Kinetic and thermodynamic characterization of HIV-1 protease inhibitors

Journal of Molecular Recognition

Volumn 17, Issue 2, 2004, Pages 106-119

  Shuman, Cynthia F ^a   Hämäläinen, Markku D ^b   Danielson, U Helena ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b BIACORE AB   (Sweden)

Author keywords

Biosensor; HIV protease; Interactions; Kinetics; Thermodynamics

Indexed keywords

AMPRENAVIR; CARBAMIC ACID DERIVATIVE; INDINAVIR; LOPINAVIR; PROTEINASE INHIBITOR; PYRIMIDINONE DERIVATIVE; RITONAVIR; SULFONAMIDE;

ARTICLE; CHEMISTRY; HUMAN IMMUNODEFICIENCY VIRUS 1; KINETICS; THERMODYNAMICS;

CARBAMATES; HIV PROTEASE INHIBITORS; HIV-1; INDINAVIR; KINETICS; PYRIMIDINONES; RITONAVIR; SULFONAMIDES; THERMODYNAMICS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 1642310506     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.655     Document Type: Article

References (46)

1. Ahlsén G, Hultén J, Shuman CF, Poliakov A, Lindgren MT, Alterman M, Samuelsson B, Hallberg A, Danielson UH. 2002. Resistance profiles of cyclic sulfamide inhibitors of HIV-1 protease. Antivir. Chem. Chemother. 13: 27-37.
2. Boden D, Markowitz M. 1998. Resistance to human immunodeficiency virus type 1 protease inhibitors. Antimicrob. Agents Chemother. 42: 2775-2783.
3. Boniface JJ, Reich Z, Lyons DS, Davis MM. 1999. Thermodynamics of T cell receptor binding to peptide-MHC: evidence for a general mechanism of molecular scanning. Proc. Natl Acad. Sci. USA 96: 11446-11451.
4. Chaires JB. 1997. Possible origin of differences between van't Hoff and calorimetric enthalpy estimates. Biophys. Chem. 64: 15-23.
5. Copeland RA. 2000. Enzymes. A Practical Introduction to Structure, Mechanism, and Data Analysis. Wiley-VCH: New York.
6. Danielson H, Lindgren MT, Markgren P-O, Nillroth U. 1998. Investigation of an allosteric site of HIV-1 proteinase involved in inhibition by Cu2+. Adv. Exp. Med. Biol. 436: 99-103.
7. Deinum J, Gustavsson L, Gyzander E, Kullman-Magnusson M, Edström A, Karlsson R. 2002. A thermodynamic characterization of the binding of thrombin inhibitors to human thrombin, combining biosensor technology, stopped-flow spectrophotometry, and microcalorimetry. Anal. Biochem. 300: 152-162.
8. Dorsey BD, Levin RB, McDaniel SL, Vacca JP, Guare JP, Darke PL, Zugay JA, Emini EA, Schleif WA, Quintero JC. 1994. L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor. J. Med. Chem. 37: 3443-3451.
9. FDA. 2003. FDA approves a once daily protease inhibitor for HIV infection. http://www.fda.gov/bbs/topics/ANSWERS/2003/ANS01233.html
10. Glaser RW. 1993. Antigen-antibody binding and mass transport by convection and diffusion to a surface: a two-dimensional computer model of binding and dissociation kinetics. Anal. Biochem. 213: 152-161.
11. Horn JR, Russell D, Lewis EA, Murphy KP. 2001. Van't Hoff and calorimetric enthalpies from isothermal titration calorimetry: are there significant discrepancies? Biochemistry 40: 1774-1778.
12. Kaldor SW, Kalish VJ, Davies JF, Shetty BV, Fritz JE, Appelt K, Burgess JA, Campanale KM, Chirgadze NY, Clawson DK, Dressman BA, Hatch SD, Khalil DA, Kosa MB, Lubbehusen PP, Muesing MA, Patick AK, Reich SH, Su KS, Tatlock JH. 1997. Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. J. Med. Chem. 40: 3979-3985.
13. Karlsson R. 1999. Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J. Mol. Recognit. 12: 285-292.
14. Karlsson R, Fält A. 1997. Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors. J. Immunol. Meth. 200: 121-133.
15. Kempf DJ, Sham HL, Marsh KC, Flentge CA, Betebenner D, Green BE, McDonald E, Vasavanonda S, Saldivar A, Wideburg NE, Kati WM, Ruiz L, Zhao C, Fino L, Patterson J, Molla A, Plattner JJ, Norbeck DW. 1998. Discovery of ritonavir, a potent inhibitor of HIV protease with high oral bioavailability and clinical efficacy. J. Med. Chem. 41: 602-617.
16. Kim EE, Baker CT, Dwyer MD, Murcko MA, Rao BG, Tung RD, Navia MA. 1995. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J. Am. Chem. Soc. 117: 1181-1182.
17. Klabe RM, Bacheler LT, Ala PJ, Erickson-Viitanen S, Meek JL. 1998. Resistance to HIV protease inhibitors: a comparison of enzyme inhibition and antiviral potency. Biochemistry 37: 8735-8742.
18. Leatherbarrow RJ. 1998. GraFit Version 5.0. Erithacus Software Ltd, Staines, U.K.
19. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. 1997. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23: 3-25.
20. Luque I, Todd MJ, Gomez J, Semo N, Freire E. 1998. Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis. Biochemistry 37: 5791-5797.
