Skip to main content
SpringerLink
Log in

In Silico-Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase

  • Protocol
  • First Online:
Allostery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 796))

  • 1436 Accesses

Abstract

Identification of allosteric binding site modulators have gained increased attention lately for their potential to be developed as selective agents with a novel chemotype and targeting perhaps a new and unique binding site with probable fewer side effects. Erythrocyte pyruvate kinase (R-PK) is an important glycolytic enzyme that can be pharmacologically modulated through its allosteric effectors for the treatment of hemolytic anemia, sickle-cell anemia, hypoxia-related diseases, and other disorders arising from erythrocyte PK malfunction. An in-silico screening approach was applied to identify novel allosteric modulators of pyruvate kinase. A small-molecules database of the National Cancer Institute (NCI), was virtually screened based on structure/ligand-based pharmacophore. The virtual screening campaign led to the identification of several compounds with similar pharmacophoric features as fructose-1,6-bisphosphate (FBP), the natural allosteric activator of the kinase. The compounds were subsequently docked into the FBP-binding site using the programs FlexX and GOLD, and their interactions with the protein were analyzed with the energy-scoring function of HINT. Seven promising candidates were obtained from the NCI and subjected to kinetics analysis, which revealed both activators and inhibitors of the R-isozyme of PK (R-PK).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kharalkar, S. S., Joshi, G. S., Musayev, F. N., Fornabaio, M., Abraham, D. J., Safo, M. K. (2007) Identification of novel allosteric regulators of human-erythrocyte pyruvate kinase. Chem Biodivers. 4, 2603–2617.

    Article  PubMed  CAS  Google Scholar 

  2. Bond, C. J., Jurica, M. S., Mesecar, A., Stoddard, B. L. (2000) Determinants of Allosteric Activation of Yeast Pyruvate Kinase and Identification of Novel Effectors Using Computational Screening. Biochemistry. 39, 15333–15343.

    Article  PubMed  CAS  Google Scholar 

  3. Conn, P. J., Arthur Christopoulos, A., Lindsley, C. W. (2009) Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders. Nature Reviews Drug Discovery. 8, 41–54.

    Article  PubMed  CAS  Google Scholar 

  4. Yanamala, N., Tirupula, K. C., Seetharaman, J. K. (2008) Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors. BMC Bioinformatics. 9(Suppl 1):S16.

    Article  PubMed  Google Scholar 

  5. Espinoza-Fonseca, L. M., Trujillo-Ferrara, J. G. (2005) Identification of multiple allosteric sites on the M1 muscarinic acetylcholine receptor. FEBS Letters. 79, 6726–6732.

    Article  Google Scholar 

  6. Kern, D., Zuiderweg, E. R. (2003) The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol., 13, 748–757.

    Article  PubMed  CAS  Google Scholar 

  7. Hardy, J. A., Wells, J. A. (2004) Searching for new allosteric sites in enzymes. Curr. Opin. Struct. Biol. 14, 706–715.

    Article  PubMed  CAS  Google Scholar 

  8. Laskowski, R. A., Gerick, F., Thornton, J. M. (2009) The structural basis of allosteric regulation in proteins. FEBS Lett. 583, 1692–8.

    Article  PubMed  CAS  Google Scholar 

  9. Kay, L. E. (2005) NMR studies of protein structure and dynamics. J. Magn. Reson. 173, 193–207.

    Article  PubMed  CAS  Google Scholar 

  10. Hummer, G., Schotte, F., Anfinrud, P. A. (2004) Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 101, 15330–15334.

    Article  PubMed  CAS  Google Scholar 

  11. Safo, M. K., Abraham, D. J. (2005) The enigma of the liganded hemoglobin end-state: A novel Quaternary structure of human carbonmonoxy hemoglobin, Biochemistry, 44, 8347–8359.

    Article  PubMed  CAS  Google Scholar 

  12. Jenkins, J. D., Musayev, F. N., Danso-Danquah, R., Abraham, D. J., Safo, M. K. (2009) Structure of relaxed-state human hemoglobin: insight into ligand uptake, transport and release. Acta Crystallogr D Biol Crystallogr., 65, 41–48.

