{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T01:51:13Z","timestamp":1783043473279,"version":"3.54.6"},"reference-count":78,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T00:00:00Z","timestamp":1669334400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T00:00:00Z","timestamp":1669334400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100008522","name":"University of Illinois at Chicago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008522","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2023,1]]},"DOI":"10.1007\/s10822-022-00490-1","type":"journal-article","created":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T16:12:38Z","timestamp":1669392758000},"page":"53-65","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Evaluation of interactions between the hepatitis C virus NS3\/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations"],"prefix":"10.1007","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0328-702X","authenticated-orcid":false,"given":"Jinhong","family":"Ren","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9825-9026","authenticated-orcid":false,"given":"Tasneem M.","family":"Vaid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2570-8120","authenticated-orcid":false,"given":"Hyun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1737-168X","authenticated-orcid":false,"given":"Isabel","family":"Ojeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8246-4081","authenticated-orcid":false,"given":"Michael E.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,11,25]]},"reference":[{"key":"490_CR1","doi-asserted-by":"publisher","first-page":"E165","DOI":"10.3390\/cells7100165","volume":"7","author":"M Barathan","year":"2018","unstructured":"Barathan M, Mohamed R, Yong YK et al (2018) Viral persistence and chronicity in hepatitis C virus infection: role of T-cell apoptosis,senescence and exhaustion. Cells 7:E165. https:\/\/doi.org\/10.3390\/cells7100165","journal-title":"Cells"},{"key":"490_CR2","doi-asserted-by":"publisher","first-page":"85","DOI":"10.4103\/jrms.JRMS_524_19","volume":"25","author":"H Khadempour-Arani","year":"2020","unstructured":"Khadempour-Arani H, Shojaeian A, Mehri-Ghahfarrokhi A et al (2020) Identifying genotype profile of chronic hepatitis C infection in Southwest Iran. J Res Med Sci 25:85. https:\/\/doi.org\/10.4103\/jrms.JRMS_524_19","journal-title":"J Res Med Sci"},{"key":"490_CR3","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.653717","author":"K Aishanjiang","year":"2021","unstructured":"Aishanjiang K, Wei X, Fu Y et al (2021) Circular RNAs and hepatocellular carcinoma: new epigenetic players with diagnostic and prognostic roles. Front Oncol. https:\/\/doi.org\/10.3389\/fonc.2021.653717","journal-title":"Front Oncol"},{"key":"490_CR4","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.3390\/jcm10081694","volume":"10","author":"L Frazzoni","year":"2021","unstructured":"Frazzoni L, Sikandar U, Metelli F et al (2021) Hepatocellular carcinoma recurrence after hepatitis C virus therapy with direct-acting antivirals. A systematic review and meta-analysis. J Clin Med 10:1694. https:\/\/doi.org\/10.3390\/jcm10081694","journal-title":"J Clin Med"},{"key":"490_CR5","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.3390\/cancers13071729","volume":"13","author":"W Teng","year":"2021","unstructured":"Teng W, Liu YC, Jeng WJ, Su CW (2021) Tertiary prevention of HCC in chronic hepatitis B or C infected patients. Cancers Basel 13:1729. https:\/\/doi.org\/10.3390\/cancers13071729","journal-title":"Cancers Basel"},{"key":"490_CR6","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1002\/hep.26744","volume":"59","author":"DB Smith","year":"2014","unstructured":"Smith DB, Bukh J, Kuiken C et al (2014) Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 59:318\u2013327. https:\/\/doi.org\/10.1002\/hep.26744","journal-title":"Hepatology"},{"key":"490_CR7","doi-asserted-by":"publisher","first-page":"17","DOI":"10.3350\/cmh.2013.19.1.17","volume":"19","author":"CW