294
Views
7
CrossRef citations to date
0
Altmetric
Research Articles

Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics

ORCID Icon, & ORCID Icon
Pages 1717-1734 | Received 05 Feb 2020, Accepted 26 Feb 2020, Published online: 11 Mar 2020

References

  • Almahmoud, S., Wang, X., Vennerstrom, J. L., & Zhong, H. A. (2019). Conformational studies of glucose transporter 1 (GLUT1) as an anticancer drug target. Molecules, 24(11), 2159. doi:10.3390/molecules24112159
  • Azam, F., Alabdullah, N. H., Ehmedat, H. M., Abulifa, A. R., Taban, I., & Upadhyayula, S. (2018). NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer’s disease: An investigation by docking, molecular dynamics, and DFT studies. Journal of Biomolecular Structure and Dynamics, 36(8), 2099–2117.
  • Biava, M., Porretta, G. C., Poce, G., Supino, S., Forli, S., Rovini, M., Cappelli, A., Manetti, F., Botta, M., Sautebin, L., Rossi, A., Pergola, C., Ghelardini, C., Vivoli, E., Makovec, F., Anzellotti, P., Patrignani, P., & Anzini, M. (2007). Cyclooxygenase-2 inhibitors. 1, 5-diarylpyrrol-3-acetic esters with enhanced inhibitory activity toward cyclooxygenase-2 and improved cyclooxygenase-2/cyclooxygenase-1 selectivity. Journal of Medicinal Chemistry, 50(22), 5403–5411. doi:10.1021/jm0707525
  • Bleumink, G. S., Feenstra, J., Sturkenboom, M. C., & Stricker, B. H. C. (2003). Nonsteroidal anti-inflammatory drugs and heart failure. Drugs, 63(6), 525–534. doi:10.2165/00003495-200363060-00001
  • Blobaum, A. L., & Marnett, L. J. (2007). Structural and functional basis of cyclooxygenase inhibition. Journal of Medicinal Chemistry, 50(7), 1425–1441. doi:10.1021/jm0613166
  • Carrillo-Jimenez, R., & Nurnberger, M. (2000). Celecoxib-induced acute pancreatitis and hepatitis: A case report. Archives of Internal Medicine, 160(4), 553–554. doi:10.1001/archinte.160.4.553
  • Chaudhary, N., & Aparoy, P. (2017). Deciphering the mechanism behind the varied binding activities of COXIBs through molecular dynamic simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies. Journal of Biomolecular Structure and Dynamics, 35(4), 868–882. doi:10.1080/07391102.2016.1165736
  • Chen, D., Oezguen, N., Urvil, P., Ferguson, C., Dann, S. M., & Savidge, T. C. (2016). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances, 2(3), e1501240. doi:10.1126/sciadv.1501240
  • Cioffi, C. L. (2017). Modulation of glycine-mediated spinal neurotransmission for the treatment of chronic pain. Journal of Medicinal Chemistry, 61(7), 2652–2679. doi:10.1021/acs.jmedchem.7b00956
  • Dhasmana, A., Raza, S., Jahan, R., Lohani, M., & Arif, J. M. (2019a). Chapter 19 – High-throughput virtual screening (HTVS) of natural compounds and exploration of their biomolecular mechanisms: An in silico approach. In M. S. Ahmad Khan, I. Ahmad, & D. Chattopadhyay (Eds.), New look to phytomedicine (pp. 523–548). Academic Press.
  • Dhasmana, A., Raza, S., Jahan, R., Lohani, M., & Arif, J. M. (2019b). High-throughput virtual screening (HTVS) of natural compounds and exploration of their biomolecular mechanisms: An in silico approach. In Mohd Sajjad Ahmad Khan, Iqbal Ahmad, & Debprasad Chattopadhyay (Eds)., New look to phytomedicine (pp. 523–548). Elsevier.
