Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data
Lenin González-Paz, María Carla Lossada, María Laura Hurtado-León, Joan Vera-Villalobos, José L Paz, Yovani Marrero-Ponce, Felix Martinez-Rios, Ysaías. J Alvarado
ACS Omega, doi:10.1021/acsomega.3c06968
Recent reports have suggested that the susceptibility of cells to SARS-CoV-2 infection can be influenced by various proteins that potentially act as receptors for the virus. To investigate this further, we conducted simulations of viral dynamics using different cellular systems (Vero E6, HeLa, HEK293, and CaLu3) in the presence and absence of drugs (anthelmintic, ARBs, anticoagulant, serine protease inhibitor, antimalarials, and NSAID) that have been shown to impact cellular recognition by the spike protein based on experimental data. Our simulations revealed that the susceptibility of the simulated cell systems to SARS-CoV-2 infection was similar across all tested systems. Notably, CaLu3 cells exhibited the highest susceptibility to SARS-CoV-2 infection, potentially due to the presence of receptors other than ACE2, which may account for a significant portion of the observed susceptibility. Throughout the study, all tested compounds showed thermodynamically favorable and stable binding to the spike protein. Among the tested compounds, the anticoagulant nafamostat demonstrated the most favorable characteristics in terms of thermodynamics, kinetics, theoretical antiviral activity, and potential safety (toxicity) in relation to SARS-CoV-2 spike proteinmediated infections in the tested cell lines. This study provides mathematical and bioinformatic models that can aid in the identification of optimal cell lines for compound evaluation and detection, particularly in studies focused on repurposed drugs and their mechanisms of action. It is important to note that these observations should be experimentally validated, and this research is expected to inspire future quantitative experiments.
Notes The authors declare no competing financial interest.
■ ACKNOWLEDGMENTS This research was supported by regular funds of the Venezuelan Institute for Scientific Research (IVIC). J.L.P. thanks the Vicerrectorado de Investigación y Postgrado of the Universidad Nacional Mayor de San Marcos for the computational resources used.
References
Abernathy, Abernathy, Stevens, A mathematical model for tumor growth and treatment using virotherapy, AIMS Math,
doi:10.3934/math.2020265Appelberg, Gupta, Svensson Akusjärvi, Ambikan, Mikaeloff et al., Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells, Emerging microbes & infections,
doi:10.1080/22221751.2020.1799723Baccam, Beauchemin, Macken, Hayden, Perelson, Kinetics of influenza A virus infection in humans, Journal of virology,
doi:10.1128/JVI.01623-05Banerjee, Eckert, Schrey, Preissner, ProTox-II: a webserver for the prediction of toxicity of chemicals, Nucleic acids research,
doi:10.1093/nar/gky318Bar-On, Flamholz, Phillips, Milo, Science Forum: SARS-CoV-2 (COVID-19) by the numbers, Elife,
doi:10.7554/eLife.57309Bollavaram, Leeman, Lee, Kulkarni, Upshaw et al., Multiple sites on SARS-CoV-2 spike protein are susceptible to proteolysis by cathepsins B, Protein science: a publication of the Protein Society,
doi:10.1002/pro.4073Campbell, Boilard, Rondina, Is there a role for the ACE2 receptor in SARS-CoV-2 interactions with platelets, Journal of Thrombosis and Haemostasis,
doi:10.1111/jth.15156Cer, Mudunuri, Stephens, Lebeda, IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding, Nucleic Acids Res,
doi:10.1093/nar/gkp253Chen, Liu, Guo, Emerging coronaviruses: Genome structure, replication, and pathogenesis, J. Med. Virol,
doi:10.1002/jmv.25681Choi, Son, Kim, Na, Uversky et al., Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination, Int. J. Biol. Macromol,
doi:10.1016/j.ijbiomac.2023.126526Chu, Chan, Yuen, Shuai, Yuan et al., Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study, Lancet. Microbe,
doi:10.1016/S2666-5247(20)30004-5Coghi, Yang, Ng, Haynes, Memo et al., A drug repurposing approach for antimalarials interfering with SARS-CoV-2 spike protein receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2), Pharmaceuticals,
