References
- Ahmed, M., Qadir, M. A., Hameed, A., Arshad, M. N., Asiri, A. M., & Muddassar, M. (2017). Azomethines, isoxazole, N-substituted pyrazoles and pyrimidine containing curcumin derivatives: Urease inhibition and molecular modeling studies. Biochemical and Biophysical Research Communications, 490(2), 434–440. https://doi.org/https://doi.org/10.1016/j.bbrc.2017.06.059
- Arora, R., Issar, U., & Kakkar, R. (2019). Identification of novel urease inhibitors: Pharmacophore modeling, virtual screening and molecular docking studies. Journal of Biomolecular Structure & Dynamics, 37(16), 4312–4326. https://doi.org/https://doi.org/10.1080/07391102.2018.1546620
- Baell, J. B., & Nissink, J. W. M. (2018). Seven year itch: Pan-assay interference compounds (PAINS) in 2017-utility and limitations. ACS Chemical Biology, 13(1), 36–44. https://doi.org/https://doi.org/10.1021/acschembio.7b00903
- Barbieri, R., Coppo, E., Marchese, A., Daglia, M., Sobarzo-Sánchez, E., Nabavi, S. F., & Nabavi, S. M. (2017). Phytochemicals for human disease: An update on plant-derived compounds antibacterial activity. Microbiological Research, 196, 44–68. https://doi.org/https://doi.org/10.1016/j.micres.2016.12.003
- Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nature Chemistry, 4(2), 90–98. https://doi.org/https://doi.org/10.1038/nchem.1243
- Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33.
- Chopdar, K. S., Dash, G. C., Mohapatra, P. K., Nayak, B., & Raval, M. K. (2019). In silico design of covalently bonding catechol-based urease inhibitors as potential candidates for treatment of Helicobacter pylori infection. International Journal of Pharma Research and Health Sciences, 7(6), 3111–3116. https://doi.org/https://doi.org/10.21276/ijprhs.2019.06.08
- Chopdar, K. S., Mohapatra, P. K., Nayak, B., & Raval, M. K. (2020). In silico screening of ZINC database for discovery of novel urease inhibitors as a remedy to gastro-duodenal ulcer caused by Helicobacter pylori. International Journal of Pharmaceutical Sciences and Drug Research, 12, 46–52.
- Cox, G. M., Mukherjee, J., Cole, G. T., Casadevall, A., & Perfect, J. R. (2000). Urease as a virulence factor in experimental cryptococcosis. Infection and Immunity, 68(2), 443–448. https://doi.org/https://doi.org/10.1128/iai.68.2.443-448.2000
- Eaton, K. A., Brooks, C. L., Morgan, D. R., & Krakowka, S. (1991). Essential role of urease in pathogenesis of gastritis induced by Helicobacter pylori in gnotobiotic piglets. Infection and Immunity, 59(7), 2470–2475. https://doi.org/https://doi.org/10.1128/IAI.59.7.2470-2475.1991
- Gilson, M. K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., & Chong, J. (2016). BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Research, 44(D1), D1045–D1063. https://doi.org/https://doi.org/10.1093/nar/gkv1072
- Golbraikh, A., & Tropsha, A. (2002). Beware of q2! Journal of Molecular Graphics and Modelling, 20(4), 269–276. https://doi.org/https://doi.org/10.1016/S1093-3263(01)00123-1
- Habala, L., Devinsky, F., & Egger, A. E. (2018). Metal complexes as urease inhibitors. Journal of Coordination Chemistry, 71(7), 907–940. https://doi.org/https://doi.org/10.1080/00958972.2018.1458228
- Hassan, S. T. S., & Sudomova, M. (2017). The development of urease inhibitors: What opportunities exist for better treatment of Helicobacter pylori infection in children? Children, 4(1), 2. https://doi.org/https://doi.org/10.3390/children4010002
- Hassan, S. T. S., & Zemlicka, M. (2016). Plant-derived urease inhibitors as alternative chemotherapeutic agents. Archiv Der Pharmazie, 349(7), 507–516. https://doi.org/https://doi.org/10.1002/ardp.201500019
- Javidfar, M., & Ahmadi, S. (2020). QSAR modelling of larvicidal phytocompounds against Aedes aegypti using index of ideality of correlation. SAR and QSAR in Environmental Research, 31(10), 717–739. https://doi.org/https://doi.org/10.1080/1062936X.2020.1806922
- Jones, B. D., Lockatell, C. V., Johnson, D. E., Warren, J. W., & Mobley, H. L. (1990). Construction of a urease-negative mutant of Proteus mirabilis: Analysis of virulence in a mouse model of ascending urinary tract infection. Infection and Immunity, 58(4), 1120–1123. https://doi.org/https://doi.org/10.1128/IAI.58.4.1120-1123.1990
- Kafarski, P. & Talma, M. (2018). Recent advances in design of new urease inhibitors: A review. Journal of Advanced Research, 13, 101–112.
- Karimi, A., Majlesi, M., & Rafieian-Kopaei, M. (2015). Herbal versus synthetic drugs; beliefs and facts. Journal of Nephropharmacology, 4(1), 27–30.
