Investigation of Simultaneous and Sequential Cooperative Homotropic Inhibitor Binding to the Catalytic Chamber of SARS-CoV-2 RNA-dependent RNA Polymerase (RdRp)

Gutfreund H. Binding and Linkage. (1991). Functional chemistry of biological macromolecules. FEBS Letters, 293(1–2), 224–224. https://onlinelibrary.wiley.com/doi/full/10.1016/0014-5793%2891%2981192-B.

Palmer, T., & Bonner, P. L. Sigmoidal kinetics and allosteric enzymes. Enzymes, 239–254 (2011). https://shop.elsevier.com/books/enzymes/palmer/978-1-904275-27-5.

Faas, G. C., Schwaller, B., Vergara, J. L. & & Mody, I. (2007). Resolving the fast kinetics of cooperative binding: Ca2+ buffering by calretinin. PLoS Biology, 5(11), 2646–2660.

Article  CAS  Google Scholar 

Velazquez-Campoy, A., Goñi, G., Peregrina, J. R., & Medina, M. (2006). Exact analysis of heterotropic interactions in proteins: Characterization of cooperative ligand binding by isothermal titration calorimetry. Biophysical Journal, 91(5), 1887–1904.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stefan, M. I., & Le Novère, N. (2013). Cooperative binding. PLOS Computational Biology, 9(6). https://pubmed.ncbi.nlm.nih.gov/23843752/.

Kirchdoerfer, R. N., & Ward, A. B. (2019). Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nature Communication, 10(1), 1–9.

Article  CAS  Google Scholar 

Gao, Y., Yan, L., & Huang, Y., et al. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peng, Q., Peng, R., & Yuan, B., et al. (2020). Structural and biochemical characterization of the nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Reports, 31(11), 107774.

Article  CAS  PubMed  Google Scholar 

Yin, W., Mao, C., & Luan, X., et al. (2020). Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science, 368(6498), 1499–1504.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lung, J., Lin, Y., & Yang, Y., et al. (2020). The potential chemical structure of anti‐SARS‐CoV‐2 RNA‐dependent RNA polymerase. Journal of Medical Virology, 92(6), 693–697. https://onlinelibrary.wiley.com/doi/10.1002/jmv.25761.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koulgi, S., Jani, V., Uppuladinne, M. V. N., Sonavane, U., & Joshi, R. (2020). Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2. RSC Advances, 10(45), 26792–26803.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gaurav, A., & Al-Nema, M. (2019). Polymerases of coronaviruses: structure, function, and inhibitors. Viral Polymerases, 271. https://doi.org/10.1016/B978-0-12-815422-9.00010-3.

Yin, W., Luan, X., & Li, Z., et al. (2021). Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nat Struct Mol Biol, 28(3), 319–325. https://doi.org/10.1038/s41594-021-00570-0.

Article  CAS  PubMed  Google Scholar 

Wiedemar, N., Hauser, D. A., & Mäser, P. (2020). 100 years of suramin. Antimicrobial Agents and Chemotherapy 64(3), e01168–19.

Yin, W., Luan, X., & Li, Z., et al. (2021). Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nature Structural & Molecular Biology, 28(3), 319–325.

Article  CAS  Google Scholar 

Metwally, K., Abo-Dya, N. E., & Alahmdi, M. I., et al. (2023). The unusual architecture of RNA-dependent RNA polymerase (RdRp)’s catalytic chamber provides a potential strategy for combination therapy against COVID-19. Molecules, 28(6), 2806 https://www.mdpi.com/1420-3049/28/6/2806/htm.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zeller, M. J., Nuthanakanti, A., Li, K., Aubé, J., Serganov, A., & Weeks, K. M. (2022). Subsite ligand recognition and cooperativity in the TPP riboswitch: implications for fragment-linking in RNA ligand discovery. ACS Chemical Biology, 17(2), 438–448. https://pubs.acs.org/doi/abs/10.1021/acschembio.1c00880.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hyde, J., Braisted, A. C., Randal, M., & Arkin, M. R. (2003). Discovery and characterization of cooperative ligand binding in the adaptive region of interleukin-2. Biochemistry, 42(21), 6475–6483. https://www.researchgate.net/publication/7146736_Discovery_and_Characterization_of_Cooperative_Ligand_Binding_in_the_Adaptive_Region_of_Interleukin-2.

Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). The protein data bank. Acta Crystallogr D Biol Crystallogr. 2002;58(Pt 6 No 1):899–907.

Allouche, A. (2012). Software news and updates gabedit—a graphical user interface for computational chemistry softwares. Journal of Computational Chemistry, 32, 174–182.

Article  Google Scholar 

Lee, T.-S., Cerutti, D. S., Mermelstein, D., Lin, C., LeGrand, S., Giese, T. J., Roitberg, A., Case, D. A., Walker, R. C., & York, D. M. (2018). GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. Journal of Chemical Information and Modeling, 58, 2043–2050.

Alamri, A. S., Alhomrani, M., & Alsanie, W. F., et al. (2022). Enhancement of haloperidol binding affinity to dopamine receptor via forming a charge-transfer complex with picric acid and 7,7,8,8-tetracyanoquinodimethane for improvement of the antipsychotic efficacy. Molecules, 27(10), 3295 https://www.mdpi.com/1420-3049/27/10/3295.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alsanie, W. F., Alamri, A. S., & Alyami, H., et al. (2022). Increasing the efficacy of seproxetine as an antidepressant using charge–transfer complexes. Molecules, 27(10), 3290 https://www.mdpi.com/1420-3049/27/10/3290.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82.

Article  CAS  PubMed  Google Scholar 

Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area method. Molecular Informatics, 31(2), 114–122.

Article  CAS  PubMed  Google Scholar 

Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://pubmed.ncbi.nlm.nih.gov/25835573/.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kolaczkowski, M., Van der Rest, M., Cybularz-Kolaczkowska, A., Soumillion, J. P., Konings, W. N., & Goffeau, A. (1996). Anticancer drugs, ionophoric peptides, and steroids as substrates of the yeast multidrug transporter Pdr5p. Journal of Biological Chemistry, 271(49), 31543–31548. https://pubmed.ncbi.nlm.nih.gov/8940170/.

Article  CAS  PubMed  Google Scholar 

Loo, T. W., Bartlett, M. C., & Clarke, D. M. (2003). Methanethiosulfonate derivatives of rhodamine and verapamil activate human P-glycoprotein at different sites. Journal of Biological Chemistry, 278(50), 50136–50141. https://pubmed.ncbi.nlm.nih.gov/14522974/.

Article  CAS  PubMed  Google Scholar 

Schumacher, M. A., Miller, M. C., & Brennan, R. G. (2004). Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein. EMBO Journal, 23(15), 2923.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mastrangelo, E., Pezzullo, M., & Tarantino, D., et al. (2012). Structure-based inhibition of Norovirus RNA-dependent RNA polymerases. Journal of Molecular Biology, 419(3–4), 198–210. https://pubmed.ncbi.nlm.nih.gov/22446684/.

Article  CAS  PubMed  Google Scholar 

Huber, R. (1987). Flexibility and rigidity, requirements for the function of proteins and protein pigment complexes. Eleventh Keilin memorial lecture. Biochemical Society Transactions, 15(6), 1009–1020. https://pubmed.ncbi.nlm.nih.gov/3502256/.

Article  CAS  PubMed  Google Scholar 

Clark, J. J., Benson, M. L., Smith, R. D., & Carlson, H. A. (2019). Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLOS Computational Biology, 15(1), e1006705. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006705.

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