doi:10.3390/ph14100954Cuervo, Grandvaux, ACE2: Evidence of role as entry receptor for SARS-CoV-2 and implications in comorbidities, Elife,
doi:10.7554/eLife.61390Czuppon, Débarre, Goncalves, Tenaillon, Perelson et al., Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action, PLoS computational biology,
doi:10.1371/journal.pcbi.1008752De Bruin, Schneider, Reus, Talmon, Ciesek et al., Ibuprofen, Flurbiprofen, Etoricoxib or Paracetamol Do Not Influence ACE2 Expression and Activity In Vitro or in Mice and Do Not Exacerbate In-Vitro SARS-CoV-2 Infection, Int. J. Mol. Sci,
doi:10.3390/ijms23031049Digre, Lindskog, The human protein atlas�spatial localization of the human proteome in health and disease, Protein Sci,
doi:10.1002/pro.3987Dittmar, Lee, Whig, Segrist, Li et al., Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2, Cell reports,
doi:10.1016/j.celrep.2021.108959Dobrindt, Hoagland, Seah, Kassim, O'shea et al., Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection, Stem Cell Rep,
doi:10.1016/j.stemcr.2021.02.010Felline, Seeber, Fanelli, webPSN v2. 0: a webserver to infer fingerprints of structural communication in biomacromolecules, Nucleic Acids Res,
doi:10.1093/nar/gkaa397Fenizia, Galbiati, Vanetti, Vago, Clerici et al., SARS-CoV-2 Entry: At the Crossroads of CD147 and ACE2, Cell,
doi:10.3390/cells10061434Fiege, Thiede, Nanda, Matchett, Moore et al., Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium, PLoS Pathogens,
doi:10.1371/journal.ppat.1009292Gesztelyi, Zsuga, Kemeny-Beke, Varga, Juhasz et al., The Hill equation and the origin of quantitative pharmacology, Archive for history of exact sciences,
doi:10.1007/s00407-012-0098-5Goncalves, Bertrand, Ke, Comets, De Lamballerie et al., Timing of antiviral treatment initiation is critical to reduce SARS-CoV-2 viral load, CPT: Pharmacometrics Syst. Pharmacol,
doi:10.1002/psp4.12543González-Paz, Alvarado, Hurtado-León, Lossada, Vera-Villalobos et al., Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors, Computers in biology and medicine,
doi:10.1016/j.compbiomed.2022.105245González-Paz, Lossada, Fernández-Materán, Paz, Vera-Villalobos et al., Can Non-steroidal Antiinflammatory Drugs Affect the Interaction Between Receptor Binding Domain of SARS-COV-2 Spike and the Human ACE2 Receptor? A Computational Biophysical Study, Front. Phys,
doi:10.3389/fphy.2020.587606Gupta, Biswal, Panda, Ray, Rana, Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin, J. Biomol. Struct. Dyn,
doi:10.1080/07391102.2020.1839564Gutiérrez-Chamorro, Riveira-Munõz, Barrios, Palau, Nevot et al., SARS-CoV-2 Infection Modulates ACE2 Function and Subsequent Inflammatory Responses in Swabs and Plasma of COVID-19 Patients, Viruses,
doi:10.3390/v13091715Hempel, Raich, Olsson, Azouz, Klingler et al., Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat, Chemical Science,
doi:10.1039/D0SC05064DHikmet, Méar, Edvinsson, Micke, Uhlén et al., The protein expression profile of ACE2 in human tissues, Molecular systems biology,
doi:10.15252/msb.20209610Hoffmann, Kleine-Weber, Schroeder, Kruger, Herrler et al., SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor, Cell,
doi:10.1016/j.cell.2020.02.052Isaac-Lam, Molecular modeling of the interaction of ligands with ACE2-SARS-CoV-2 spike protein complex, silico pharmacology,
doi:10.1007/s40203-021-00114-wJafary, Jafari, Ganjalikhany, In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensinconverting enzyme 2, Sci. Rep,
doi:10.1038/s41598-021-86380-2Kalhor, Sadeghi, Abolhasani, Kalhor, Rahimi, Repurposing of the approved small molecule drugs in order to inhibit SARS-CoV-2 S protein and human ACE2 interaction through virtual screening approaches, J. Biomol. Struct. Dyn,
doi:10.1080/07391102.2020.1824816Kasahara, Terazawa, Itaya, Goto, Nakamura et al., myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling, Biophysics and Physicobiology,
doi:10.2142/biophysico.BSJ-2020013Keyaerts, Vijgen, Maes, Neyts, Ranst, Growth kinetics of SARS-coronavirus in Vero E6 cells, Biochem. Biophys. Res. Commun,