- Krieger, E., & Vriend, G. (2014). YASARA view – Molecular graphics for all devices - from smartphones to workstations. Bioinformatics (Oxford, England), 30(20), 2981–2982. https://doi.org/https://doi.org/10.1093/bioinformatics/btu426
- Kumar, A., & Chauhan, S. (2018). Use of simplified molecular input line entry system and molecular graph based descriptors in prediction and design of pancreatic lipase inhibitors. Future Medicinal Chemistry, 10(13), 1603–1622. https://doi.org/https://doi.org/10.4155/fmc-2018-0024
- Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics (Oxford, England), 33(22), 3658–3660. https://doi.org/https://doi.org/10.1093/bioinformatics/btx491
- Loes, A. N., Ruyle, L., Arvizu, M., Gresko, K. E., Wilson, A. L., & Deutch, C. E. (2014). Inhibition of urease activity in the urinary tract pathogen Staphylococcus saprophyticus. Letters in Applied Microbiology, 58(1), 31–41. https://doi.org/https://doi.org/10.1111/lam.12153
- Mangal, M., Sagar, P., Singh, H., Raghava, G. P. S., & Agarwal, S. M. (2013). NPACT: Naturally occurring plant-based anti-cancer compound-activity-target database. Nucleic Acids Research, 41(D1), D1124–D1129. https://doi.org/https://doi.org/10.1093/nar/gks1047
- Modolo, L. V., da-Silva, C. J., Brandão, D. S., & Chaves, I. S. (2018). A minireview on what we have learned about urease inhibitors of agricultural interest since mid-2000s. Journal of Advanced Research, 13, 29–37. https://doi.org/https://doi.org/10.1016/j.jare.2018.04.001
- NagoorMeeran, M. F., Goyal, S. N., Suchal, K., Sharma, C., Patil, C. R., & Ojha, S. K. (2018). Pharmacological properties, molecular mechanisms, and pharmaceutical development of asiatic acid: A pentacyclic triterpenoid of therapeutic promise. Frontiers Pharmacology, 9, 892.
- Roy, P., & Roy, K. (2008). On some aspects of variable selection for partial least squares regression models. QSAR & Combinatorial Science, 27(3), 302–313. https://doi.org/https://doi.org/10.1002/qsar.200710043
- Roy, P. P., Paul, S., Mitra, I., & Roy, K. (2009). On two novel parameters for validation of predictive QSAR models. Molecules (Basel, Switzerland), 14(5), 1660–1701. https://doi.org/https://doi.org/10.3390/molecules14051660
- Rutherford, J. C. (2014). The emerging role of urease as a general microbial virulence factor. PLoS Pathogens, 10(5), e1004062. https://doi.org/https://doi.org/10.1371/journal.ppat.1004062
- Todeschini, R., & Consonni, V. (2000). Handbook of molecular descriptors. Wiley-VCH.
- Toropov, A. A., Toropova, A. P., Lombardo, A., Roncaglioni, A., Benfenati, E., & Gini, G. (2011). CORAL: Building up the model for bio-concentration factor and defining it’s applicability domain. European Journal of Medicinal Chemistry, 46(4), 1400–1403. https://doi.org/https://doi.org/10.1016/j.ejmech.2011.01.018
- Toropov, A. A., Toropova, A. P., & Raska, I. (2008). QSPR modeling of octanol/water partition coefficient for vitamins by optimal descriptors calculated with SMILES. European Journal of Medicinal Chemistry, 43(4), 714–740. https://doi.org/https://doi.org/10.1016/j.ejmech.2007.05.007
- Toropova, A. P., & Toropov, A. A. (2017). The index of ideality of correlation: A criterion of predictability of QSAR models for skin permeability. Science of the Total Environment, 586, 466–472. https://doi.org/https://doi.org/10.1016/j.scitotenv.2017.01.198
- Toropova, A. P., Toropov, A. A., Veselinovic, J. B., Miljkovic, F. N., & Veselinovic, A. M. (2014). QSAR models for HEPT derivates as NNRTI inhibitors based on Monte Carlo method. European Journal of Medicinal Chemistry, 77, 298–305. https://doi.org/https://doi.org/10.1016/j.ejmech.2014.03.013
- Trott, O., & Olson, A. J. (2010). AutoDockVina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461.
- Tsuda, M., Karita, M., Morshed, M. G., Okita, K., & Nakazawa, T. A. (1994). A urease-negative mutant of Helicobacter pylori constructed by allelic exchange mutagenesis lacks the ability to colonize the nude mouse stomach. Infection and Immunity, 62(8), 3586–3589. https://doi.org/https://doi.org/10.1128/IAI.62.8.3586-3589.1994
- Ul-Haq, Z., Ashraf, S., Al-Majid, A. M., & Barakat, A. (2016). 3D-QSAR studies on barbituric acid derivatives as urease inhibitors and the effect of charges on the quality of a model. International Journal of Molecular Sciences, 17(5), 657. https://doi.org/https://doi.org/10.3390/ijms17050657
- Xiao, Z. P., Wang, X. D., Peng, Z. Y., Huang, S., Yang, P., Li, Q. S., Zhou, L. H., Hu, X. J., Wu, L. J., Zhou, Y., & Zhu, H. L. (2012). Molecular docking, kinetics study, and structure-activity relationship analysis of quercetin and its analogous as Helicobacter pylori urease inhibitors. Journal of Agricultural and Food Chemistry, 60(42), 10572–10577. https://doi.org/https://doi.org/10.1021/jf303393n
- Yang, X., Koohi-Moghadam, M., Wang, R., Chang, Y.-Y., Woo, P. C. Y., Wang, J., Li, H., & Sun, H. (2018). Metallochaperone UreG serves as a new target for design of urease inhibitor: A novel strategy for development of antimicrobials. PLoS Biology, 16(1), e2003887. https://doi.org/https://doi.org/10.1371/journal.pbio.2003887
- Zhang, Y., & Skolnick, J. (2005). TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 33(7), 2302–2309. https://doi.org/https://doi.org/10.1093/nar/gki524