{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:27:24Z","timestamp":1791354444395,"version":"4.3.1"},"reference-count":67,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2018M3A9A7057263"],"award-info":[{"award-number":["NRF-2018M3A9A7057263"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Basic Science Research Program","award":["2017R1D1A3B03035738"],"award-info":[{"award-number":["2017R1D1A3B03035738"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Drug resistance is a core issue in cancer chemotherapy. A known folate antagonist, methotrexate (MTX) inhibits human dihydrofolate reductase (hDHFR), the enzyme responsible for the catalysis of 7,8-dihydrofolate reduction to 5,6,7,8-tetrahydrofolate, in biosynthesis and cell proliferation. Structural change in the DHFR enzyme is a significant cause of resistance and the subsequent loss of MTX. In the current study, wild type hDHFR and double mutant (engineered variant) F31R\/Q35E (PDB ID: 3EIG) were subject to computational study. Structure-based pharmacophore modeling was carried out for wild type (WT) and mutant (MT) (variant F31R\/Q35E) hDHFR structures by generating ten models for each. Two pharmacophore models, WT-pharma and MT-pharma, were selected for further computations, and showed excellent ROC curve quality. Additionally, the selected pharmacophore models were validated by the Guner-Henry decoy test method, which yielded high goodness of fit for WT-hDHFR and MT-hDHFR. Using a SMILES string of MTX in ZINC15 with the selections of \u2018clean\u2019, in vitro and in vivo options, 32 MTX-analogs were obtained. Eight analogs were filtered out due to their drug-like properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment tests and Lipinski\u2019s Rule of five. WT-pharma and MT-pharma were further employed as a 3D query in virtual screening with drug-like MTX analogs. Subsequently, seven screening hits along with a reference compound (MTX) were subjected to molecular docking in the active site of WT- and MT-hDHFR. Through a clustering analysis and examination of protein-ligand interactions, one compound was found with a ChemPLP fitness score greater than that of MTX (reference compound). Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM\/PBSA binding free energy. In conclusion, we report on an MTX analog which is capable of inhibiting hDHFR in wild type form, as well as in cases where the enzyme acquires resistance to drugs during chemotherapy treatment.<\/jats:p>","DOI":"10.3390\/molecules25153510","type":"journal-article","created":{"date-parts":[[2020,8,3]],"date-time":"2020-08-03T07:45:57Z","timestamp":1596440757000},"page":"3510","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics"],"prefix":"10.3390","volume":"25","author":[{"given":"Rabia Mukhtar","family":"Rana","sequence":"first","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shailima","family":"Rampogu","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6929-8878","authenticated-orcid":false,"given":"Noman Bin","family":"Abid","sequence":"additional","affiliation":[{"name":"Division of Life Science and Applied Life Science (BK 21), College of Natural Sciences, Gyeongsang National University, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Zeb","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6566-7496","authenticated-orcid":false,"given":"Shraddha","family":"Parate","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gihwan","family":"Lee","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanghwa","family":"Yoon","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumi","family":"Kim","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghwan","family":"Kim","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keun Woo","family":"Lee","sequence":"additional","affiliation":[{"name":"Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,7,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1200\/JCO.1993.11.1.5","article-title":"Ode to methotrexate","volume":"11","author":"Bertino","year":"1993","journal-title":"J. Clin. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1038\/nrc3599","article-title":"Cancer drug resistance: An evolving paradigm","volume":"13","author":"Holohan","year":"2013","journal-title":"Nat. Rev. Cancer"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.ijpddr.2016.09.003","article-title":"Human dihydrofolate reductase influences the sensitivity of the malaria parasite Plasmodium falciparum to ketotifen - A cautionary tale in screening transgenic parasites","volume":"6","author":"Tran","year":"2016","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2441","DOI":"10.1096\/fasebj.4.8.2185970","article-title":"Dihydrofolate reductase as a therapeutic target","volume":"4","author":"Schweitzer","year":"1990","journal-title":"Faseb J."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"7532","DOI":"10.1021\/jm800776a","article-title":"Synthetic and crystallographic studies of a new inhibitor series targeting Bacillus anthracis dihydrofolate reductase","volume":"51","author":"Beierlein","year":"2008","journal-title":"J. Med. Chem."