Quercetin and Luteolin Are Single-digit Micromolar Inhibitors of the SARS-CoV-2 RNA-dependent RNA Polymerase
Federico Munafò, Elisa Donati, Nicoletta Brindani, Giuliano Ottonello, Andrea Armirotti, Marco De Vivo
doi:10.21203/rs.3.rs-1149846/v1
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. Among the viral proteins, RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and has emerged as one of the most promising targets for pharmacological intervention against SARS-CoV-2. To this end, we experimentally tested luteolin and quercetin for their ability to inhibit the RdRp enzyme. These two compounds are ancestors of avonoid natural compounds known for a variety of basal pharmacological activities. Luteolin and quercetin returned a single-digit IC 50 of 4.6 µM and 6.9 µM, respectively. Then, through dynamic docking simulations, we identi ed possible binding modes of these compounds to a recently published cryo-EM structure of RdRp. Collectively, these data indicate that these two compounds are a valid starting point for further optimization and development of a new class of RdRp inhibitors to treat SARS-CoV-2 and potentially other viral infections.
Supporting Information. Supplementary gures reporting the: i) chromatography analysis of luteolin and quercetin (pages S2−S3), ii) chemical structures of luteolin and quercetin in different protonation states (page S4), iii) docking scores (page S5), iv) MD analysis (pages S6-S9).
Supplementary Files This is a list of supplementary les associated with this preprint. Click to download.
References
Abian, Structural stability of SARS-CoV-2 3CLpro and identi cation of quercetin as an inhibitor by experimental screening, Int J Biol Macromol,
doi:10.1016/j.ijbiomac.2020.07.235Arencibia, Synthesis, Dynamic Docking, Biochemical Characterization, and in Vivo Pharmacokinetics Studies of Novel Topoisomerase II Poisons with Promising Antiproliferative Activity, J Med Chem,
doi:10.1021/acs.jmedchem.9b01760Bayly, Cieplak, Cornell, Kollman, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, The Journal of Physical Chemistry,
doi:10.1021/j100142a004Bussi, Donadio, Parrinello, Canonical sampling through velocity rescaling, J Chem Phys,
doi:10.1063/1.2408420Carta, Quinoline tricyclic derivatives. Design, synthesis and evaluation of the antiviral activity of three new classes of RNA-dependent RNA polymerase inhibitors, Bioorg Med Chem,
doi:10.1016/j.bmc.2011.10.009Casalino, AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics, The International Journal of High Performance Computing Applications,
doi:10.1177/10943420211006452Choudhry, Chinese Therapeutic Strategy for Fighting COVID-19 and Potential Small-Molecule Inhibitors against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), J Med Chem,
doi:10.1021/acs.jmedchem.0c00626De, Vivo, Cavalli, Recent advances in dynamic docking for drug discovery, WIREs Computational Molecular Science,
doi:10.1002/wcms.1320Derosa, Ma Oli, D'angelo, Di Pierro, A role for quercetin in coronavirus disease 2019 (COVID-19), Phytother Res,
doi:10.1002/ptr.6887Deshmukh, Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease, Structure,
doi:10.1016/j.str.2021.06.002Friesner, Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy, J Med Chem,
doi:10.1021/jm0306430Geronimo, Vidossich, Donati, Vivo, Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology, WIREs Computational Molecular Science,
doi:10.1002/wcms.1534Goris, Repositioning microbial biotechnology against COVID-19: the case of microbial production of avonoids, Microb Biotechnol,
doi:10.1111/1751-7915.13675Halgren, Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening, J Med Chem,
doi:10.1021/jm030644sHess, P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation, J Chem Theory Comput,
doi:10.1021/ct700200bHuang, Song, Huang, Sun, Pharmacological Therapeutics Targeting RNA-Dependent RNA Polymerase, Proteinase and Spike Protein: From Mechanistic Studies to Clinical Trials for COVID-19
Jockusch, A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19, Antiviral Res,
doi:10.1016/j.antiviral.2020.104857Joung, Cheatham, Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations, J Phys Chem B,
doi:10.1021/jp8001614Lee, Investigation of the pharmacophore space of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) NTPase/helicase by dihydroxychromone derivatives, Bioorg Med Chem Lett,
doi:10.1016/j.bmcl.2009.07.009Naydenova, Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP, Proc Natl Acad Sci U S A,
doi:10.1073/pnas.2021946118Nguyen, Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in Pichia pastoris, Biotechnol Lett,
doi:10.1007/s10529-011-0845-8Ortega, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II alpha over beta, J Med Chem,
doi:10.1021/acs.jmedchem.0c00774Palermo, An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quanti ed by comparative analysis centered on the clinical candidate F14512, Chem Commun (Camb),
doi:10.1039/c5cc05065kPalermo, Favia, Convertino, De Vivo, The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition, ChemMedChem,
doi:10.1002/cmdc.201500507Parrinello, Rahman, Polymorphic transitions in single crystals: A new molecular dynamics method, Journal of Applied Physics,
doi:10.1063/1.328693Picarazzi, Vicenti, Saladini, Zazzi, Mori, Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge, Molecules,
doi:10.3390/molecules25235695Shaldam, Yahya, Mohamed, Abdel-Daim, Al Naggar, In silico screening of potent bioactive compounds from honeybee products against COVID-19 target enzymes, Environ Sci Pollut Res Int,
doi:10.1007/s11356-021-14195-9Steinmann, Buer, Pietschmann, Steinmann, Anti-infective properties of epigallocatechin-3-gallate (EGCG), a component of green tea, Br J Pharmacol,
doi:10.1111/bph.12009Tian, RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic, Eur J Med Chem,
doi:10.1016/j.ejmech.2021.113201Wang, Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro, Cell Res,
doi:10.1038/s41422-020-0282-0Wang, Wolf, Caldwell, Kollman, Case, Development and testing of a general amber force eld, J Comput Chem,
doi:10.1002/jcc.20035Yan, Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis, Cell,
doi:10.1016/j.cell.2020.11.016Yin, Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir, Science,
doi:10.1126/science.abc1560Zhang, Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations, ACS Cent Sci,
doi:10.1021/acscentsci.1c00039Zhao, Quinoline and Quinazoline Derivatives Inhibit Viral RNA Synthesis by SARS-CoV-2
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