Kim","year":"2013","unstructured":"Kim CW, Chang K-M (2013) Hepatitis C virus: virology and life cycle. Clin Mol Hepatol 19:17\u201325. https:\/\/doi.org\/10.3350\/cmh.2013.19.1.17","journal-title":"Clin Mol Hepatol"},{"key":"490_CR8","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1126\/science.285.5424.110","volume":"285","author":"V Lohmann","year":"1999","unstructured":"Lohmann V, Korner F, Koch J-O et al (1999) Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285:110\u2013113","journal-title":"Science"},{"key":"490_CR9","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1016\/j.chom.2014.10.008","volume":"16","author":"D Paul","year":"2014","unstructured":"Paul D, Madan V, Bartenschlager R (2014) Hepatitis C virus RNA replication and assembly: living on the fat of the land. Cell Host Microbe 16:569\u2013579","journal-title":"Cell Host Microbe"},{"key":"490_CR10","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/S0092-8674(00)81351-3","volume":"87","author":"JL Kim","year":"1996","unstructured":"Kim JL, Morgenstern KA, Lin C et al (1996) Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87:343\u2013355. https:\/\/doi.org\/10.1016\/S0092-8674(00)81351-3","journal-title":"Cell"},{"key":"490_CR11","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/S0092-8674(00)81350-1","volume":"87","author":"RA Love","year":"1996","unstructured":"Love RA, Parge HE, Wickersham JA et al (1996) The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 87:331\u2013342","journal-title":"Cell"},{"key":"490_CR12","doi-asserted-by":"publisher","first-page":"e0236447","DOI":"10.1371\/journal.pone.0236447","volume":"15","author":"HTL Tran","year":"2020","unstructured":"Tran HTL, Morikawa K, Anggakusuma, et al (2020) OCIAD1 is a host mitochondrial substrate of the hepatitis C virus NS3-4A protease. PLoS ONE 15:e0236447. https:\/\/doi.org\/10.1371\/journal.pone.0236447","journal-title":"PLoS ONE"},{"key":"490_CR13","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-3-642-27340-7_5","volume":"369","author":"D Moradpour","year":"2013","unstructured":"Moradpour D, Penin F (2013) Hepatitis C virus proteins: from structure to function. Curr Top Microbiol Immunol 369:113\u2013142. https:\/\/doi.org\/10.1007\/978-3-642-27340-7_5","journal-title":"Curr Top Microbiol Immunol"},{"key":"490_CR14","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1021\/jm400164c","volume":"57","author":"Y Jiang","year":"2014","unstructured":"Jiang Y, Andrews SW, Condroski KR et al (2014) Discovery of danoprevir (ITMN-191\/R7227), a highly selective and potent inhibitor of hepatitis C virus (HCV) NS3\/4A protease. J Med Chem 57:1753\u20131769","journal-title":"J Med Chem"},{"key":"490_CR15","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1038\/nbt.2020","volume":"29","author":"AD Kwong","year":"2011","unstructured":"Kwong AD, Kauffman RS, Hurter P, Mueller P (2011) Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus. Nat Biotechnol 29:993\u20131003","journal-title":"Nat Biotechnol"},{"key":"490_CR16","doi-asserted-by":"publisher","first-page":"11972","DOI":"10.1021\/acs.jmedchem.1c00554","volume":"64","author":"D Nageswara Rao","year":"2021","unstructured":"Nageswara Rao D, Zephyr J, Henes M et al (2021) Discovery of quinoxaline-based p1\u2013p3 macrocyclic ns3\/4a protease inhibitors with potent activity against drug-resistant hepatitis C virus variants. J Med Chem 64:11972\u201311989. https:\/\/doi.org\/10.1021\/acs.jmedchem.1c00554","journal-title":"J Med Chem"},{"key":"490_CR17","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1021\/acsmedchemlett.5b00425","volume":"7","author":"SF Neelamkavil","year":"2016","unstructured":"Neelamkavil SF, Agrawal S, Bara T et al (2016) Discovery of MK-8831, a novel spiro-proline macrocycle as a pan-genotypic HCV-NS3\/4a protease inhibitor. ACS Med Chem Lett 7:111\u2013116","journal-title":"ACS Med Chem Lett"},{"key":"490_CR18","doi-asserted-by":"publisher","first-page":"1673","DOI":"10.1021\/jm401507s","volume":"57","author":"\u00c5 