},{"key":"ref_6","first-page":"392","article-title":"Review paper The possibilities and principles of methotrexate treatment of psoriasis-the updated knowledge","volume":"6","year":"2014","journal-title":"Magdal. Czarnecka-Oper. Postep Derm Alergol"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/0163-7258(85)90083-X","article-title":"The cellular pharmacology of methotrexate","volume":"28","author":"Goldman","year":"1985","journal-title":"Pharmacol. Ther."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1182\/blood.V76.1.44.44","article-title":"Accumulation of methotrexate and methotrexate polyglutamates in lymphoblasts at diagnosis of childhood acute lymphoblastic leukemia: A pilot prognostic factor analysis","volume":"76","author":"Whitehead","year":"1990","journal-title":"Blood"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5776","DOI":"10.1016\/S0021-9258(19)70697-8","article-title":"Enzymatic synthesis of folylpolyglutamates. Characterization of the reaction and its products","volume":"255","author":"McGuire","year":"1980","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"9720","DOI":"10.1016\/S0021-9258(17)39298-0","article-title":"Enhanced inhibition of thymidylate synthase by methotrexate polyglutamates","volume":"260","author":"Allegra","year":"1985","journal-title":"J. Biol. Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"4881","DOI":"10.1073\/pnas.82.15.4881","article-title":"Inhibition of phosphoribosylaminoimidazolecarboxamide transformylase by methotrexate and dihydrofolic acid polyglutamates","volume":"82","author":"Allegra","year":"1985","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1056\/NEJM198311033091805","article-title":"The pharmacology and clinical use of methotrexate","volume":"309","author":"Jolivet","year":"1983","journal-title":"N. Engl. J. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2495","DOI":"10.1073\/pnas.80.9.2495","article-title":"Isolation and expression of an altered mouse dihydrofolate reductase cDNA","volume":"80","author":"Simonsen","year":"1983","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"9501","DOI":"10.1016\/S0021-9258(19)68791-0","article-title":"Properties of an altered dihydrofolate reductase encoded by amplified genes in cultured mouse fibroblasts","volume":"256","author":"Haber","year":"1981","journal-title":"J. Biol. Chem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3524","DOI":"10.1016\/S0021-9258(18)94097-4","article-title":"Amplification of a polymorphic dihydrofolate reductase gene expressing an enzyme with decreased binding to methotrexate in a human colon carcinoma cell line, HCT-8R4, resistant to this drug","volume":"264","author":"Srimatkandada","year":"1989","journal-title":"J. Biol. Chem."},{"key":"ref_16","first-page":"38","article-title":"Phenotypic expression in Escherichia coli and nucleotide sequence of two Chinese hamster lung cell cDNAs encoding different dihydrofolate reductases","volume":"4","author":"Melera","year":"1984","journal-title":"Mol. Cell. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"8317","DOI":"10.1016\/S0021-9258(19)39074-X","article-title":"Identification and characterization of a mutation in the dihydrofolate reductase gene from the methotrexate-resistant Chinese hamster ovary cell line Pro-3 MtxRIII","volume":"265","author":"Dicker","year":"1990","journal-title":"J. Biol. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"7025","DOI":"10.1093\/nar\/18.23.7025","article-title":"Isolation and characterization of a variant dihydrofolate reductase cDNA from methotrexate-resistant murine L5178Y cells","volume":"18","author":"Mclvor","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"9547","DOI":"10.1016\/S0021-9258(17)36916-8","article-title":"Methotrexate-resistant variants of human dihydrofolate reductase. Effects of Phe31 substitutions","volume":"269","author":"Chundurus","year":"1994","journal-title":"J. Biol. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"8124","DOI":"10.1021\/bi00247a005","article-title":"Conversion of Arginine to Lysine at Position 70 of Human Dihydrofolate Reductase: Generation of a Methotrexate-Insensitive Mutant Enzyme","volume":"30","author":"Thompson","year":"1991","journal-title":"Biochemistry"},{"key":"ref_21","first-page":"430","article-title":"Variants of human dihydrofolate reductase with substitutions at Leucine-22: Effect on catalytic and inhibitor binding properties","volume":"49","author":"Waltham","year":"1996","journal-title":"Mol. Pharm."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5057","DOI":"10.1074\/jbc.270.10.5057","article-title":"Methotrexate-resistant variants of human dihydrofolate reductase with substitutions of leucine 22. Kinetics, crystallography, and potential as selectable markers","volume":"270","author":"Lewis","year":"1995","journal-title":"J. Biol. Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1177\/1087057108318783","article-title":"2-tier bacterial and in vitro selection of active and methotrexate-resistant variants of human dihydrofolate reductase","volume":"13","author":"Fossati","year":"2008","journal-title":"J. Biomol. Screen."