doi:10.1016/j.bbrc.2005.02.085Kim, Melgoza, Jiang, Guo, The effect of reninangiotensin-aldosterone system inhibitors on organ-specific ace2 expression in zebrafish and its implications for COVID-19, Sci. Rep,
doi:10.1038/s41598-021-03244-5Kishimoto, Uemura, Sanaki, Sato, Hall et al., TMPRSS11D and TMPRSS13 Activate the SARS-CoV-2 Spike Protein, Viruses,
doi:10.3390/v13030384Kitagawa, Arai, Iida, Mukai, Furukawa et al., A phase I study of high dose camostat mesylate in healthy adults provides a rationale to repurpose the TMPRSS2 inhibitor for the treatment of COVID-19, Clinical and translational science,
doi:10.1111/cts.13052Kumar, Ter Ellen, Bouma, Troost, Van De Pol et al., Moxidectin and Ivermectin Inhibit SARS-CoV-2 Replication in Vero E6 Cells but Not in Human Primary Bronchial Epithelial Cells, Antimicrob. Agents Chemother,
doi:10.1128/AAC.01543-21Kumari, Kumar, Dhankhar, Dalal, Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA, J. Biomol. Struct. Dyn,
doi:10.1080/07391102.2022.2071340Kyrou, Randeva, Spandidos, Karteris, Not only ACE2�the quest for additional host cell mediators of SARS-CoV-2 infection: Neuropilin-1 (NRP1) as a novel SARS-CoV-2 host cell entry mediator implicated in COVID-19, Signal transduction and targeted therapy,
doi:10.1038/s41392-020-00460-9Li, Li, Huang, Wu, Liu et al., Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs, Proc. Natl. Acad. Sci. U. S. A,
doi:10.1073/pnas.2010470117Liu, Han, Blair, Kenst, Qin et al., SARS-CoV-2 Infects Endothelial Cells In Vivo and In Vitro, Frontiers in cellular and infection microbiology,
doi:10.3389/fcimb.2021.701278Liu, Wang, Zhou, Zhao, Zhang et al., Potential role of ACE2 in coronavirus disease 2019 (COVID-19) prevention and management, Journal of translational internal medicine,
doi:10.2478/jtim-2020-0003Matsuyama, Kawase, Nao, Shirato, Ujike et al., The Inhaled Steroid Ciclesonide Blocks SARS-CoV-2 RNA Replication by Targeting the Viral Replication-Transcription Complex in Cultured Cells, Journal of virology,
doi:10.1128/JVI.01648-20Moon, Hong, Bae, Treatment effect of nafamostat mesylate in patients with COVID-19 pneumonia: study protocol for a randomized controlled trial, Trials,
doi:10.1186/s13063-021-05760-1Mosquera-Yuqui, Lopez-Guerra, Moncayo-Palacio, Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations, J. Biomol. Struct. Dyn,
doi:10.1080/07391102.2020.1835716Murgolo, Therien, Howell, Klein, Koeplinger et al., SARS-CoV-2 tropism, entry, replication, and propagation: Considerations for drug discovery and development, PLoS pathogens,
doi:10.1371/journal.ppat.1009225Nguyen, Binder, Boianelli, Meyer-Hermann, Hernandez-Vargas, Ebola virus infection modeling and identifiability problems, Frontiers in microbiology,
doi:10.3389/fmicb.2015.00257Nguyen, Hernández-Vargas, Parameter Estimation in Mathematical Models of Viral Infections Using R, Methods in molecular biology,
doi:10.1007/978-1-4939-8678-1_25Park, Kim, Park, Maharjan, Kim et al., Differential Signaling and Virus Production in Calu-3 Cells and Vero Cells upon SARS-CoV-2 Infection, Biomolecules & therapeutics,
doi:10.4062/biomolther.2020.226Peixoto, Monteiro, Rocha, Veiga-Fernandes, Quantification of multiple gene expression in individual cells, Genome research,
doi:10.1101/gr.2890204Quiroga, Villarreal, Vinardo, A scoring function based on autodock vina improves scoring, docking, and virtual screening, PloS one,
doi:10.1371/journal.pone.0155183Rajah, Hubert, Bishop, Saunders, Robinot et al., SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation, EMBO J,
doi:10.15252/embj.2021108944Reus, Schneider, Ulshöfer, Henke, Bojkova et al., Characterization of ACE Inhibitors and AT1R Antagonists with Regard to Their Effect on ACE2 Expression and Infection with SARS-CoV-2 Using a Caco-2 Cell Model, Life,
doi:10.3390/life11080810Rothlin, Vetulli, Duarte, Pelorosso, Telmisartan as tentative angiotensin receptor blocker therapeutic for COVID-19, Drug Dev. Res,