Rosenquist","year":"2014","unstructured":"Rosenquist \u00c5, Samuelsson B, Johansson P-O et al (2014) Discovery and development of simeprevir (TMC435), a HCV NS3\/4A protease inhibitor. J Med Chem 57:1673\u20131693","journal-title":"J Med Chem"},{"key":"490_CR19","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1021\/ml400466p","volume":"5","author":"U Shah","year":"2014","unstructured":"Shah U, Jayne C, Chackalamannil S et al (2014) Novel quinoline-based P2\u2013P4 macrocyclic derivatives as pan-genotypic HCV NS3\/4a protease inhibitors. ACS Med Chem Lett 5:264\u2013269","journal-title":"ACS Med Chem Lett"},{"key":"490_CR20","doi-asserted-by":"publisher","first-page":"4161","DOI":"10.1128\/AAC.00324-12","volume":"56","author":"V Summa","year":"2012","unstructured":"Summa V, Ludmerer SW, McCauley JA et al (2012) MK-5172, a selective inhibitor of hepatitis C virus NS3\/4a protease with broad activity across genotypes and resistant variants. Antimicrob Agents Chemother 56:4161\u20134167","journal-title":"Antimicrob Agents Chemother"},{"key":"490_CR21","doi-asserted-by":"publisher","first-page":"493","DOI":"10.2147\/TCRM.S66731","volume":"10","author":"I Gentile","year":"2014","unstructured":"Gentile I, Buonomo AR, Zappulo E et al (2014) Asunaprevir, a protease inhibitor for the treatment of hepatitis C infection. Ther Clin Risk Manag. 10:493\u2013504. https:\/\/doi.org\/10.2147\/TCRM.S66731","journal-title":"Ther Clin Risk Manag."},{"key":"490_CR22","doi-asserted-by":"publisher","first-page":"2443","DOI":"10.1021\/jm9015526","volume":"53","author":"JA McCauley","year":"2010","unstructured":"McCauley JA, McIntyre CJ, Rudd MT et al (2010) Discovery of vaniprevir (MK-7009), a macrocyclic hepatitis C virus NS3\/4a protease inhibitor. J Med Chem 53:2443\u20132463. https:\/\/doi.org\/10.1021\/jm9015526","journal-title":"J Med Chem"},{"key":"490_CR23","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.3851\/Imp2359","volume":"17","author":"A Agarwal","year":"2012","unstructured":"Agarwal A, Zhang B, Olek E et al (2012) Rapid and sharp decline in HCV upon monotherapy with NS3 protease inhibitor, ACH-1625. Antivir Ther 17:1533\u20131539. https:\/\/doi.org\/10.3851\/Imp2359","journal-title":"Antivir Ther"},{"key":"490_CR24","doi-asserted-by":"publisher","first-page":"2629","DOI":"10.1016\/j.bmcl.2012.01.017","volume":"22","author":"XC Sheng","year":"2012","unstructured":"Sheng XC, Appleby T, Butler T et al (2012) Discovery of GS-9451: an acid inhibitor of the hepatitis C virus NS3\/4A protease. Bioorg Med Chem Lett 22:2629\u20132634","journal-title":"Bioorg Med Chem Lett"},{"key":"490_CR25","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1021\/acs.orglett.5b00418","volume":"17","author":"H Li","year":"2015","unstructured":"Li H, Scott JP, Chen C et al (2015) Synthesis of bis-macrocyclic HCV protease inhibitor MK-6325 via intramolecular sp2\u2013sp3 Suzuki-Miyaura coupling and ring closing metathesis. Org Lett 17:1533\u20131536. https:\/\/doi.org\/10.1021\/acs.orglett.5b00418","journal-title":"Org Lett"},{"key":"490_CR26","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1093\/cid\/cir774","volume":"54","author":"AA Butt","year":"2012","unstructured":"Butt AA, Kanwal F (2012) Boceprevir and telaprevir in the management of hepatitis C virus-infected patients. Clin Infect Dis 54:96\u2013104. https:\/\/doi.org\/10.1093\/cid\/cir774","journal-title":"Clin Infect Dis"},{"key":"490_CR27","doi-asserted-by":"publisher","first-page":"3261","DOI":"10.2174\/0929867321666140706125950","volume":"21","author":"I Gentile","year":"2014","unstructured":"Gentile I, Borgia F, Riccardo Buonomo A et al (2014) ABT-450: a novel protease inhibitor for the treatment of hepatitis C virus infection. Curr Med Chem 21:3261\u20133270","journal-title":"Curr Med Chem"},{"key":"490_CR28","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1128\/AAC.02264-15","volume":"60","author":"EJ Lawitz","year":"2016","unstructured":"Lawitz EJ, O\u2019Riordan