  • Doak, B. C., Over, B., Giordanetto, F., & Kihlberg, J. (2014). Oral druggable space beyond the rule of 5: Insights from drugs and clinical candidates. Chemistry & Biology, 21(9), 1115–1142. doi:10.1016/j.chembiol.2014.08.013
  • Dogné, J.-M., Supuran, C. T., & Pratico, D. J. J. o M. C. (2005). Adverse cardiovascular effects of the coxibs. Journal of Medicinal Chemistry, 48(7), 2251–2257. doi:10.1021/jm0402059
  • Edmeads, J. (1983). The physiology of pain: A review. Progress in Neuro-Psychopharmacology & Biological Psychiatry, 7(4-6), 413–419. doi:10.1016/0278-5846(83)90004-0
  • Giulio, P., & Tuccinardi, T. (2018). Consensus docking in drug discovery. Current Bioactive Compounds, 14, 1–9. doi:10.2174/1573407214666181023114820
  • Gong, P., Du, J., Wang, D., Cao, B., Tian, M., Wang, Y., Sun, L., Ji, S., & Liu, Z. (2018). Fluorinated graphene as an anticancer nanocarrier: An experimental and DFT study. Journal of Materials Chemistry B, 6(18), 2769–2777. doi:10.1039/C8TB00102B
  • Han, Y., Zhang, J., Hu, C. Q., Zhang, X., Ma, B., & Zhang, P. (2019). In silico ADME and toxicity prediction of ceftazidime and its impurities. Frontiers in Pharmacology, 10, 434. doi:10.3389/fphar.2019.00434
  • Houston, D. R., & Walkinshaw, M. D. (2013). Consensus docking: Improving the reliability of docking in a virtual screening context. Journal of Chemical Information and Modeling, 53(2), 384–390. doi:10.1021/ci300399w
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
  • Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52(7), 1757–1768. doi:10.1021/ci3001277
  • Johnson, E. R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A. J., & Yang, W. (2010). Revealing noncovalent interactions. Journal of the American Chemical Society, 132(18), 6498–6506. doi:10.1021/ja100936w
  • Kang, Y.-J., Mbonye, U. R., DeLong, C. J., Wada, M., & Smith, W. L. (2007). Regulation of intracellular cyclooxygenase levels by gene transcription and protein degradation. Progress in Lipid Research, 46(2), 108–125. doi:10.1016/j.plipres.2007.01.001
  • Knapp, B., Lederer, N., Omasits, U., & Schreiner, W. (2010). vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD. Journal of Computational Chemistry, 31(16), 2868–2873. doi:10.1002/jcc.21581
  • Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E., 3rd. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. doi:10.1021/ar000033j
  • Lagzian, M., Qasemi, A., Kaviani, P., & Mohammadi, M. (2018). Identification of new promising plant-based lead compounds for inhibition of prokaryotic replicative DNA polymerases: Combination of in silico and in vitro studies. Journal of Biomolecular Structure and Dynamics, 37, 4222–4237.
  • Lee, M. R., & Sun, Y. (2007). Improving docking accuracy through molecular mechanics generalized born optimization and scoring. Journal of Chemical Theory and Computation, 3(3), 1106–1119. doi:10.1021/ct6003406
  • Lefebvre, C., Khartabil, H., Boisson, J. C., Contreras‐García, J., Piquemal, J. P., & Hénon, E. (2018). The independent gradient model: A new approach for probing strong and weak interactions in molecules from wave function calculations. ChemPhysChem, 19(6), 724–735. doi:10.1002/cphc.201701325
  • Limongelli, V., Bonomi, M., Marinelli, L., Gervasio, F. L., Cavalli, A., Novellino, E., & Parrinello, M. (2010). Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proceedings of the National Academy of Sciences, 107(12), 5411–5416. doi:10.1073/pnas.0913377107
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. doi:10.1016/S0169-409X(96)00423-1
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. doi:10.1016/j.addr.2012.09.019
  • Lipinski, C. A. (2004). Lead-and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. doi:10.1016/j.ddtec.2004.11.007
  • Lu, T., & Chen, F. (2012). Multiwfn: A multifunctional wavefunction analyzer. Journal of Computational Chemistry, 33(5), 580–592. doi:10.1002/jcc.22885
  • Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. doi:10.1021/jm060522a
  • McGettigan, P., & Henry, D. (2000). Current problems with non-specific COX inhibitors. Current Pharmaceutical Design, 6(17), 1693–1724. doi:10.2174/1381612003398690
  • Medzhitov, R. (2010). Inflammation 2010: New adventures of an old flame. Cell, 140(6), 771–776. doi:10.1016/j.cell.2010.03.006
  • Oda, A., Tsuchida, K., Takakura, T., Yamaotsu, N., & Hirono, S. (2006). Comparison of consensus scoring strategies for evaluating computational models of protein–ligand complexes. Journal of Chemical Information and Modeling 46(1), 380–391. doi:10.1021/ci050283k
  • Oniga, S., Pacureanu, L., Stoica, C., Palage, M., Crăciun, A., Rusu, L. R., Crisan, E. L., & Araniciu, C. (2017). COX inhibition profile and molecular docking studies of some 2-(trimethoxyphenyl)-thiazoles. Molecules, 22(9), 1507. doi:10.3390/molecules22091507
  • Ounissi, M., Kameli, A., Tigrine, C., & Rachedi, F. Z. (2018). Computer-aided identification of natural lead compounds as cyclooxygenase-2 inhibitors using virtual screening and molecular dynamic simulation. Computational Biology and Chemistry, 77, 1–16.