    Article  PubMed  Google Scholar 

  13. Safo, M. K., Moure, C. M., Burnett, J. C., Joshi, G. S., Abraham, D. J. (2001) High-resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector. Protein Sci. 10, 951–957.

    Article  PubMed  CAS  Google Scholar 

  14. Safo, M. K., Boyiri, T., Burnett, J. C., Danso-Danquah, R., Moure, C. M., Joshi, G. S., Abraham, D. J. (2002) X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites. Acta Crystallogr D Biol Crystallogr. 58, 634–644.

    Article  PubMed  Google Scholar 

  15. Marden, M. C., Cabanes-Macheteau, M., Babes, A., Kiger, L., Griffon, N., Poyart, C., Boyiri, T., Safo, M. K., Abraham, D. J. (2002) Control of the allosteric equilibrium of hemoglobin by cross-linking agents. Protein Sci. 11, 1376–1383.

    Article  PubMed  CAS  Google Scholar 

  16. Safo, M. K., Abdulmalik, O., Danso-Danquah, R., Burnett, J. C., Nokuri, S., Joshi, G. S., Musayev, F. N., Asakura, T., Abraham, D. J. (2004) Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds. J. Med. Chem. 9, 4665–4676.

    Article  Google Scholar 

  17. Abdulmalik, O., Safo, M. K., Chen, Q., Yang, J., Brugnara, C., Ohene-Frempong, K., Abraham, D. J., Asakura, T. (2005) 5-Hydroxymethyl-2-furfural modifies intracellular sickle haemoglobin and inhibits sickling of red blood cells. Br. J. Haematol. 128, 552–561.

    Article  PubMed  CAS  Google Scholar 

  18. Nnamani, I. N., Joshi, G. S., Danso-Danquah, R., Abdulmalik, O., Asakura, T., Abraham, D. J., Safo, M. K. (2008) Pyridyl derivatives of benzaldehyde as potential antisickling agents. Chem. Biodivers. 9, 1762–1769.

    Article  Google Scholar 

  19. Palmer, A. G. III, Grey, M. J., Wang, C. (2005) Solution NMR spin relaxation methods for characterizing chemical exchange in high molecular-weight systems. Methods Enzymol. 394, 430–465.

    Article  PubMed  CAS  Google Scholar 

  20. Korzhnev, D. M., Kloiber, K., Kay, L. E. (2004) Multiple-quantum relaxation dispersion NMR spectroscopy probing millisecond time-scale dynamics in proteins: theory and application. J. Am. Chem. Soc. 126, 7320–7329.

    Article  PubMed  CAS  Google Scholar 

  21. Korzhnev, D. M., Salvatella, X., Vendruscolo, M., Di Nardo, A. A., Davidson, A. R., Dobson, C. M., Kay, L. E. (2004) Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature. 430, 586–590.

    Article  PubMed  CAS  Google Scholar 

  22. Dennis, M. S., Eigenbrot, C., Skelton, N. J., Ultsch, M. H., Santell, L., Dwyer, M. A., O’Connell, M. P., Lazarus, R. A. (2000) Peptide exosite inhibitors of factor VIIa as anticoagulants. Nature. 404, 465–470.

    Article  PubMed  CAS  Google Scholar 

  23. Dennis, M. S., Roberge, M., Quan, C., Lazarus, R. A. (2001) Selection and characterization of a new class of peptide exosite inhibitors of coagulation factor VIIa. Biochemistry. 40, 9513–9521.

    Article  PubMed  CAS  Google Scholar 

  24. Roberge, M., Santell, L., Dennis, M. S., Eigenbrot, C., Dwyer, M. A., Lazarus, R. A. (2001) A novel exosite on coagulation factor VIIa and its molecular interactions with a new class of peptide inhibitors. Biochemistry. 40, 9522–9531.

