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.
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.
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.
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.
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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