Novel potential inhibitors for adenylylsulfate reductase to control souring of water in oil industries

References

• Almeida, P. F., Almeida, R. C. C., Carvalho, E. B., Ramos-de-Souza, E., Carvalho, A. S., Silva, C. H. T. P., & Taft, C. A. (2006). Overview of sulfate-reducing bacteria and strategies to control biosulfide generation in oil waters. In C. A. Taft (Ed.), Modern biotechnology in medicinal chemistry and industry (pp. 183–195). Kerala: Research Signpost.
   Google Scholar
• American Public Health Association (1998). Standard methods for the examination of water and wastewater (20th ed.). Washington, DC: Author.
   Google Scholar
• Barillari, C., Taylor, J., Viner, R., & Essex, J. W. (2007). Classification of water molecules in protein binding sites. Journal American Chemical Society, 129, 2577–2587.
   PubMed Web of Science ®Google Scholar
• Beech, I. B., & Sunner, J. (2004). Biocorrosion: Towards understanding interactions between biofilms and metals. Current Opinion in Biotechnology, 15, 181–186.
   PubMed Web of Science ®Google Scholar
• Bendall, D. S. (1996). Interprotein electron transfer. In D. S. Bendall (Ed.), Protein electron transfer (pp. 43–64). Oxford: Bios Scientific.
   Google Scholar
• Bizzarri, A. R., & Cannistraro, S. (1998). Molecular dynamics simulation of plastocyanin potential energy fluctuations: 1/f noise. Physics Letters A, 267, 257–270.
   Google Scholar
• Carvalho, A. S., Almeida, P. F., Souza, E. R., & Roque, M. R. A. (2010). Brazil Patent No. BR 1013438-7. Rio de Janeiro: Instituto Nacional de Propriedade Intelectual.
   Google Scholar
• Chia-en, A., Chang, W. C., & Michael, K. G. (2007). Ligand configurational entropy and protein binding. Proceeding of the National Academy of Sciences of the United States of America, 104, 1534–1539.
   PubMed Web of Science ®Google Scholar
• Cozzini, P., Fornabaio, M., Marabotti, A., Abraham, D. J., Kellogg, G. E., & Mozzarelli, A. (2004). Free energy of ligand binding to protein: Evaluation of the contribution of water molecules by computational methods. Current Medicinal Chemistry, 11, 3093–3118.
   PubMed Web of Science ®Google Scholar
• Decard, G. M., & Nikaido, H. (1976). Outer membrane of gram-negative bacteria molecular-sieving function of cell-wall. Journal Bacteriology, 128, 325–336.
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2011). The PyMOL molecular graphics system (Version 1.4.1). San Carlos, CA: DeLano Scientific LLC. Retrieved from www.pymol.org
   Google Scholar
• dos Santos, E. S., Gritta, D., Taft, C., Almeida, P. F., & Ramos-de-Souza, E. (2010). Molecular dynamics simulation of the adenylylsulfate reductase from hyperthermophilic Archaeoglobus fulgidus. Molecular Simulation, 36, 190–203.
   Google Scholar
• dos Santos, E. S., Ramos-de-Souza, E., & Almeida, P. F. (2010). Brazil patent No. BR1005035-3. Rio de Janeiro: Instituto Nacional de Propriedade Intelectual.
   Google Scholar
• Eisenberg, D., & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature, 319, 199–203.
   PubMed Web of Science ®Google Scholar
• Filikov, A. V., Mohan, V., Vickers, T. A., Griffey, R. H., Cook, P. D., Abagyan, R. A., & James, T. L. (2000). Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. Computer-Aided Molecular Design, 14, 593–610.
   PubMed Web of Science ®Google Scholar
• Fleming, P. J., & Richards, F. M. (2000). Protein packing: Dependence on protein size, secondary structure and amino acid composition. Journal of Molecular Biology, 299, 487–498.
   PubMed Web of Science ®Google Scholar
• Frederick, K. K., Marlow, M. S., Valentine, K. G., & Wand, A. J. (2007). Conformational entropy in molecular recognition by proteins. Nature, 448, 325–329.
   PubMed Web of Science ®Google Scholar
• Grigoriev, F. V., Luschekina, S. V., Romanov, A. N., Sulimov, V. B., & Nikitina, E. A. (2007). Computation of entropy contribution to protein–ligand binding free energy. Biochemistry (Moscow), 72, 785–792.
   PubMed Web of Science ®Google Scholar
• Greene, E. A., Hubert, C., Nemati, M., Jenneman, G. E., & Voordouw, G. (2003). Nitrite reductase activity of sulphate-reducing bacteria prevents their inhibition by nitrate-reducing, sulphide oxidizing bacteria. Environmental Microbiology, 5, 607–617.
   PubMed Web of Science ®Google Scholar
• Guimarães, C. R. W., & Mathiowetz, A. M. (2010). Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations. Journal of Chemical Information and Modeling, 50, 547–559.
   PubMed Web of Science ®Google Scholar
• Guimarães, C. R. W., & Cardozo, M. (2008). MM-GB/SA rescoring of docking poses in structure-based lead optimization. Journal of Chemical Information and Modeling, 48, 958–970.
   PubMed Web of Science ®Google Scholar
• Han, L. Y., Lin, H. H., Li, Z. R., Zheng, C. J., Cao, Z. W., Xie, B., & Chen, Y. Z. (2006). PEARLS: Program for energetic analysis of receptor-ligand system. Journal of Chemical Information and Modeling, 46, 445–450.