  • Pajouhesh, H., & Lenz, G. R. (2005). Medicinal chemical properties of successful central nervous system drugs. NeuroRX, 2(4), 541–553. doi:10.1602/neurorx.2.4.541
  • Palacio-Rodríguez, K., Lans, I., Cavasotto, C. N., & Cossio, P. (2019). Exponential consensus ranking improves the outcome in docking and receptor ensemble docking. Scientific Reports, 9(1), 5142. doi:10.1038/s41598-019-41594-3
  • Paulino, M., Alvareda, E., Iribarne, F., Miranda, P., Espinosa, V., Aguilera, S., & Pardo, H. (2016). Toward the understanding of the molecular basis for the inhibition of COX-1 and COX-2 by phenolic compounds present in Uruguayan propolis and grape pomace. Journal of Biomolecular Structure and Dynamics, 34(12), 2643–2657. doi:10.1080/07391102.2015.1124808
  • Pérez, D. J., Sarabia, O., Villanueva-García, M., Pineda-Urbina, K., Ramos-Organillo, Á., Gonzalez-Gonzalez, J., Gómez-Sandoval, Z., & Razo-Hernández, R. S. (2017). In silico receptor-based drug design of X, Y-benzenesulfonamide derivatives as selective COX-2 inhibitors. Comptes Rendus Chimie, 20(2), 169–180. doi:10.1016/j.crci.2016.05.015
  • Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. doi:10.1002/jcc.20289
  • Plewczynski, D., Łażniewski, M., Von Grotthuss, M., Rychlewski, L., & Ginalski, K. (2011). VoteDock: Consensus docking method for prediction of protein–ligand interactions. Journal of Computational Chemistry, 32(4), 568–581. doi:10.1002/jcc.21642
  • Ramírez, D., & Caballero, J. (2016). Is it reliable to use common molecular docking methods for comparing the binding affinities of enantiomer pairs for their protein target? International Journal of Molecular Sciences, 17(4), 525. doi:10.3390/ijms17040525
  • Rao, P., Knaus, E. E. J. J. o P., & Sciences, P. (2008). Evolution of nonsteroidal anti-inflammatory drugs (NSAIDs): Cyclooxygenase (COX) inhibition and beyond. Journal of Pharmacy & Pharmaceutical Sciences, 11(2), 81–110. doi:10.18433/J3T886
  • Razzaghi-Asl, N., Mirzayi, S., Mahnam, K., & Sepehri, S. (2018). Identification of COX-2 inhibitors via structure-based virtual screening and molecular dynamics simulation. Journal of Molecular Graphics and Modelling, 83, 138–152. doi:10.1016/j.jmgm.2018.05.010
  • Roche, V. F. (2009). A receptor-grounded approach to teaching nonsteroidal antiinflammatory drug chemistry and structure-activity relationships. American Journal of Pharmaceutical Education, 73(8), 143. doi:10.5688/aj7308143
  • Saleh, G., Gatti, C., & Presti, L. L. (2012). Non-covalent interaction via the reduced density gradient: Independent atom model vs experimental multipolar electron densities. Computational and Theoretical Chemistry, 998, 148–163. doi:10.1016/j.comptc.2012.07.014
  • Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. doi:10.1093/nar/gkv315
  • Sani, F. D., Shakibapour, N., Beigoli, S., Sadeghian, H., Hosainzadeh, M., & Chamani, J. (2018). Changes in binding affinity between ofloxacin and calf thymus DNA in the presence of histone H1: Spectroscopic and molecular modeling investigations. Journal of Luminescence, 203, 599–608. doi:10.1016/j.jlumin.2018.06.083
  • Sárosi, M.-B., Neumann, W., Lybrand, T. P., & Hey-Hawkins, E. (2017). Molecular modeling of the interactions between carborane-containing analogs of indomethacin and cyclooxygenase-2. Journal of Chemical Information and Modeling, 57(8), 2056–2067. doi:10.1021/acs.jcim.7b00113