    Article  PubMed  CAS  Google Scholar 

  25. Hardy, J. A., Lam, J., Nguyen, J. T., O’Brien, T., Wells, J. A. (2004) Discovery of an allosteric site in the caspases. Proc. Natl. Acad. Sci. USA. 101, 12461–12466.

    Article  PubMed  CAS  Google Scholar 

  26. Heddle, J. G., Okajima, T., Scott, D. J., Akashi, S., Park, S. Y., Tame, J. R. (2007) Dynamic allostery in the ring protein TRAP. J. Mol. Biol. 371, 154–167.

    Article  PubMed  CAS  Google Scholar 

  27. Yu, P., Lasagna, M., Pawlyk, A.C., Reinhart, G.D., Pettigrew, D.W. (2007) IIAGlc inhibition of glycerol kinase: a communications network tunes protein motions at the allosteric site. Biochemistry. 46, 12355–12365.

    Article  PubMed  CAS  Google Scholar 

  28. Swain, J. F., Gierasch L. M. (2006) The changing landscape of protein allostery. Current Opinion in Structural Biology. 16,102–108.

    Article  PubMed  CAS  Google Scholar 

  29. Hilser, V. J., Dowdy, D., Oas, T. G., Freire, E. (1998) The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc Natl Acad Sci USA. 95, 9903–9908.

    Article  PubMed  CAS  Google Scholar 

  30. Freire, E. (2000) Can allosteric regulation be predicted from structure? Proc Natl Acad Sci USA, 97, 11680–11682.

    Article  PubMed  CAS  Google Scholar 

  31. Freire, E. (1999) The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc Natl Acad Sci USA. 96, 10118–22.

    Article  PubMed  CAS  Google Scholar 

  32. Lockless, S. W., Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 286, 295–299.

    Article  PubMed  CAS  Google Scholar 

  33. Suel, G. M., Lockless, S. W., Wall, M. A., Ranganathan, R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59–69.

    Article  PubMed  Google Scholar 

  34. Hatley, M. E., Lockless, S. W., Gibson, S. K., Gilman, A. G., Ranganathan, R. (2003) Allosteric determinants in guanine nucleotide-binding proteins. Proc. Natl. Acad. Sci. USA. 100, 14445–14450.

    Article  PubMed  CAS  Google Scholar 

  35. Shulman, A. I., Larson, C., Mangelsdorf, D. J., Ranganathan, R. (2004) Structural determinants of allosteric ligand activation in RXR heterodimers. Cell. 116, 417–429.

    Article  PubMed  CAS  Google Scholar 

  36. Bleicher, K. H., Böhm, H., Müller, K., Alanine, A. I. (2003) Hit and lead generation: beyond high-throughput screening. Nature Reviews Drug Discovery. 2, 369–378.

    Article  PubMed  CAS  Google Scholar 

  37. Walters, W. P., Murcko, A., Murcko, M. A. (1999) Recognizing molecules with drug-like properties. Curr. Opin. Chem. Bio. 3, 384–387.

    Article  CAS  Google Scholar 

  38. Walters, W. P., Stahl, M. T., Murcko, M. A. (1998) Virtual screening – an overview. Drug Discovery Today. 3, 160–178.

    Article  CAS  Google Scholar 

  39. Smith, A. (2002) Screening for drug discovery: the leading question. Nature. 418, 483–459.

    Article  Google Scholar 

  40. Schneider, G., Böhm, H. (2002) Virtual screening and fast automated docking methods. Drug Discovery Today, 7, 64–70.

    PubMed  CAS  Google Scholar 

  41. Oprea, T. I. (2002) On the information content of 2D and 3D descriptors for QSAR. J. Braz. Chem. Soc. 13, 811–815.

    Article  CAS  Google Scholar 

  42. Todeschini, R., Consonni, V. (2000) Handbook of molecular descriptors. Wiley-VCH: Weinheim.

    Book  Google Scholar 

  43. Brown, R.D., Martin, Y.C. (1997) The information content of 2D and 3D structural descriptors relevant to ligand–receptor binding. J. Chem. Inf. Comput. Sci. 37, 1–9.