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"9945","DOI":"10.1021\/bi00199a017","article-title":"Critical role of phenylalanine 34 of human dihydrofolate reductase in substrate and inhibitor binding and in catalysis","volume":"33","author":"Nakano","year":"1994","journal-title":"Biochemistry"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3426","DOI":"10.1021\/jm980081y","article-title":"Structure-based design and synthesis of lipophilic 2,4-diamino-6-substituted quinazolines and their evaluation as inhibitors of dihydrofolate reductases and potential antitumor agents","volume":"41","author":"Gangjee","year":"1998","journal-title":"J Med Chem"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1107\/S0907444904030422","article-title":"Understanding the role of Leu22 variants in methotrexate resistance: Comparison of wild-type and Leu22Arg variant mouse and human dihydrofolate reductase ternary crystal complexes with methotrexate and NADPH","volume":"61","author":"Cody","year":"2005","journal-title":"Acta Cryst. D. Biol. Cryst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"13897","DOI":"10.1021\/bi971711l","article-title":"Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523","volume":"36","author":"Cody","year":"1997","journal-title":"Biochemistry"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1107\/S0907444903001951","article-title":"Analysis of two polymorphic forms of a pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolate binary complex with human dihydrofolate reductase","volume":"59","author":"Cody","year":"2003","journal-title":"Acta Cryst. D. Biol. Cryst."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1107\/S0907444903014963","article-title":"Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase","volume":"59","author":"Cody","year":"2003","journal-title":"Acta Cryst. D. Biol. Cryst."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1107\/S0907444904002094","article-title":"Structure determination of tetrahydroquinazoline antifolates in complex with human and Pneumocystis carinii dihydrofolate reductase: Correlations between enzyme selectivity and stereochemistry","volume":"60","author":"Cody","year":"2004","journal-title":"Acta Cryst.. D. Biol. Cryst."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"20079","DOI":"10.1074\/jbc.M109.018010","article-title":"Multiple Conformers in Active Site of Human Dihydrofolate Reductase F31R\/Q35E Double Mutant Suggest Structural Basis for Methotrexate Resistance","volume":"284","author":"Volpato","year":"2009","journal-title":"J. Biol. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/j.jmb.2007.07.076","article-title":"Increasing methotrexate resistance by combination of active-site mutations in human dihydrofolate reductase","volume":"373","author":"Volpato","year":"2007","journal-title":"J. Mol. Biol."},{"key":"ref_33","first-page":"2069","article-title":"Comparison of the protection of cells from antifolates by transduced human dihydrofolate reductase mutants","volume":"8","author":"Patel","year":"1997","journal-title":"Hum. Gene."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1124\/pr.112.007336","article-title":"Computational methods in drug discovery","volume":"66","author":"Sliwoski","year":"2014","journal-title":"Pharmacol. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/S1367-5931(97)80108-1","article-title":"Computational approaches for combinatorial library design and molecular diversity analysis","volume":"1","author":"Blaney","year":"1997","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1960","DOI":"10.1126\/science.287.5460.1960","article-title":"Drug discovery: A historical perspective","volume":"287","author":"Drews","year":"2000","journal-title":"Science (80-. )."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1038\/aps.2012.109","article-title":"Computational drug discovery","volume":"33","author":"Kong","year":"2012","journal-title":"Acta Pharm. Sin."},{"key":"ref_38","first-page":"1","article-title":"Optimized peptide based inhibitors targeting the dihydrofolate reductase pathway in cancer OPEN","volume":"8","author":"Singh","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1021\/acs.jcim.5b00559","article-title":"ZINC 15\u2014Ligand Discovery for Everyone","volume":"55","author":"Sterling","year":"2015","journal-title":"J. Chem. Inf. Model."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3072","DOI":"10.1529\/biophysj.104.050286","article-title":"Comparison of Multiple Molecular Dynamics Trajectories Calculated for the Drug-Resistant HIV-1 Integrase T66I\/M154I Catalytic Domain","volume":"88","author":"Brigo","year":"2005","journal-title":"Biophys. J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2014\/502618","article-title":"Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A","volume":"2014","author":"Swetha","year":"2014","journal-title":"Adv. Bioinform."},{"key":"ref_42","first-page":"2535","article-title":"A study on dihydrofolate reductase and its inhibitors: A review","volume":"4","author":"Rao","year":"2013","journal-title":"Int. J"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/path.1706","article-title":"Molecular mechanisms of drug resistance","volume":"205","author":"Longley","year":"2005","journal-title":"J. Pathol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1146\/annurev.biophys.33.110502.133613","article-title":"Structure, dynamics, and catalytic function of dihydrofolate reductase","volume":"33","author":"Schnell","year":"2004","journal-title":"Annu. Rev. Biophys. Biomol. Struct"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Raimondi, M.V., Randazzo, O., Franca, M.L., Barone, G., Vignoni, E., Rossi, D., and Collina, S. (2019). DHFR Inhibitors: Reading the Past for Discovering Novel Anticancer Agents. Molecules, 24.","DOI":"10.3390\/molecules24061140"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3424","DOI":"10.2174\/1381612824666180810162944","article-title":"The development of pharmacophore modeling: Generation and recent applications in drug discovery","volume":"24","author":"Lu","year":"2018","journal-title":"Curr. Pharm. Des."