  • Shakibapour, N., Dehghani Sani, F., Beigoli, S., Sadeghian, H., & Chamani, J. (2019). Multi-spectroscopic and molecular modeling studies to reveal the interaction between propyl acridone and calf thymus DNA in the presence of histone H1: Binary and ternary approaches. Journal of Biomolecular Structure and Dynamics, 37(2), 359–371. doi:10.1080/07391102.2018.1427629
  • Sharif-Barfeh, Z., Beigoli, S., Marouzi, S., Rad, A. S., Asoodeh, A., & Chamani, J. (2017). Multi-spectroscopic and HPLC studies of the interaction between estradiol and cyclophosphamide with human serum albumin: Binary and ternary systems. Journal of Solution Chemistry, 46(2), 488–504. doi:10.1007/s10953-017-0590-2
  • Sharifi-Rad, A., Mehrzad, J., Darroudi, M., Saberi, M. R., & Chamani, J. (2020). Oil-in-water nanoemulsions comprising Berberine in olive oil: Biological activities, binding mechanisms to human serum albumin or holo-transferrin, and QMMD simulations. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2020.1724568
  • Sohilait, M. R., Pranowo, H. D., & Haryadi, W. (2017). Molecular docking analysis of curcumin analogues with COX-2. Bioinformation, 13(11), 356–359. doi:10.6026/97320630013356
  • Tavares, M. T., Primi, M. C., Silva, N. A., Carvalho, C. F., Cunha, M. R., & Parise-Filho, R. (2016). Using an in silico approach to teach 3D pharmacodynamics of the drug–target interaction process focusing on selective COX2 inhibition by Celecoxib. Journal of Chemical Education, 94(3), 380–387. doi:10.1021/acs.jchemed.6b00288
  • Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. J. J. o m c. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. doi:10.1021/jm020017n
  • Vecchio, A. J., Simmons, D. M., & Malkowski, M. G. (2010). Structural basis of fatty acid substrate binding to cyclooxygenase-2. Journal of Biological Chemistry, 285(29), 22152–22163. doi:10.1074/jbc.M110.119867
  • Wang, J. L., Limburg, D., Graneto, M. J., Springer, J., Hamper, J. R. B., Liao, S., Pawlitz, J. L., Kurumbail, R. G., Maziasz, T., Talley, J. J., Kiefer, J. R., & Carter, J. (2010). The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life. Bioorganic & Medicinal Chemistry Letters, 20(23), 7159–7163. doi:10.1016/j.bmcl.2010.07.054
  • Wang, R., & Wang, S. J. (2001). How does consensus scoring work for virtual library screening? An idealized computer experiment. Journal of Chemical Information and Computer Sciences, 41(5), 1422–1426. doi:10.1021/ci010025x
  • Williams, T., Kelley, C., Campbell, J., Kotz, D., & Lang, R. (1990). Gnuplot, An Interactive Plotting Program, The Free Software Foundation.
  • Wu, J., Wang, J., Liu, J., Yang, Y., Cheng, J., Wang, Z., Zhou, J., & Cen, K. (2017). Moisture removal mechanism of low-rank coal by hydrothermal dewatering: Physicochemical property analysis and DFT calculation. Fuel, 187, 242–249. doi:10.1016/j.fuel.2016.09.071
  • Zarghi, A., & Arfaei, S. (2011). Selective COX-2 inhibitors: A review of their structure-activity relationships. Iranian Journal of Pharmaceutical Research: IJPR, 10(4), 655–683.
  • Zolfagharzadeh, M., Pirouzi, M., Asoodeh, A., Saberi, M. R., & Chamani, J. (2014). A comparison investigation of DNP-binding effects to HSA and HTF by spectroscopic and molecular modeling techniques. Journal of Biomolecular Structure and Dynamics, 32(12), 1936–1952. doi:10.1080/07391102.2013.843062

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.