{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T13:48:56Z","timestamp":1787838536824,"version":"build-2784847793"},"reference-count":41,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Graphics and Modelling"],"published-print":{"date-parts":[[2023,5]]},"DOI":"10.1016\/j.jmgm.2023.108422","type":"journal-article","created":{"date-parts":[[2023,1,21]],"date-time":"2023-01-21T02:38:05Z","timestamp":1674268685000},"page":"108422","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"special_numbering":"C","title":["Roxadustat and its failure: A comparative dynamic study"],"prefix":"10.1016","volume":"120","author":[{"given":"Kainat","family":"Gul","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naila","family":"Zaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syed Sikander","family":"Azam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmgm.2023.108422_bib1","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1182\/blood-2018-06-856500","article-title":"Anemia of inflammation","volume":"133","author":"Weiss","year":"2019","journal-title":"Blood"},{"key":"10.1016\/j.jmgm.2023.108422_bib2","doi-asserted-by":"crossref","first-page":"6964","DOI":"10.1021\/acs.jmedchem.7b01686","article-title":"Prolyl hydroxylase inhibitors: a breakthrough in the therapy of anemia associated with chronic diseases","volume":"61","author":"Joharapurkar","year":"2018","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108422_bib3","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1681\/ASN.2011111078","article-title":"Mechanisms of anemia in CKD","volume":"23","author":"Babitt","year":"2012","journal-title":"J. Am. Soc. Nephrol."},{"key":"10.1016\/j.jmgm.2023.108422_bib4","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1016\/j.jfma.2018.03.017","article-title":"Physiology and pathophysiology of renal erythropoietin-producing cells","volume":"117","author":"Shih","year":"2018","journal-title":"J. Formos. Med. Assoc."},{"key":"10.1016\/j.jmgm.2023.108422_bib5","first-page":"39","article-title":"Renal anemia: a nephrologist's view","volume":"15","author":"Tsagalis","year":"2011","journal-title":"Hippokratia"},{"key":"10.1016\/j.jmgm.2023.108422_bib6","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1093\/ndt\/gfv302","article-title":"Randomized placebo-controlled dose-ranging and pharmacodynamics study of roxadustat (FG-4592) to treat anemia in nondialysis-dependent chronic kidney disease (NDD-CKD) patients","volume":"30","author":"Besarab","year":"2015","journal-title":"Nephrol. Dial. Transplant."},{"key":"10.1016\/j.jmgm.2023.108422_bib7","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/ndt\/16.suppl_7.25","article-title":"Hyporesponsiveness to recombinant human erythropoietin","volume":"16","author":"Dr\u00fceke","year":"2001","journal-title":"Nephrol. Dial. Transplant."},{"key":"10.1016\/j.jmgm.2023.108422_bib8","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1053\/j.ajkd.2007.09.015","article-title":"Exploring relative mortality and epoetin alfa dose among hemodialysis patients","volume":"51","author":"Bradbury","year":"2008","journal-title":"Am. J. Kidney Dis."},{"key":"10.1016\/j.jmgm.2023.108422_bib9","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1053\/j.ajkd.2012.07.014","article-title":"Dose of erythropoiesis-stimulating agents and adverse outcomes in CKD: a metaregression analysis","volume":"61","author":"Koulouridis","year":"2013","journal-title":"Am. J. Kidney Dis."},{"key":"10.1016\/j.jmgm.2023.108422_bib10","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1056\/NEJMoa1005109","article-title":"Erythropoietic response and outcomes in kidney disease and type 2 diabetes","volume":"363","author":"Solomon","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jmgm.2023.108422_bib11","doi-asserted-by":"crossref","first-page":"5725","DOI":"10.1021\/acs.jmedchem.8b01596","article-title":"Small-molecule modulators of the hypoxia-inducible factor pathway: development and therapeutic applications","volume":"62","author":"Li","year":"2019","journal-title":"J. Med. Chem."},{"key":"10.1016\/j.jmgm.2023.108422_bib12","series-title":"Discovery of Prolyl Hydroxylase 2 Inhibitors with New Chemical Scaffolds as in Vivo Active Erythropoietin Inducers through a Combined Virtual Screening Strategy","first-page":"270","author":"Yu","year":"2020"},{"key":"10.1016\/j.jmgm.2023.108422_bib13","first-page":"1","article-title":"United States securities and exchange commission form 10-Q","volume":"94043","author":"One","year":"2010","journal-title":"Exchange Organ. Behav. Teach J."