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1111\/j.1432-1033.1988.tb14108.x","article-title":"Crystal structure of human dihydrofolate reductase complexed with folate","volume":"174","author":"Oefner","year":"1988","journal-title":"Eur. J. Biochem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1016\/j.jbi.2005.02.008","article-title":"The use of receiver operating characteristic curves in biomedical informatics","volume":"38","author":"Lasko","year":"2005","journal-title":"J. Biomed. Inform."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1021\/jm049092j","article-title":"Virtual screening workflow development guided by the \u201creceiver operating characteristic\u201d curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4","volume":"48","author":"Triballeau","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Herrera-Mayorga, V., Lara-Ram\u00edrez, E.E., Chac\u00f3n-Vargas, K.F., Aguirre-Alvarado, C., Rodr\u00edguez-P\u00e1ez, L., Alc\u00e1ntara-Farf\u00e1n, V., Cordero-Mart\u00ednez, J., Nogueda-Torres, B., Reyes-Espinosa, F., and Bocanegra-Garc\u00eda, V. (2019). Structure-based virtual screening and in vitro evaluation of new trypanosoma cruzi cruzain inhibitors. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20071742"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.addr.2012.09.019","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"64","author":"Lipinski","year":"2012","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Ramasamy, S., Chin, S.P., Sukumaran, S.D., Buckle, M.J.C., Kiew, L.V., and Chung, L.Y. (2015). In Silico and in vitro analysis of bacoside A aglycones and its derivatives as the constituents responsible for the cognitive effects of Bacopa monnieri. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0126565"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1002\/cpch.27","article-title":"Overview of methods and strategies for conducting virtual small molecule screening","volume":"Volume 9","author":"Fradera","year":"2017","journal-title":"Current Protocols in Chemical Biology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/protein\/15.3.185","article-title":"Molecular dynamics simulations as a tool for improving protein stability","volume":"15","author":"Pikkemaat","year":"2002","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"4552","DOI":"10.1016\/j.bmc.2007.04.011","article-title":"Structure-based design, synthesis and preliminary evaluation of selective inhibitors of dihydrofolate reductase from Mycobacterium tuberculosis","volume":"15","author":"Smith","year":"2007","journal-title":"Bioorg. Med. Chem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1111\/febs.13662","article-title":"Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities","volume":"283","author":"Bhosle","year":"2016","journal-title":"Febs J."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e1501240","DOI":"10.1126\/sciadv.1501240","article-title":"Regulation of protein-ligand binding affinity by hydrogen bond pairing","volume":"2","author":"Chen","year":"2016","journal-title":"Sci. Adv."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Liu, J., Su, M., Liu, Z., Li, J., Li, Y., and Wang, R. (2017). Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1750-5"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1021\/ci500081m","article-title":"Comparative assessment of scoring functions on an updated benchmark: 2. evaluation methods and general results","volume":"54","author":"Li","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1021\/ct800557h","article-title":"Thermostat artifacts in replica exchange molecular dynamics simulations","volume":"5","author":"Rosta","year":"2009","journal-title":"J. Chem. Theory Comput."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2359","DOI":"10.1002\/jcc.21816","article-title":"SwissParam: A fast force field generation tool for small organic molecules","volume":"32","author":"Zoete","year":"2011","journal-title":"J. Comput. Chem."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity-rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"064703","DOI":"10.1063\/1.4891578","article-title":"Challenges in first-principles NPT molecular dynamics of Soft Porous Crystals: A case study on MIL-53(Ga)","volume":"141","author":"Haigis","year":"2014","journal-title":"J. Chem. Phys."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1002\/jcc.21773","article-title":"Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5","volume":"32","author":"Abraham","year":"2011","journal-title":"J. Comput. Chem."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1021\/ci500020m","article-title":"g_mmpbsa \u2014A GROMACS Tool for High-Throughput MM-PBSA Calculations","volume":"54","author":"Kumari","year":"2014","journal-title":"J. Chem. Inf. 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