    Article  CAS  Google Scholar 

  44. Willet, P. (2006) Similarity-based virtual screening using 2D fingerprints. Drug Discovery Today. 11, 1046–1053.

    Article  Google Scholar 

  45. Willet, P. (1998) Chemical similarity searching. J. Chem. Inf. Comput. Sci. 38, 983–996.

    Article  Google Scholar 

  46. Sheridan, R. P., Kearsley, S. K. (2002) Why do we need so many chemical similarity search methods? Drug Discovery Today. 7, 903–911.

    Article  PubMed  Google Scholar 

  47. Eckert, H, Bajorath, J. (2007) Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discovery Today. 12, 225–233.

    Article  PubMed  CAS  Google Scholar 

  48. Mason, J.S., Morize, I., Menard, P.R., Cheney, D.L., Hulme, C., and Labaudiniere, R.F. (1999) New 4-point pharmacophore method for molecular similarity and diversity applications: Overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. 42, 3251–3264.

    Article  PubMed  CAS  Google Scholar 

  49. Matter, H. & Pötter, T. (1999) Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets. J. Chem. Inf. Comput. Sci. 39, 1211–1225.

    Article  CAS  Google Scholar 

  50. Patel, Y., Gillet, V. J., Bravi, G., Leach, A. R. (2002) A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. J. Comput. Aided Mol. Des. 16, 653–81.

    Article  CAS  Google Scholar 

  51. McGregor, M. J., Muskal, S. M. (1999) Pharmacophore Fingerprinting. 1. Application to QSAR and Focused Library Design. J. Chem. Inf. Comput. Sci. 39, 569–574.

    Article  PubMed  CAS  Google Scholar 

  52. McGregor, M. J., Muskal, S. M. (2000) Pharmacophore Fingerprinting. 2. Application to Primary Library Design. J. Chem. Inf. Comput. Sci. 40, 117–125.

    Article  PubMed  CAS  Google Scholar 

  53. Tropsha, A, Golbraikh, A. (2007) Predictive QSAR Modeling Workflow, Model Applicability Domains, and Virtual Screening. Curr. Pharm. Des. 13, 3494–3504.

    Article  PubMed  CAS  Google Scholar 

  54. Bissantz, C., Folkers, G., Rognan, D. (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 43, 4759–4767.

    Article  PubMed  CAS  Google Scholar 

  55. Joseph-McCarthy, D. (1999) Computational approaches to structure-based ligand design. Pharmacology & Therapeutics. 84, 179–191.

    Article  CAS  Google Scholar 

  56. Anderson, A.C. (2003) The Process of structure-based drug design. Chemistry & Biology. 10, 787–797.

    Article  CAS  Google Scholar 

  57. Kitchen, D. B.; Decornez, H.; Furr, J. R.; and Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov. 3, 935–949.

    Article  PubMed  CAS  Google Scholar 

  58. Ferrara, P., Gohlke, H., Price, D. J., Klebe, G., Brooks III, C. L. (2004) Assessing scoring functions for protein–ligand interactions. J. Med. Chem. 47, 3032–3047.

    Article  PubMed  CAS  Google Scholar 

  59. Gohlke, H., Klebe, G. (2002) Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41, 2644–2676.

    Article  CAS  Google Scholar 

  60. Oloff, S., Zhang, S., Sukumar, N., Breneman, C., Tropsha, A. (2006). Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI). J. Chem. Inf. Model. 46, 844–851.

    Article  PubMed  CAS  Google Scholar 

  61. Reid, D., Sadjad, B. S., Zsoldos, Z., Simon, A. (2008) LASSO – ligand activity by surface similarity order: a new tool for ligand based virtual screening. Journal of Computer-Aided Molecular Design. 22, 479–487.

    Article  PubMed  CAS  Google Scholar 

  62. Zsoldos, Z., Reid, D., Simon, A., Sadjad, S. B., Johnson, A. P. (2006) eHiTS: a new fast, exhaustive flexible ligand docking system. J. Mol. Graph. Model. 7, 421–435.

