MDPI 2019-02-11 /pmc/articles/PMC6406960/ /pubmed/30754680 http://dx.doi.org/10.3390/jcm8020233 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Rana, Rabia Mukhtar Rampogu, Shailima Zeb, Amir Son, Minky Park, Chanin Lee, Gihwan Yoon, Sanghwa Baek, Ayoung Parameswaran, Sarvanan Park, Seok Ju Lee, Keun Woo In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title | In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title_full | In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title_fullStr | In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title_full_unstemmed | In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title_short | In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics |
title_sort | in silico study probes potential inhibitors of human dihydrofolate reductase for cancer therapeutics |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406960/ https://www.ncbi.nlm.nih.gov/pubmed/30754680 http://dx.doi.org/10.3390/jcm8020233 |
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