},{"key":"10.1016\/j.jmgm.2023.108422_bib14","doi-asserted-by":"crossref","first-page":"5286","DOI":"10.1039\/C7RA12259D","article-title":"Discovery of VEGFR2 inhibitors by integrating na\u00efve Bayesian classification, molecular docking and drug screening approaches","volume":"8","author":"Kang","year":"2018","journal-title":"RSC Adv"},{"key":"10.1016\/j.jmgm.2023.108422_bib15","first-page":"2278","article-title":"Ligand based pharmacophore modeling and virtual screening for novel antidiabetics targeting PPAR-gamma","author":"Bairy","year":"2019","journal-title":"Int. J. Innovative Technol. Explor. Eng."},{"key":"10.1016\/j.jmgm.2023.108422_bib16","doi-asserted-by":"crossref","first-page":"8388","DOI":"10.1021\/ja204075s","article-title":"Computer review of ChemDraw ultra 12.0","volume":"133","author":"Cousins","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.jmgm.2023.108422_bib17","first-page":"1","article-title":"Open Babel: an open chemical toolbox - 1758-2946-3-33.pdf","volume":"3","author":"O'Boyle","year":"2011","journal-title":"J. Cheminf."},{"key":"10.1016\/j.jmgm.2023.108422_bib18","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.molstruc.2012.06.032","article-title":"A combined ligand and structure based approach to design potent PPAR-alpha agonists","volume":"1028","author":"V Dhoke","year":"2012","journal-title":"J. Mol. Struct."},{"key":"10.1016\/j.jmgm.2023.108422_bib19","doi-asserted-by":"crossref","first-page":"5832","DOI":"10.1007\/s00044-013-0571-y","article-title":"The discovery of potential cyclin A\/CDK2 inhibitors: a combination of 3D QSAR pharmacophore modeling, virtual screening, and molecular docking studies","volume":"22","author":"Ece","year":"2013","journal-title":"Med. Chem. Res."},{"key":"10.1016\/j.jmgm.2023.108422_bib20","doi-asserted-by":"crossref","DOI":"10.1155\/2014\/812148","article-title":"Ligand based pharmacophore modeling and virtual screening studies to design novel HDAC2 inhibitors","volume":"2014","author":"Kandakatla","year":"2014","journal-title":"Adv. Bioinformatics."},{"key":"10.1016\/j.jmgm.2023.108422_bib21","series-title":"Recent Advances in Developing Inhibitors for Hypoxia-Inducible Factor Prolyl Hydroxylases and Their Therapeutic Implications","first-page":"20551","author":"Kim","year":"2015"},{"key":"10.1016\/j.jmgm.2023.108422_bib22","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general Amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jmgm.2023.108422_bib23","series-title":"Amber 2016 Reference Manual (Covers Amber16 and AmberTools16)","first-page":"3","author":"Case","year":"2016"},{"key":"10.1016\/j.jmgm.2023.108422_bib24","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1080\/00268978800101881","article-title":"An analysis of the accuracy of Langevin and molecular dynamics algorithms","volume":"65","author":"Pastor","year":"1988","journal-title":"Mol. Phys."},{"key":"10.1016\/j.jmgm.2023.108422_bib25","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V","article-title":"A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations","volume":"22","author":"Kr\u00e4utler","year":"2001","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jmgm.2023.108422_bib26","doi-asserted-by":"crossref","first-page":"6606","DOI":"10.1039\/C7CP07869B","article-title":"Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder","volume":"20","author":"Xue","year":"2018","journal-title":"Phys. Chem. Chem. Phys."},{"key":"10.1016\/j.jmgm.2023.108422_bib27","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1063\/1.439486","article-title":"Molecular dynamics simulations at constant pressure and\/or temperature","volume":"72","author":"Andersen","year":"1980","journal-title":"J. Chem. Phys."},{"key":"10.1016\/j.jmgm.2023.108422_bib28","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1007\/s12539-018-0299-y","article-title":"Subtractive genomics, molecular docking and molecular dynamics simulation revealed LpxC as a potential drug target against multi-drug resistant Klebsiella pneumoniae","volume":"11","author":"Ahmad","year":"2019","journal-title":"Interdiscipl. Sci. Comput. Life Sci."