WD, Asatryan A et al (2016) Potent antiviral activities of the direct-acting antivirals ABT-493 and ABT-530 with three-day monotherapy for hepatitis C virus genotype 1 infection. Antimicrob Agents Chemother 60:1546\u20131555","journal-title":"Antimicrob Agents Chemother"},{"key":"490_CR29","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1111\/j.1365-2893.2012.01617.x","volume":"19","author":"F Poordad","year":"2012","unstructured":"Poordad F, Dieterich D (2012) Treating hepatitis C: current standard of care and emerging direct-acting antiviral agents. J Viral Hepat 19:449\u2013464. https:\/\/doi.org\/10.1111\/j.1365-2893.2012.01617.x","journal-title":"J Viral Hepat"},{"key":"490_CR30","unstructured":"Classification of Direct-Acting Antiviral Agents in HCV Treatment Regimens. https:\/\/hepatitis.va.gov\/hcv\/treatment\/hcv-daa-class.asp"},{"key":"490_CR31","doi-asserted-by":"publisher","first-page":"103247","DOI":"10.1016\/j.drugpo.2021.103247","volume":"96","author":"A Amoako","year":"2021","unstructured":"Amoako A, Ortiz-Paredes D, Engler K et al (2021) Patient and provider perceived barriers and facilitators to direct acting antiviral hepatitis C treatment among priority populations in high income countries: A knowledge synthesis. Int J Drug Policy 96:103247. https:\/\/doi.org\/10.1016\/j.drugpo.2021.103247","journal-title":"Int J Drug Policy"},{"key":"490_CR32","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.3390\/diagnostics12051177","volume":"12","author":"CM Danilescu","year":"2022","unstructured":"Danilescu CM, Ionescu M, Sandulescu DL et al (2022) Perceived stress in hepatitis C Virus infected patients under the DAA-based therapy. Diagnostics 12:1177. https:\/\/doi.org\/10.3390\/diagnostics12051177","journal-title":"Diagnostics"},{"key":"490_CR33","doi-asserted-by":"publisher","first-page":"101626","DOI":"10.1016\/j.clinre.2021.101626","volume":"45","author":"S Roger","year":"2021","unstructured":"Roger S, Ducancelle A, Le Guillou-Guillemette H et al (2021) HCV virology and diagnosis. Clin Res Hepatol Gastroenterol 45:101626","journal-title":"Clin Res Hepatol Gastroenterol"},{"key":"490_CR34","doi-asserted-by":"publisher","first-page":"291","DOI":"10.3390\/vaccines9030291","volume":"9","author":"R Velazquez-Moctezuma","year":"2021","unstructured":"Velazquez-Moctezuma R, Augestad EH, Castelli M et al (2021) Mechanisms of hepatitis C virus escape from vaccine-relevant neutralizing antibodies. Vaccines Basel 9:291. https:\/\/doi.org\/10.3390\/vaccines9030291","journal-title":"Vaccines Basel"},{"key":"490_CR35","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1007\/s12272-017-0949-3","volume":"40","author":"G Jin","year":"2017","unstructured":"Jin G, Lee J, Lee K (2017) Chemical genetics-based development of small molecules targeting hepatitis C virus. Arch Pharm Res 40:1021\u20131036. https:\/\/doi.org\/10.1007\/s12272-017-0949-3","journal-title":"Arch Pharm Res"},{"key":"490_CR36","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1097\/QCO.0000000000000319","volume":"29","author":"DM Forton","year":"2016","unstructured":"Forton DM (2016) How much of a problem is resistance in treating hepatitis C? Curr Opin Infect Dis 29:625\u2013631. https:\/\/doi.org\/10.1097\/QCO.0000000000000319","journal-title":"Curr Opin Infect Dis"},{"key":"490_CR37","doi-asserted-by":"publisher","first-page":"679","DOI":"10.3390\/microorganisms10040679","volume":"10","author":"AA Shoun","year":"2022","unstructured":"Shoun AA, Abozahra R, Baraka K et al (2022) Identifying different mutation sites leading to resistance to the Direct-Acting Antiviral (DAA) sofosbuvir in hepatitis C virus patients from Egypt. Microorganisms 10:679. https:\/\/doi.org\/10.3390\/microorganisms10040679","journal-title":"Microorganisms"},{"key":"490_CR38","doi-asserted-by":"publisher","first-page":"371","DOI":"10.3851\/IMP3303","volume":"24","author":"SB Park","year":"2019","unstructured":"Park SB, Boyer A, Hu Z et al (2019) Discovery and characterization of a novel HCV inhibitor