doi:10.1002/ddr.21679Saraswat, Riaz, Patel, In-silico study for the screening and preparation of ionic liquid-AVDs conjugate to combat COVID-19 surge, J. Mol. Liq,
doi:10.1016/j.molliq.2022.119277Saraswat, Singh, Patel, A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds, Journal of molecular liquids,
doi:10.1016/j.molliq.2021.115298Schroeder, Pott, Niemeyer, Veith, Richter et al., Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics, Lancet Microbe,
doi:10.1016/S2666-5247(21)00027-6Shamsi, Mohammad, Anwar, Alajmi, Hussain et al., Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy, Bioscience Reports,
doi:10.1042/BSR20201256Shilts, Crozier, Greenwood, Lehner, Wright, No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor, Sci. Rep,
doi:10.1038/s41598-020-80464-1Smart, Fawkes, Goggin, Pennick, Rainsford et al., A narrative review of the potential pharmacological influence and safety of ibuprofen on coronavirus disease 19 (COVID-19), ACE2, and the immune system: a dichotomy of expectation and reality, Inflammopharmacology,
doi:10.1007/s10787-020-00745-zSulaiman, Chung, Angel, Tsay, Wu et al., Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome, Nat. Microbiol,
doi:10.1038/s41564-021-00961-5Ter Ellen, Dinesh Kumar, Bouma, Troost, Van De Pol et al., Resveratrol and Pterostilbene Inhibit SARS-CoV-2 Replication in Air-Liquid Interface Cultured Human Primary Bronchial Epithelial Cells, Viruses,
doi:10.3390/v13071335Terrier, Dilly, Pizzorno, Chalupska, Humpolickova et al., Antiviral Properties of the NSAID Drug Naproxen Targeting the Nucleoprotein of SARS-CoV-2 Coronavirus, Molecules,
doi:10.3390/molecules26092593Tiwari, Fuglebakk, Hollup, Skjaerven, Cragnolini et al., WEBnm@ v2.0: Web server and services for comparing protein flexibility, BMC Bioinformatics,
doi:10.1186/s12859-014-0427-6Vincent, Bergeron, Benjannet, Erickson, Rollin et al., Chloroquine is a potent inhibitor of SARS coronavirus infection and spread, Virology journal,
doi:10.1186/1743-422X-2-69Viveiros, Gheblawi, Aujla, Sosnowski, Seubert et al., Sex-and age-specific regulation of ACE2: Insights into severe COVID-19 susceptibility, Journal of molecular and cellular cardiology,
doi:10.1016/j.yjmcc.2021.11.003Wang, Qiu, Hou, Deng, Xu et al., AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells, Cell Res,
doi:10.1038/s41422-020-00460-yWang, Wang, Li, Lei, Wang et al., farPPI: a webserver for accurate prediction of proteinligand binding structures for small-molecule PPI inhibitors by MM/ PB(GB)SA methods, Bioinformatics,
doi:10.1093/bioinformatics/bty879Wysocki, Lores, Ye, Soler, Batlle, Kidney and lung ACE2 expression after an ACE inhibitor or an Ang II receptor blocker: implications for COVID-19, Journal of the American Society of Nephrology,
doi:10.1681/ASN.2020050667Xie, Ying, Xie, Smpbs, Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation, J. Comput. Chem,
doi:10.1002/jcc.24703Yamamoto, Matsuyama, Li, Takeda, Kawaguchi et al., Identification of nafamostat as a potent inhibitor of Middle East respiratory syndrome coronavirus S proteinmediated membrane fusion using the split-protein-based cell-cell fusion assay, Antimicrob. Agents Chemother,
doi:10.1128/AAC.01043-16Yu, Organoids: a new model for SARS-CoV-2 translational research, International. Journal of Stem Cells,
doi:10.15283/ijsc20169Zhang, Chu, Han, Shuai, Deng et al., SARS-CoV-2 infects human neural progenitor cells and brain organoids, Cell research,
doi:10.1038/s41422-020-0390-xZhuravel, Khmelnitskiy, Burlaka, Gritsan, Goloshchekin et al., Nafamostat in hospitalized patients with moderate to severe COVID-19 pneumonia: a randomised Phase II clinical trial, EClinicalMedicine,
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{'key': 'ref25/cit25', 'doi-asserted-by': 'publisher', 'DOI': '10.1128/JVI.01623-05'},
{ 'key': 'ref26/cit26',
'doi-asserted-by': 'publisher',
'DOI': '10.1007/978-1-4939-8678-1_25'},
{'key': 'ref27/cit27', 'doi-asserted-by': 'publisher', 'DOI': '10.3934/math.2020265'},
{'key': 'ref28/cit28', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/pro.3987'},
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