    CAS  Google Scholar 

  63. Bajorath, J. (2002) Integration of virtual and high-throughput screening. Nat. Rev. Drug Discov. 1, 882–894.

    Article  PubMed  CAS  Google Scholar 

  64. Larsen, T. M., Laughlin, L. T., Holden, H. M., Rayment, I., Reed, G. H. (1994) Structure of rabbit muscle pyruvate kinase complexed with Mn2+, K+, and pyruvate. Biochemistry. 24, 6301–6309.

    Article  Google Scholar 

  65. Muirhead, H., Clayden, D. A., Barford, D., Lorimer, C. G., Fothergill-Gilmore, L. A., Schiltz, E., Schmitt, W. (1986) The structure of cat muscle pyruvate kinase. EMBO J. 5, 475–481.

    PubMed  CAS  Google Scholar 

  66. Valentini, G., Chiarelli, L., Fortin, R., Speranza, M. L., Galizzi, A., Mattevi, A. (2000) The allosteric regulation of pyruvate kinase. J. Biol. Chem. 275, 18145–18152.

    Article  PubMed  CAS  Google Scholar 

  67. Laughlin, L. T., Reed, G. H. (1997) The monovalent cation requirement of rabbit muscle pyruvate kinase is eliminated by substitution of lysine for glutamate 117. Arch. Biochem. Biophys. 1997, 348, 262–267.

    Article  Google Scholar 

  68. Early, C. N., Britt, B. M. (1998) Sequence similarities of glyceraldehyde-3-phosphate dehydrogenases, phosphoglycerate kinases, and pyruvate kinases are species optimal temperature-dependent. Eur. Biophys. J. 27, 409–410.

    Article  PubMed  CAS  Google Scholar 

  69. Ernest, I., Opperdoes, F. R., Michels, P. A. (1994) Cloning and sequence analysis of the gene encoding pyruvate kinase in Trypanoplasma borelli. Biochem. Biophys. Res. Commun. 201, 727–732.

    Article  PubMed  CAS  Google Scholar 

  70. Ikeda, Y., Noguchi, T. (1998) Allosteric regulation of pyruvate kinase M2 isozyme involves a cysteine residue in the intersubunit contact. J. Biol. Chem. 273, 12227 12233.

    Google Scholar 

  71. Fothergill-Gillmore, L. A., Rigden, D. J., Michels, P. A., Phillips, S. E. (2000) Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties. Biochem. Soc. Trans. 28, 186–190.

    PubMed  CAS  Google Scholar 

  72. Mattevi, A., Bolognesi, M., Valentini, G. (1996) The allosteric regulation of pyruvate kinase. FEBS Lett. 389, 15–19.

    Article  PubMed  CAS  Google Scholar 

  73. Jurica, M. S., Mesecar, A., Heath, P. J., Shi, W., Nowak, T., Stoddard, B. L. (1998) The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate. Structure. 6, 195–210.

    Article  PubMed  CAS  Google Scholar 

  74. K. J. Johannes, K. J., Hess, B. (1973) Allosteric kinetics of pyruvate kinase of Saccharomyces carlsbergensis. J. Mol Biol. 76, 181–205.

    Google Scholar 

  75. Palmer, T. N., Odedra, B. R. (1982) l-Phenylalanine inhibition of muscle pyruvate kinase. Biosci. Rep. 2, 825–833.

    Article  PubMed  CAS  Google Scholar 

  76. Mapungwana, S. M., Davies, D. R. (1982) The effect of fructose on pyruvate kinase activity in isolated hepatocytes. Inhibition by allantoin and alanine. Biochem. J. 208, 171–178.

    CAS  Google Scholar 

  77. Del Valle, P., Busto, F., De Arriaga, D., Soler, J. (1990) ATP inhibition of Phycomyces pyruvate kinase: a kinetic study of the inhibitory effects on the allosteric kinetics shown by the enzyme. J. Enzyme Inhib. 3, 219–228.