21. Markgren P-O, Hämäläinen M, Danielson UH. 1998. Screening of compounds interacting with HIV-1 proteinase using optical biosensor technology. Anal. Biochem. 265: 340-350.
22. Markgren P-O, Hämäläinen M, Danielson UH. 2000. Kinetic analysis of the interaction between HIV-1 protease and inhibitors using optical biosensor technology. Anal. Biochem. 279: 71-78.
23. Markgren P-O, Lindgren MT, Gertow K, Karlsson R, Hämälä inen M, Danielson UH. 2001. Determination of interaction kinetic constants for HIV-1 protease inhibitors using optical biosensor technology. Anal. Biochem. 291: 207-218.
24. Markgren P-O, Hämäläinen M, Schaal W, Karlen A, Hallberg A, Danielson UH. 2002. Relationships between structure and interaction kinetics for HIV-1 protease inhibitors. J. Med. Chem. 45: 5430-5439.
25. Miller V. 2001. International perspectives on antiretroviral resistance. Resistance to protease inhibitors. J. Acquir. Immune Defic. Syndr. 26(suppl. 1): S34-S50.
26. Myszka DG. 1999. Improving biosensor analysis. J. Mol. Recognit. 12: 279-284.
27. Myszka DG. 2000. Kinetic, equilibrium, and thermodynamic analysis of macromolecular interactions with BIACORE. Meth. Enzymol. 323: 325-340.
28. Naghibi H, Tamura A, Sturtevant JM. 1995. Significant discrepancies between van't Hoff and calorimetric enthalpies. Proc. Natl. Acad. Sci. USA 92: 5597-5599.
29. Navia MA, Chaturvedi PR. 1996. Design principles for orally bioavailable drugs. Drug Discov. Today 1: 179-189.
30. NIAID. 2003. NIAID. www.niaid.nih.gov/daids/dtpdb/fdadrug.htm
31. Nillroth U, Vrang L, Markgren P-O, Hultén J, Hallberg A, Danielson UH. 1997. Human immunodeficiency virus type 1 proteinase resistance to symmetric cyclic urea inhibitor analogs. Antimicrob. Agents Chemother. 41: 2383-2388.
32. Price NC, Dwek RA, Ratcliff RG, Wormald MR. 2001. Principles and Problems in Physical Chemistry for Biochemists. Oxford University Press: Oxford.
33. Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. 2003. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucl. Acids Res. 31: 298-303.
34. Roberts NA, Martin JA, Kinchington D, Broadhurst AV, Craig JC, Duncan IB, Galpin SA, Handa BK, Kay J, Kröhn A. 1990. Rational design of peptide-based HIV proteinase inhibitors. Science 248: 358-361.
35. Robinson BS, Riccardi KA, Gong YF, Guo Q, Stock DA, Blair WS, Terry BJ, Deminie CA, Djang F, Colonno RJ, Lin PF. 2000. BMS-232632, a highly potent human immunodeficiency virus protease inhibitor that can be used in combination with other available antiretroviral agents. Antimicrob. Agents Chemother. 44: 2093-2099.
36. Roos H, Karlsson R, Nilshans H, Persson A. 1998. Thermodynamic analysis of protein interactions with biosensor technology. J. Mol. Recognit. 11: 204-210.
37. Sham HL, Kempf DJ, Molla A, Marsh KC, Kumar GN, Chen CM, Kati W, Stewart K, Lal R, Hsu A, Betebenner D, Korneyeva M, Vasavanonda S, McDonald E, Saldivar A, Wideburg N, Chen X, Niu P, Park C, Jayanti V, Grabowski B, Granneman GR, Sun E, Japour AJ, Norbeck DW. 1998. ABT-378, a highly potent inhibitor of the human immunodeficiency virus protease. Antimicrob. Agents Chemother. 42: 3218-3224.
38. Shuman CF, Markgren P-O, Hämäläinen M, Danielson UH. 2003. Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants. Antiviral Res. 58: 235-242.
39. Statistica. 2002. STATISTICA (data analysis software system), version 6. www.statsoft.com. StatSoft, Inc.
40. Stoll V, Qin W, Stewart KD, Jakob C, Park C, Walter K, Simmer RL, Helfrich R, Bussiere D, Kao J, Kempf D, Sham HL, Norbeck DW. 2002. X-ray crystallographic structure of ABT-378 (lopinavir) bound to HIV-1 protease. Bioorg. Med. Chem. 10: 2803-2806.
41. Tomasselli AG, Heinrikson RL. 2000. Targeting the HIV-protease in AIDS therapy: a current clinical perspective. Biochim. Biophys. Acta 1477: 189-214.
42. Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD. 2002. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 45: 2615-2623.
43. Velazquez-Campoy A, Freire E. 2001. Incorporating target heterogeneity in drug design. J. Cell Biochem. Suppl. (suppl. 37): 82-88.
44. Velazquez-Campoy A, Todd MJ, Freire E. 2000. HIV-1 protease inhibitors: enthalpic versus entropic optimization of the binding affinity. Biochemistry 39: 2201-2207.
45. Velazquez-Campoy A, Kiso Y, Freire E. 2001. The binding energetics of first- and second-generation HIV-1 protease inhibitors: implications for drug design. Arch. Biochem. Biophys. 390: 169-175.
46. Wang W, Kollman PA. 2001. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc. Natl Acad. Sci. USA 98: 14937-14942.