   PubMed Web of Science ®Google Scholar
• Harano, Y. (2012). Application of hydration thermodynamics to the evaluation of protein structures and protein-ligand binding. Entropy, 14, 1443–1468.
   Web of Science ®Google Scholar
• Karplus, M., Ichiye, T., & Pettitt, B. M. (1987). Configurational entropy of native proteins. Biophysical Journal, 52, 1083–1085.
   PubMed Web of Science ®Google Scholar
• Klapper, M. H. (1971). On the nature of protein interior. Biochemica et Biophysica Acta, 229, 557–566.
   PubMed Web of Science ®Google Scholar
• Lee, B., & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55, 379–400.
   PubMed Web of Science ®Google Scholar
• Marcus, R. A., & Sutin, N. (1985). Electron transfers in chemistry and biology. Biochimica Biophysica Acta, 811, 265–322.
   Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutodockTools4: Automated docking with selective receptor flexiblity. Journal Computational Chemistry, 16, 2785–2791.
   Web of Science ®Google Scholar
• Moser, C. C., Keske, J. M., Warncke, K., Farid, R. S., & Dutton, P. L. (1992). Nature of biological electron transfer. Nature, 366, 796–802.
   Google Scholar
• Mulder, M. H. V., van Voorthuizen, E. M., Peeters, J. M. M. (2005). Membrane Characterization. In: A. I. Schafer, A. G. Fane, T. D. Waite (Eds). Nanofiltration principles and applicatons, chapter 5 (pp. 89–117). Sydney: Elsevier.
   Google Scholar
• Nemati, M., Jenneman, G. E., & Voordouw, G. (2001). Impact of nitrate-mediated microbial control of souring in oil reservoirs on the extent of corrosion. Biotechnology Progress, 17, 852–859.
   Google Scholar
• O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 1–14.
   PubMed Web of Science ®Google Scholar
• Pinsetta, F. R., Taft, C. A., & Silva, C. H. T. P. (2013). Rational design of novel potential p38α MAPK inhibitors with drug-like properties using pharmacophore and similarity-based virtual screening procedures. Current Bioactive Compounds, 9, 3–13.
   Google Scholar
• Postgate, J. R. (1984). The sulphate-reducing bacteria (2nd ed.). Cambridge: Cambridge University Press.
   Google Scholar
• Robertson, J. W. F., Rodrigues, C. G., Stanford, V. M., Rubison, K. A., Krasilnikov, O. V., & Kasianowicz, J. J. (2007). Single-molecule mass spectrometry in solution using a solitary nanopore. Proceedings of the National Academy of Sciences of the USA, 104, 8207–8211.
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numeral integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.
   Web of Science ®Google Scholar
• Santos, A. F. J., Batista, L. L. F., Lima, J. B. T., Almeida, R. C. C., Roque, M. R. A., Ramos-de-Souza, E., & Almeida, P. F. (2010). Evaluation of the fluorescence in situ hybridization technique for detection of eubacteria and sulfate-reducing bacteria from samples of water in oil fields. Chemical Engineering Transactions, 20, 139–144.
   Google Scholar
• Schuettelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica, D60, 1355–1363.
   Web of Science ®Google Scholar
• Schiffer, A., Fritz, G., Kroneck, P. M. H., & Ermler, U. (2006). Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5-phosphosulfate reductase based on the structural characterization of different enzymatic states. Biochemistry, 45, 2960–2967.
   PubMed Web of Science ®Google Scholar
• Taft, C. A., & da Silva, C. H. T. P. (2013). Comments on the paper ‘Levinthal’s question, revisited, and answered’. Journal of Biomolecular Structure and Dynamics, J31, 1001–1002.
   Google Scholar
• Tsai, J., Taylor, R., Chothia, C., & Gerstein, M. (1999). The packing density in proteins: Standard radii and volumes. Journal of Molecular Biology, 290, 253–266.
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, O. J. (2010). Autodock Vina: Improving speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computation Chemistry, 31, 455–461.
   PubMed Web of Science ®Google Scholar
• Van der Spoel, D., Lindahl, E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.
   PubMed Web of Science ®Google Scholar
• Vik, E. A., Janbu, A. O., Garshol, F., Henninge, L. B., Engebretsen, S., Kuijvenhoven, C., … Hendriks, W. P. (2007). Nitrate based souring mitigation produced water – Side effects and challenges from the Draugen produced water re-injecting pilot. Houston, TX: SPE International Symposium on oilfield chemistry.
   Google Scholar
• Voordouw, G., Nemati, M., & Jenneman, G. E. (2002). Use of nitrate reducing, sulfide-oxidising bacteria to reduce souring in oil fields: Interactions with SRB and effects on corrosion. Corrosion, 34, 1–6.
   Google Scholar
• Vorov, O. K., Livesay, D. R., & Jacobs, D. J. (2008). Conformational entropy of an ideal cross-linking polymer chain. Entropy, 10, 285–308.
   Google Scholar
• Wesson, L., & Eisenberg, D. (1992). Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Science, 1, 227–235.
   PubMed Web of Science ®Google Scholar
• Zhou, Y., Vitkup, D., & Karplus, M. (1999). Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state. Journal of Molecular Biology, 285, 1371–1375.
   PubMed Web of Science ®Google Scholar
• Zuo, R., Ornek, D., Syrett, B. C., Green, R. M., Hsu, C.-H., Mansfeld, F. B., & Wood, T. K. (2004). Inhibiting mild steel corrosion from sulfate-reducing bacteria using antimicrobial-producing biofilms in Three-Mile-Island process water. Applied Microbiology and Biotechnology, 64, 275–283.
   PubMed Web of Science ®Google Scholar