    Article  PubMed  Google Scholar 

  78. Lee, J. C. (2008) Modulation of allostery of pyruvate kinase by shifting of an ensemble of microstates. Acta Biochim Biophys Sin. 40, 663–669.

    Article  PubMed  CAS  Google Scholar 

  79. Black, J. A., Henderson, M. H. (1972) Activation and inhibition of human erythrocyte pyruvate kinase by organic phosphates, amino acids, dipeptides and anions. Biochimica et Biophysica Acta (BBA) – Enzymology. 284, 115–127.

    Google Scholar 

  80. Fenton, A. W., Blair, J. B. (2002) Kinetic and Allosteric Consequences of Mutations in the Subunit and Domain Interfaces and the Allosteric Site of Yeast Pyruvate Kinase. Archives of Biochemistry and Biophysics. 397, 28–39.

    Article  PubMed  CAS  Google Scholar 

  81. Valentine, W. N., Tanaka, K. R., Miwa, S. (1961) A specific erythrocyte glycolytic enzyme defect (pyruvate kinase) in three subjects with congenital non-spherocytic hemolytic anemia. Trans. Assoc. Am. Physicians. 74, 100–110.

    PubMed  CAS  Google Scholar 

  82. Zanella, A., Bianchi, P. (2000) Red cell pyruvate kinase deficiency: from genetics to clinical manifestations. Baillieres Best Pract. Res. Clin. Haematol. 13, 57–81.

    Article  PubMed  CAS  Google Scholar 

  83. Abraham, D. J., Mehanna, A. S., Wireko, F. C., Whitney, J., Thomas, R. P., Orringer, E. P. (1991) Vanillin, a potential agent for the treatment of sickle cell anemia. Blood 77, 1334–1341.

    PubMed  CAS  Google Scholar 

  84. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., Bourne, P. E. (2000) The protein data bank. Nucl. Acids. Res. 28, 235–242.

    Article  PubMed  CAS  Google Scholar 

  85. Rarey, M., Kramer, B., Lengauer, T., Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 23, 470–489.

    Article  Google Scholar 

  86. Jones, G., Willett, P., Glen, R. C., Leach, A. R., Taylor, R. J. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267, 727–748.

    Article  PubMed  CAS  Google Scholar 

  87. Kellogg, G. E., Abraham, D. J. (2000) Hydrophobicity: is LogP(o/w) more than the sum of its parts? Eur. J. Med. Chem. 35, 651–661.

    Article  CAS  Google Scholar 

  88. Cozzini, P., Fornabaio, M., Marabotti, A., Abraham, D. J., Kellogg, G. E., Mozzarelli, A. (2002) Simple, intuitive calculations of free energy of binding for protein–ligand complexes. 1. Models without explicit constrained water. J. Med. Chem. 45, 2469–2483.

    Article  PubMed  CAS  Google Scholar 

  89. Spyrakis, F., Amadasi, A., Fornabaio, M., Abraham, D. J., Mozzarelli, A., Kellogg, G. E., Cozzini, P. (2007) The consequences of scoring docked ligand conformations using free energy correlations. Eur. J. Med. Chem. 42, 921–933.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicinal Chemistry, School of Pharmacy & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA

    Ashutosh Tripathi & Martin K. Safo

Authors
  1. Ashutosh Tripathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin K. Safo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Martin K. Safo .

Editor information

Editors and Affiliations

  1. , Dept. Biochemistry & Molecular Biology, University of Kansas Medical Center, Rainbow Blvd. 3901, Kansas City, 66160, Kansas, USA

    Aron W. Fenton

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Tripathi, A., Safo, M.K. (2012). In Silico-Screening Approaches for Lead Generation: Identification of Novel Allosteric Modulators of Human-Erythrocyte Pyruvate Kinase. In: Fenton, A. (eds) Allostery. Methods in Molecular Biology, vol 796. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-334-9_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-334-9_19

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-333-2

  • Online ISBN: 978-1-61779-334-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation