Rational approach to AIDS drug design through structural biology.

The discovery and development of more than a dozen drugs in the past 15 years for the treatment of AIDS offer an excellent example of progress in the field of rational drug design. At this time, the principal targets are reverse transcriptase and protease, enzymes encoded by the human immunodeficiency virus. The introduction of protease inhibitors, in particular, has drastically decreased the mortality and morbidity associated with AIDS. This review presents the methods used to develop such drugs and discusses the remaining problems, such as the rapid emergence of drug resistance.

[1]  A Wlodawer,et al.  Structural and biochemical studies of retroviral proteases. , 2000, Biochimica et biophysica acta.

[2]  R. Swanstrom,et al.  Human immunodeficiency virus type-1 protease inhibitors: therapeutic successes and failures, suppression and resistance. , 2000, Pharmacology & therapeutics.

[3]  J. Condra,et al.  In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors , 1995, Nature.

[4]  A. Leach Molecular Modelling: Principles and Applications , 1996 .

[5]  A Wlodawer,et al.  Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures. , 1994, Protein engineering.

[6]  J. A. Aviña-Zubieta,et al.  Reduction in hospitalization costs, morbidity, disability, and mortality in patients with aids treated with protease inhibitors. , 2000, Archives of medical research.

[7]  PatrickY.-S. Lam,et al.  Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. , 1994, Science.

[8]  S. Vasavanonda,et al.  Antiviral and pharmacokinetic properties of C2 symmetric inhibitors of the human immunodeficiency virus type 1 protease , 1991, Antimicrobial Agents and Chemotherapy.

[9]  Y. Pommier,et al.  HIV-1 Integrase as a Target for Antiviral Drugs , 1997 .

[10]  L J Davis,et al.  Active human immunodeficiency virus protease is required for viral infectivity. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[11]  W. M. Sanders,et al.  Design and synthesis of HIV protease inhibitors. Variations of the carboxy terminus of the HIV protease inhibitor L-682,679. , 1991, Journal of medicinal chemistry.

[12]  A. Wlodawer,et al.  Drugs Targeted at HIV — Successes and Resistance , 2002 .

[13]  K. Goa,et al.  Amprenavir , 2000, Drugs.

[14]  P. Darke,et al.  L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor. , 1994, Journal of medicinal chemistry.

[15]  D. Davies,et al.  The structure and function of the aspartic proteinases. , 1990 .

[16]  Dale J. Kempf,et al.  In Vitro Selection and Characterization of Human Immunodeficiency Virus Type 1 Variants with Increased Resistance to ABT-378, a Novel Protease Inhibitor , 1998, Journal of Virology.

[17]  David A. Stock,et al.  BMS-232632, a Highly Potent Human Immunodeficiency Virus Protease Inhibitor That Can Be Used in Combination with Other Available Antiretroviral Agents , 2000, Antimicrobial Agents and Chemotherapy.

[18]  Baoguang Zhao,et al.  Three-dimensional structure of a simian immunodeficiency virus protease/inhibitor complex. Implications for the design of human immunodeficiency virus type 1 and 2 protease inhibitors. , 1993, Biochemistry.

[19]  A. Tomasselli,et al.  The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors. , 1993, The Journal of biological chemistry.

[20]  M. Jaskólski,et al.  Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. , 1989, Science.

[21]  I. Weber,et al.  Molecular mechanics analysis of inhibitor binding to HIV-1 protease. , 1992, Protein engineering.

[22]  Erik De Clercq,et al.  Potent and selective inhibition of HIV-1 replication in vitro by a novel series of TIBO derivatives , 1990, Nature.

[23]  M. Hatada,et al.  Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. , 1991, Journal of medicinal chemistry.

[24]  D. Norbeck,et al.  Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease. , 1990, Science.

[25]  T. Halgren,et al.  A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. , 1995, Journal of medicinal chemistry.

[26]  R M Stroud,et al.  Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[27]  M. Moroni,et al.  Susceptibility to PNU-140690 (Tipranavir) of Human Immunodeficiency Virus Type 1 Isolates Derived from Patients with Multidrug Resistance to Other Protease Inhibitors , 2000, Antimicrobial Agents and Chemotherapy.

[28]  J. Louis,et al.  Structural and kinetic analysis of drug resistant mutants of HIV-1 protease. , 2000, European journal of biochemistry.

[29]  K. Appelt,et al.  Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S. Gulnik,et al.  HIV protease: enzyme function and drug resistance. , 2000, Vitamins and hormones.

[31]  P Murray-Rust,et al.  X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease. , 1994, Biochemistry.

[32]  S. Thaisrivongs,et al.  Structure-based discovery of Tipranavir disodium (PNU-140690E): a potent, orally bioavailable, nonpeptidic HIV protease inhibitor. , 1999, Biopolymers.

[33]  D K Gehlhaar,et al.  De novo design of enzyme inhibitors by Monte Carlo ligand generation. , 1995, Journal of medicinal chemistry.

[34]  J F Davies,et al.  Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. , 1997, Journal of medicinal chemistry.

[35]  William J. Greenlee Renin Inhibitors , 2004, Pharmaceutical Research.

[36]  J. Erickson Design and structure of symmetry-based inhibitors of HIV-1 protease , 1993 .

[37]  A. Engelman,et al.  Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. , 1994, Science.

[38]  M. Murcko,et al.  Free energy perturbation studies on binding of A-74704 and its diester analog to HIV-1 protease. , 1996, Protein engineering.

[39]  G L Verdine,et al.  Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. , 1998, Science.

[40]  I B Duncan,et al.  Rational design of peptide-based HIV proteinase inhibitors. , 1990, Science.

[41]  P A Kollman,et al.  Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease. , 1991, Journal of medicinal chemistry.

[42]  T. Miyata,et al.  Retroviral protease-like sequence in the yeast transposon Ty 1 , 1985, Nature.

[43]  P. Darke,et al.  L-735,524: an orally bioavailable human immunodeficiency virus type 1 protease inhibitor. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[44]  V. Mikol,et al.  Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. , 1998, Journal of molecular biology.

[45]  A. Tomasselli,et al.  Targeting the HIV-protease in AIDS therapy: a current clinical perspective. , 2000, Biochimica et biophysica acta.

[46]  Gerhard Klebe,et al.  Recent developments in structure-based drug design , 2000, Journal of Molecular Medicine.

[47]  Y. Kiso,et al.  Solution conformations of KNI-272, a tripeptide HIV protease inhibitor designed on the basis of substrate transition state: determined by NMR spectroscopy and simulated annealing calculations. , 1996, Bioorganic & medicinal chemistry.

[48]  A. D. Clark,et al.  Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[49]  C. Zechel,et al.  Combinatorial Synthesis of Small Organic Molecules , 1996 .

[50]  C M Cook,et al.  The three-dimensional x-ray crystal structure of HIV-1 protease complexed with a hydroxyethylene inhibitor. , 1991, Advances in experimental medicine and biology.

[51]  S Vajda,et al.  Empirical free energy as a target function in docking and design: application to HIV‐1 protease inhibitors , 1996, FEBS letters.

[52]  V. Turk,et al.  Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Wlodawer,et al.  Structure-based inhibitors of HIV-1 protease. , 1993, Annual review of biochemistry.

[54]  A Caflisch,et al.  Monte Carlo docking of oligopeptides to proteins , 1992, Proteins.

[55]  A Tropsha,et al.  Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HIV protease. , 1992, Protein engineering.

[56]  M. Murcko,et al.  Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .

[57]  R L Jernigan,et al.  A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design , 1995, Protein science : a publication of the Protein Society.

[58]  S. Freer,et al.  Design of enzyme inhibitors using iterative protein crystallographic analysis. , 1991, Journal of medicinal chemistry.

[59]  P. Dean,et al.  Recent advances in structure-based rational drug design. , 2000, Current opinion in structural biology.

[60]  M. Navia,et al.  Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1 , 1989, Nature.

[61]  B. Larder,et al.  Mutations in Retroviral Genes Associated with Drug Resistance , 1996 .

[62]  Ian M. Brereton,et al.  Ionization states of the catalytic residues in HIV-1 protease , 1996, Nature Structural Biology.

[63]  S. Vasavanonda,et al.  ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[64]  W. Guerra Zidovudine in asymptomatic human immunodeficiency virus infection. A controlled trial in persons with fewer than 500 CD4-positive cells per cubic millimeter , 1991 .

[65]  B. Podlogar,et al.  Design, synthesis, and conformational analysis of a novel macrocyclic HIV-protease inhibitor. , 1994, Journal of medicinal chemistry.

[66]  Mark L. Pearson,et al.  Complete nucleotide sequence of the AIDS virus, HTLV-III , 1985, Nature.

[67]  T. Steitz,et al.  Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion. , 1994, Structure.

[68]  R. Stroud,et al.  Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor. , 1993, Biochemistry.

[69]  E Harper,et al.  On the size of the active site in proteases: pronase. , 1972, Biochemical and biophysical research communications.

[70]  A Wlodawer,et al.  Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.

[71]  R T Walker,et al.  Highly specific inhibition of human immunodeficiency virus type 1 by a novel 6-substituted acyclouridine derivative. , 1989, Biochemical and biophysical research communications.