targeting the late stage of HCV life cycle. Antivir Ther 24:371\u2013381. https:\/\/doi.org\/10.3851\/IMP3303","journal-title":"Antivir Ther"},{"key":"490_CR39","doi-asserted-by":"publisher","first-page":"2551","DOI":"10.1016\/S0968-0896(03)00179-2","volume":"11","author":"A Johansson","year":"2003","unstructured":"Johansson A, Poliakov A, \u00c5kerblom E et al (2003) Acyl sulfonamides as potent protease inhibitors of the hepatitis C virus full-Length NS3 (Protease-Helicase\/NTPase): A comparative study of different C-terminals. Bioorg Med Chem 11:2551\u20132568. https:\/\/doi.org\/10.1016\/S0968-0896(03)00179-2","journal-title":"Bioorg Med Chem"},{"key":"490_CR40","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1021\/jm401338c","volume":"57","author":"SR LaPlante","year":"2014","unstructured":"LaPlante SR, Nar H, Lemke CT et al (2014) Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. J Med Chem 57:1777\u20131789","journal-title":"J Med Chem"},{"key":"490_CR41","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1016\/j.bmc.2005.08.045","volume":"14","author":"R R\u00f6nn","year":"2006","unstructured":"R\u00f6nn R, Sabnis YA, Gossas T et al (2006) Exploration of acyl sulfonamides as carboxylic acid replacements in protease inhibitors of the hepatitis C virus full-length NS3. Bioorg Med Chem 14:544\u2013559. https:\/\/doi.org\/10.1016\/j.bmc.2005.08.045","journal-title":"Bioorg Med Chem"},{"key":"490_CR42","doi-asserted-by":"publisher","first-page":"2245","DOI":"10.1021\/ci300177p","volume":"52","author":"R Chaudhuri","year":"2012","unstructured":"Chaudhuri R, Lee H, Truong L et al (2012) Identification of non-macrocyclic small molecule inhibitors against the NS3\/4A Serine protease of hepatitis C virus through in silico screening. J Chem Inf Model 52:2245\u20132256. https:\/\/doi.org\/10.1021\/ci300177p","journal-title":"J Chem Inf Model"},{"key":"490_CR43","doi-asserted-by":"publisher","first-page":"e75144","DOI":"10.1371\/journal.pone.0075144","volume":"8","author":"H Lee","year":"2013","unstructured":"Lee H, Zhu T, Patel K et al (2013) High-throughput screening (HTS) and hit validation to identify small molecule inhibitors with activity against NS3\/4A proteases from multiple hepatitis C virus genotypes. PLoS ONE 8:e75144","journal-title":"PLoS ONE"},{"key":"490_CR44","doi-asserted-by":"publisher","first-page":"2349","DOI":"10.1016\/j.bmcl.2019.06.009","volume":"29","author":"J Ren","year":"2019","unstructured":"Ren J, Ojeda I, Patel M et al (2019) Exploring small molecules with pan-genotypic inhibitory activities against hepatitis C virus NS3\/4A serine protease. Bioorg Med Chem Lett 29:2349\u20132353. https:\/\/doi.org\/10.1016\/j.bmcl.2019.06.009","journal-title":"Bioorg Med Chem Lett"},{"key":"490_CR45","doi-asserted-by":"publisher","first-page":"11796","DOI":"10.1002\/chem.202000642","volume":"26","author":"TM Vaid","year":"2020","unstructured":"Vaid TM, Chalmers DK, Scott DJ, Gooley PR (2020) INPHARMA-based determination of ligand binding modes at \u03b11 -adrenergic receptors explains the molecular basis of subtype selectivity. Chem Weinh Bergstr Ger 26:11796\u201311805. https:\/\/doi.org\/10.1002\/chem.202000642","journal-title":"Chem Weinh Bergstr Ger"},{"key":"490_CR46","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/s42269-022-00796-y","volume":"46","author":"S Ejeh","year":"2022","unstructured":"Ejeh S, Uzairu A, Shallangwa GA et al (2022) In silico design and pharmacokinetics investigation of some novel hepatitis C virus NS5B inhibitors: pharmacoinformatics approach. Bull Natl Res Cent 46:109. https:\/\/doi.org\/10.1186\/s42269-022-00796-y","journal-title":"Bull Natl Res Cent"},{"key":"490_CR47","doi-asserted-by":"publisher","first-page":"e1563","DOI":"10.1002\/wcms.1563","volume":"12","author":"R Friedman","year":"2022","unstructured":"Friedman R (2022) Computational studies of protein\u2013drug binding affinity changes upon mutations in the drug target. WIREs Comput Mol Sci 12:e1563. https:\/\/doi.org\/10.1002\/wcms.1563","journal-title":"WIREs