},{"key":"10.1016\/j.jmgm.2023.108422_bib29","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmgm.2020.107585","article-title":"Journal of Molecular Graphics and Modelling Role of ring positioning and preferential occupation of ligand obtained through molecular dynamics simulation of peptidoglycan associated lipoprotein (Pal)","volume":"98","author":"Ahmad","year":"2020","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/j.jmgm.2023.108422_bib30","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0924-2031(99)00014-4","article-title":"Deriving the 3D structure of organic molecules from their infrared spectra","volume":"19","author":"Hemmer","year":"1999","journal-title":"Vib. Spectrosc."},{"key":"10.1016\/j.jmgm.2023.108422_bib31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00894-018-3601-3","article-title":"AFD : an application for bi-molecular interaction using axial frequency distribution","volume":"24","author":"Raza","year":"2018","journal-title":"J. Mol. Model."},{"key":"10.1016\/j.jmgm.2023.108422_bib32","doi-asserted-by":"crossref","first-page":"3556","DOI":"10.1016\/j.jcp.2011.01.048","article-title":"Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming","volume":"230","author":"Levine","year":"2011","journal-title":"J. Comput. Phys."},{"key":"10.1016\/j.jmgm.2023.108422_bib33","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.jmgm.2017.03.002","article-title":"Molecular dynamics simulation studies of novel \u03b2-lactamase inhibitor","volume":"74","author":"Ul Haq","year":"2017","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/j.jmgm.2023.108422_bib34","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.jmgm.2023.108422_bib35","doi-asserted-by":"crossref","first-page":"6825","DOI":"10.1073\/pnas.0409005102","article-title":"Calculation of absolute protein-ligand binding free energy from computer simulations","volume":"102","author":"Woo","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.jmgm.2023.108422_bib36","doi-asserted-by":"crossref","first-page":"2436","DOI":"10.1002\/jcc.24467","article-title":"Calculating protein-ligand binding affinities with MMPBSA: method and error analysis","volume":"37","author":"Wang","year":"2016","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.jmgm.2023.108422_bib37","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1002\/minf.201100135","article-title":"Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method","volume":"31","author":"Homeyer","year":"2012","journal-title":"Mol. Inform."},{"key":"10.1016\/j.jmgm.2023.108422_bib38","doi-asserted-by":"crossref","first-page":"12788","DOI":"10.1021\/acs.chemrev.0c00534","article-title":"Thermodynamics and kinetics of drug-target binding by molecular simulation","volume":"120","author":"Decherchi","year":"2020","journal-title":"Chem. Rev."},{"key":"10.1016\/j.jmgm.2023.108422_bib39","series-title":"MMPBSA . Py : an E Ffi Cient Program for End-State Free Energy Calculations","author":"Miller","year":"2012"},{"key":"10.1016\/j.jmgm.2023.108422_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2021.e07463","article-title":"QSAR, molecular docking and ADMET properties in silico studies of novel 4,5,6,7-tetrahydrobenzo[D]-thiazol-2-Yl derivatives derived from dimedone as potent anti-tumor agents through inhibition of C-Met receptor tyrosine kinase","volume":"7","author":"Daoui","year":"2021","journal-title":"Heliyon"},{"key":"10.1016\/j.jmgm.2023.108422_bib41","first-page":"16","article-title":"First record of the ground beetle trechoblemus postilenatus (Coleoptera, carabidae) in primorskii krai, far east","volume":"165","author":"Sundukov","year":"2006","journal-title":"Entomology (Tokyo)"}],"container-title":["Journal of Molecular Graphics and Modelling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326323000207?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326323000207?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T21:12:01Z","timestamp":1761081121000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1093326323000207"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5]]},"references-count":41,"alternative-id":["S1093326323000207"],"URL":"https:\/\/doi.org\/10.1016\/j.jmgm.2023.108422","relation":{},"ISSN":["1093-3263"],"issn-type":[{"value":"1093-3263","type":"print"}],"subject":[],"published":{"date-parts":[[2023,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Roxadustat and its failure: A comparative dynamic study","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Graphics and Modelling","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmgm.2023.108422","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"108422"}}