[72]  T. Steitz,et al.  Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. , 1992, Science.

[73]  H. B. Schock,et al.  Mutational Anatomy of an HIV-1 Protease Variant Conferring Cross-resistance to Protease Inhibitors in Clinical Trials , 1996, The Journal of Biological Chemistry.

[74]  J. Adams,et al.  Inhibition of HIV-1 replication by a nonnucleoside reverse transcriptase inhibitor. , 1990, Science.

[75]  P. Jadhav,et al.  Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV. , 1997, Journal of medicinal chemistry.

[76]  Erik De Clercq,et al.  The role of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infection , 1998 .

[77]  T. Yamazaki,et al.  Secondary structure and signal assignments of human-immunodeficiency-virus-1 protease complexed to a novel, structure-based inhibitor. , 1994, European journal of biochemistry.

[78]  A M Hassell,et al.  A symmetric inhibitor binds HIV-1 protease asymmetrically. , 1993, Biochemistry.

[79]  M. Shibuya,et al.  Murine leukemia virus maturation: protease region required for conversion from "immature" to "mature" core form and for virus infectivity. , 1985, Virology.

[80]  B. Sadler,et al.  In vitro antiviral activity of 141W94 (VX-478) in combination with other antiretroviral agents. , 1996, Antiviral research.

[81]  L. Tong,et al.  Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with a reduced amide inhibitor and comparison with HIV-1 protease structures. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[82]  S. Hirono,et al.  Solution structure of HIV-1 protease-allophenylnorstatine derivative inhibitor complex obtained from molecular dynamics simulation. , 1994, Chemical & pharmaceutical bulletin.

[83]  K Osterlund,et al.  Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor. , 1997, Journal of medicinal chemistry.

[84]  L. Peiperl Antiretroviral Treatments to Reduce Mother-to-Child Transmission of HIV , 2001, HIV clinical trials.

[85]  A Wlodawer,et al.  Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. , 1998, Annual review of biophysics and biomolecular structure.

[86]  Sergio H. Rotstein,et al.  GroupBuild: a fragment-based method for de novo drug design , 1994 .

[87]  P Murray-Rust,et al.  A series of penicillin-derived C2-symmetric inhibitors of HIV-1 proteinase: structural and modeling studies. , 1993, Journal of medicinal chemistry.

[88]  A Wlodawer,et al.  X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[89]  A. D. Rodrigues,et al.  Pharmacokinetic enhancement of inhibitors of the human immunodeficiency virus protease by coadministration with ritonavir , 1997, Antimicrobial agents and chemotherapy.

[90]  Alexander Wlodawer,et al.  Database of three-dimensional structures of HIV proteinases , 1997, Nature Structural Biology.

[91]  G. Marshall,et al.  Effect of hydroxyl group configuration in hydroxyethylamine dipeptide isosteres on HIV protease inhibition. Evidence for multiple binding modes. , 1991, Journal of medicinal chemistry.

[92]  J. Tavel Ongoing trials in HIV protease inhibitors , 2000, Expert opinion on investigational drugs.

[93]  A. Cross,et al.  Clinical Efficacy of Monotherapy with Stavudine Compared with Zidovudine in HIV-Infected, Zidovudine-Experienced Patients , 1997, Annals of Internal Medicine.

[94]  K. Appelt,et al.  Crystal structures of HIV-1 protease-inhibitor complexes , 1993 .

[95]  R. Hameed,et al.  Amprenavir: a new human immunodeficiency virus type 1 protease inhibitor. , 2000, Clinical therapeutics.

[96]  Dale J. Kempf,et al.  ABT-378, a Highly Potent Inhibitor of the Human Immunodeficiency Virus Protease , 1998, Antimicrobial Agents and Chemotherapy.

[97]  R M Stroud,et al.  Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. , 1998, Biochemistry.

[98]  The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant , 1996, FEBS letters.

[99]  J. Condra,et al.  Clinically effective HIV-1 protease inhibitors , 1997 .

[100]  J L Meek,et al.  Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. , 1996, Chemistry & biology.

[101]  T. Yasunaga,et al.  Inhibition of retroviral protease activity by an aspartyl proteinase inhibitor , 1987, Nature.

[102]  John P. Overington,et al.  X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes , 1989, Nature.

[103]  K D Watenpaugh,et al.  Tipranavir (PNU-140690): a potent, orally bioavailable nonpeptidic HIV protease inhibitor of the 5,6-dihydro-4-hydroxy-2-pyrone sulfonamide class. , 1998, Journal of medicinal chemistry.