Comput Mol Sci"},{"key":"490_CR48","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1080\/07391102.2020.1839561","volume":"40","author":"I Hdoufane","year":"2022","unstructured":"Hdoufane I, Bjij I, Oubahmane M et al (2022) In silico design and analysis of NS4B inhibitors against hepatitis C virus. J Biomol Struct Dyn 40:1915\u20131929. https:\/\/doi.org\/10.1080\/07391102.2020.1839561","journal-title":"J Biomol Struct Dyn"},{"key":"490_CR49","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1515\/pac-2021-1104","volume":"94","author":"R Hussain","year":"2022","unstructured":"Hussain R, Khalid H, Fatmi MQ (2022) HCV genotype-specific drug discovery through structure-based virtual screening. Pure Appl Chem 94:809\u2013818. https:\/\/doi.org\/10.1515\/pac-2021-1104","journal-title":"Pure Appl Chem"},{"key":"490_CR50","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1007\/s10822-021-00389-3","volume":"35","author":"H Sahakyan","year":"2021","unstructured":"Sahakyan H (2021) Improving virtual screening results with MM\/GBSA and MM\/PBSA rescoring. J Comput Aided Mol Des 35:731\u2013736. https:\/\/doi.org\/10.1007\/s10822-021-00389-3","journal-title":"J Comput Aided Mol Des"},{"key":"490_CR51","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.24011","volume":"36","author":"PC Su","year":"2015","unstructured":"Su PC, Tsai CC, Mehboob S et al (2015) Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM\/MM-GBSA ligand binding energies of F-tularensis enoyl-ACP reductase (FabI). J Comput Chem 36:1859\u20131873. https:\/\/doi.org\/10.1002\/jcc.24011","journal-title":"J Comput Chem"},{"key":"490_CR52","doi-asserted-by":"publisher","first-page":"1700","DOI":"10.1021\/acs.jpcb.1c09424","volume":"126","author":"Y-X Zhu","year":"2022","unstructured":"Zhu Y-X, Sheng Y-J, Ma Y-Q, Ding H-M (2022) Assessing the performance of screening MM\/PBSA in Protein-ligand interactions. J Phys Chem B 126:1700\u20131708. https:\/\/doi.org\/10.1021\/acs.jpcb.1c09424","journal-title":"J Phys Chem B"},{"key":"490_CR53","doi-asserted-by":"publisher","first-page":"21052","DOI":"10.1073\/pnas.1110534108","volume":"108","author":"N Schiering","year":"2011","unstructured":"Schiering N, D\u2019Arcy A, Villard F et al (2011) A macrocyclic HCV NS3\/4A protease inhibitor interacts with protease and helicase residues in the complex with its full-length target. Proc Natl Acad Sci 108:21052\u201321056","journal-title":"Proc Natl Acad Sci"},{"key":"490_CR54","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1021\/ci800298z","volume":"49","author":"O Korb","year":"2009","unstructured":"Korb O, St\u00fctzle T, Exner TE (2009) Empirical scoring functions for advanced protein\u2212ligand docking with plants. J Chem Inf Model 49:84\u201396. https:\/\/doi.org\/10.1021\/ci800298z","journal-title":"J Chem Inf Model"},{"key":"490_CR55","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1002\/prot.10465","volume":"52","author":"ML Verdonk","year":"2003","unstructured":"Verdonk ML, Cole JC, Hartshorn MJ et al (2003) Improved protein\u2013ligand docking using GOLD. Proteins Struct Funct Bioinforma 52:609\u2013623","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"490_CR56","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/S1056-8719(02)00166-1","volume":"46","author":"HC Cheng","year":"2001","unstructured":"Cheng HC (2001) The power issue: determination of KB or Ki from IC50: a closer look at the Cheng-Prusoff equation, the Schild plot and related power equations. J Pharmacol Toxicol Methods 46:61\u201371. https:\/\/doi.org\/10.1016\/S1056-8719(02)00166-1","journal-title":"J Pharmacol Toxicol Methods"},{"key":"490_CR57","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1002\/jcc.10378","volume":"25","author":"M Feig","year":"2004","unstructured":"Feig M, Onufriev A, Lee Michael S et al (2004) Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 25:265\u2013284. https:\/\/doi.org\/10.1002\/jcc.10378","journal-title":"J Comput Chem"},{"key":"490_CR58","doi-asserted-by":"publisher","first-page":"20986","DOI":"10.1073\/pnas.1006370107","volume":"107","author":"KP Romano","year":"2010","unstructured":"Romano KP, Ali A, Royer WE, Schiffer CA (2010) Drug resistance against HCV NS3\/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proc Natl Acad Sci U A 107:20986\u201320991. https:\/\/doi.org\/10.1073\/pnas.1006370107","journal-title":"Proc Natl Acad Sci U A"},{"key":"490_CR59","doi-asserted-by":"publisher","first-page":"2428","DOI":"10.1016\/j.bmcl.2019.03.037","volume":"29","author":"JG Taylor","year":"2019","unstructured":"Taylor JG, Zipfel S, Ramey K et al (2019) Discovery of the pan-genotypic hepatitis C virus NS3\/4A protease inhibitor voxilaprevir (GS-9857): a component of Vosevi\u00ae. Bioorg Med Chem Lett 29:2428\u20132436. https:\/\/doi.org\/10.1016\/j.bmcl.2019.03.037","journal-title":"Bioorg Med Chem Lett"},{"key":"490_CR60","doi-asserted-by":"publisher","first-page":"8205","DOI":"10.1074\/jbc.M510246200","volume":"281","author":"M Yi","year":"2006","unstructured":"Yi M, Tong X, Skelton A et al (2006) Mutations conferring resistance to SCH6, a novel hepatitis C virus NS3\/4A protease inhibitor. Reduced RNA replication fitness and partial rescue by second-site mutations. J Biol Chem 281:8205\u20138215. https:\/\/doi.org\/10.1074\/jbc.M510246200","journal-title":"J Biol Chem"},{"key":"490_CR61","unstructured":"Arasappan A, Bennett F, Bogen SL et al (2021) RCSB PDB - 3LON: HCV NS3-4a protease domain with ketoamide inhibitor narlaprevir. www.rcsb.org\/structure\/3LON. Accessed 1 Aug 2022"},{"key":"490_CR62","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1016\/j.bmcl.2010.02.063","volume":"20","author":"F Bennett","year":"2010","unstructured":"Bennett F, Huang Y, Hendrata S et al (2010) The introduction of P4 substituted 1-methylcyclohexyl groups into Boceprevir: a change in direction in the search for a second generation HCV NS3 protease inhibitor. Bioorg Med Chem Lett 20:2617\u20132621. https:\/\/doi.org\/10.1016\/j.bmcl.2010.02.063","journal-title":"Bioorg Med Chem Lett"},{"key":"490_CR63","doi-asserted-by":"publisher","first-page":"8744","DOI":"10.1021\/jp101031v","volume":"114","author":"J Heyda","year":"2010","unstructured":"Heyda J, Mason PE, Jungwirth P (2010) Attractive interactions between side chains of histidine-histidine and histidine-arginine-based cationic dipeptides in water. J Phys Chem B 114:8744\u20138749. https:\/\/doi.org\/10.1021\/jp101031v","journal-title":"J Phys Chem B"},{"key":"490_CR64","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.ab.2012.01.006","volume":"423","author":"H Lee","year":"2012","unstructured":"Lee H, Torres J, Truong L et al (2012) Reducing agents affect inhibitory activities of compounds: results from multiple drug targets. Anal Biochem 423:46\u201353","journal-title":"Anal Biochem"},{"key":"490_CR65","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","volume":"27","author":"GM Sastry","year":"2013","unstructured":"Sastry GM, Adzhigirey M, Day T et al (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27:221\u2013234. https:\/\/doi.org\/10.1007\/s10822-013-9644-8","journal-title":"J Comput Aided Mol Des"},{"key":"490_CR66","doi-asserted-by":"publisher","first-page":"11225","DOI":"10.1021\/ja9621760","volume":"118","author":"WL Jorgensen","year":"1996","unstructured":"Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS All-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225\u201311236. https:\/\/doi.org\/10.1021\/ja9621760","journal-title":"J Am Chem Soc"},{"key":"490_CR67","volume-title":"Schr\u00f6dinger Release 2022\u20132: LigPrep","author":"L Schr\u00f6dinger","year":"2022","unstructured":"Schr\u00f6dinger L (2022) Schr\u00f6dinger Release 2022\u20132: LigPrep. Schr\u00f6dinger, LLC, New York"},{"key":"490_CR68","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera\u2014A visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612. https:\/\/doi.org\/10.1002\/jcc.20084","journal-title":"J Comput Chem"},{"key":"490_CR69","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1002\/jcc.540150503","volume":"15","author":"R Abagyan","year":"1994","unstructured":"Abagyan R, Totrov M, Kuznetsov D (1994) ICM\u2014A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488\u2013506. https:\/\/doi.org\/10.1002\/jcc.540150503","journal-title":"J Comput Chem"},{"key":"490_CR70","unstructured":"Case DA, Babin V, Berryman J, et al (2014) Amber 14"},{"key":"490_CR71","doi-asserted-by":"publisher","first-page":"W511","DOI":"10.1093\/nar\/gkr288","volume":"39","author":"E Vanquelef","year":"2011","unstructured":"Vanquelef E, Simon S, Marquant G et al (2011) R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Res 39:W511\u2013W517. https:\/\/doi.org\/10.1093\/nar\/gkr288","journal-title":"Nucleic Acids Res"},{"key":"490_CR72","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"JM Wang","year":"2004","unstructured":"Wang JM, Wolf RM, Caldwell JW et al (2004) Development and testing of a general amber force field. J Comput Chem 25:1157\u20131174. https:\/\/doi.org\/10.1002\/jcc.20035","journal-title":"J Comput Chem"},{"key":"490_CR73","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N\u22c5log(N) method for Ewald sums in large systems. J Chem Phys 98:10089\u201310092. https:\/\/doi.org\/10.1063\/1.464397","journal-title":"J Chem Phys"},{"key":"490_CR74","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V","volume":"22","author":"V Kr\u00e4utler","year":"2001","unstructured":"Kr\u00e4utler V, van Gunsteren WF, H\u00fcnenberger PH (2001) A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J Comput Chem 22:501\u2013508. https:\/\/doi.org\/10.1002\/1096-987X(20010415)22:5%3c501::AID-JCC1021%3e3.0.CO;2-V","journal-title":"J Comput Chem"},{"key":"490_CR75","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe DR, Cheatham TE III (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9:3084\u20133095","journal-title":"J Chem Theory Comput"},{"key":"490_CR76","doi-asserted-by":"publisher","first-page":"10140","DOI":"10.1039\/C7CP00841D","volume":"19","author":"L Duan","year":"2017","unstructured":"Duan L, Feng G, Wang X et al (2017) Effect of electrostatic polarization and bridging water on CDK2\u2013ligand binding affinities calculated using a highly efficient interaction entropy method. Phys Chem Chem Phys 19:10140\u201310152","journal-title":"Phys Chem Chem Phys"},{"key":"490_CR77","doi-asserted-by":"publisher","first-page":"5722","DOI":"10.1021\/jacs.6b02682","volume":"138","author":"L Duan","year":"2016","unstructured":"Duan L, Liu X, Zhang JZ (2016) Interaction entropy: a new paradigm for highly efficient and reliable computation of protein\u2013ligand binding free energy. J Am Chem Soc 138:5722\u20135728","journal-title":"J Am Chem Soc"},{"key":"490_CR78","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/srep31488","volume":"6","author":"LL Duan","year":"2016","unstructured":"Duan LL, Feng GQ, Zhang QG (2016) Large-scale molecular dynamics simulation: effect of polarization on thrombin-ligand binding energy. Sci Rep 6:1\u201311","journal-title":"Sci Rep"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-022-00490-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-022-00490-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-022-00490-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,10]],"date-time":"2023-01-10T16:02:31Z","timestamp":1673366551000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-022-00490-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,25]]},"references-count":78,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1]]}},"alternative-id":["490"],"URL":"https:\/\/doi.org\/10.1007\/s10822-022-00490-1","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,25]]},"assertion":[{"value":"20 August 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 November 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests related to the content of this article.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}