101
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Abstract
Virtually all the compounds that are currently used, or under advanced clinical trial, for the treatment of HIV infections, belong to one of the following classes: (i) nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs): i.e. zidovudine, didanosine, zalcitabine, stavudine, lamivudine, abacavir, emtricitabine, tenofovir (PMPA) disoproxil fumarate; (ii) non-nucleoside reverse transcriptase inhibitors (NNRTIs): i.e. nevirapine, delavirdine, efavirenz, emivirine; and (iii) protease inhibitors (PIs): i.e. saquinavir, ritonavir, indinavir, nelfinavir and amprenavir. In addition, various other events in the HIV replicative cycle are potential targets for chemotherapeutic intervention: (i) viral adsorption, through binding to the viral envelope glycoprotein gp120; (ii) viral entry, through blockade of the viral coreceptors CXCR4 and CCR5; (iii) virus-cell fusion; (iv) viral assembly and disassembly; (v) proviral DNA integration; (vi) viral mRNA transcription. Also, new NRTIs, NNRTIs and PIs have been developed that possess respectively improved metabolic characteristics, or increased activity against NNRTI-resistant HIV strains or, as in the case of PIs, a different, non-peptidic scaffold. Given the multitude of molecular targets with which anti-HIV agents can interact, one should be cautious in extrapolating from cell-free enzymatic assays to the mode of action of these agents in intact cells.
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Affiliation(s)
- E De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium.
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102
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Abstract
The design of new HIV protease inhibitors requires an improved understanding of the physical basis of inhibitor/protein binding. Here, the binding affinities of seven aliphatic cyclic ureas to HIV-1 protease are calculated using a predominant states method and an implicit solvent model based upon finite difference solutions of the Poisson-Boltzmann equation. The calculations are able to reproduce the observed U-shaped trend of binding free energy as a function of aliphatic chain length. Interestingly, the decrease in affinity for the longest chains is attributable primarily to the energy cost of partly desolvating charged aspartic and arginine groups at the mouths of the active site. Even aliphatic chains too short to contact these charged groups directly are subject to considerable desolvation penalties. We are not aware of other systems where binding affinity trends have been attributed to long-ranged electrostatic desolvation of ionized groups. A generalized Born/surface area solvation model yields a much smaller change in desolvation energy with chain length and, therefore, does not reproduce the experimental binding affinity trends. This result suggests that the generalized Born model should be used with caution for complex, partly desolvated systems like protein binding sites. We also find that changing the assumed protonation state of the active site aspartyl dyad significantly affects the computed binding affinity trends. The protonation state of the aspartyl dyad in the presence of cyclic ureas is discussed in light of the observation that the monoprotonated state reproduces the experimental results best.
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Affiliation(s)
- K L Mardis
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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103
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Kuhelj R, Rizzo CJ, Chang CH, Jadhav PK, Towler EM, Korant BD. Inhibition of human endogenous retrovirus-K10 protease in cell-free and cell-based assays. J Biol Chem 2001; 276:16674-82. [PMID: 11278433 DOI: 10.1074/jbc.m008763200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A full-length and C-terminally truncated version of human endogenous retrovirus (HERV)-K10 protease were expressed in Escherichia coli and purified to homogeneity. Both versions of the protease efficiently processed HERV-K10 Gag polyprotein substrate. HERV-K10 Gag was also cleaved by human immunodeficiency virus, type 1 (HIV-1) protease, although at different sites. To identify compounds that could inhibit protein processing dependent on the HERV-K10 protease, a series of cyclic ureas that had previously been shown to inhibit HIV-1 protease was tested. Several symmetric bisamides acted as very potent inhibitors of both the truncated and full-length form of HERV-K10 protease, in subnanomolar or nanomolar range, respectively. One of the cyclic ureas, SD146, can inhibit the processing of in vitro translated HERV-K10 Gag polyprotein substrate by HERV-K10 protease. In addition, in virus-like particles isolated from the teratocarcinoma cell line NCCIT, there is significant accumulation of Gag and Gag-Pol precursors upon treatment with SD146, suggesting the compound efficiently blocks HERV-K Gag processing in cells. This is the first report of an inhibitor able to block cell-associated processing of Gag polypeptides of an endogenous retrovirus.
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Affiliation(s)
- R Kuhelj
- Department of Virology, Experimental Station, DuPont Pharmaceuticals, Wilmington, Delaware 19880, USA
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104
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Shi F, Deng Y, SiMa T, Yang H. A novel ZrO2–SO42− supported palladium catalyst for syntheses of disubstituted ureas from amines by oxidative carbonylation. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00124-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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105
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Dougherty JM, Probst DA, Robinson RE, Moore JD, Klein TA, Snelgrove KA, Hanson PR. Ring-Closing Metathesis Strategies to Cyclic Sulfamide Peptidomimetics. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00885-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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106
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Abstract
Virtually all the compounds that are currently used, or under advanced clinical trial, for the treatment of HIV infections, belong to one of the following classes: (i) nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), (ii) non-nucleoside reverse transcriptase inhibitors (NNRTIs) and (iii) protease inhibitors (PIs). In addition to the reverse transcriptase and protease step, various other events in the HIV replicative cycle are potential targets for chemotherapeutic intervention: (i) viral adsorption, through binding to the viral envelope glycoprotein gp120 (polysulphates, polysulphonates, polyoxometalates, zintevir, negatively charged albumins); (ii) viral entry, through blockade of the viral coreceptors CXCR4 and CCR5 [bicyclams (AMD3100), polyphemusins (T22), TAK-779]; (iii) virus-cell fusion, through binding to the viral glycoprotein gp41 [T-20 (DP-178), siamycins, betulinic acid derivatives]; (iv) viral assembly and disassembly, through NCp7 zinc finger-targeted agents [2,2'-dithiobisbenzamides (DIBAs), azadicarbonamide (ADA)]; (v) proviral DNA integration, through integrase inhibitors such as L-chicoric acid; (vi) viral mRNA transcription, through inhibitors of the transcription (transactivation) process (peptoid CGP64222, fluoroquinolone K-12, Streptomyces product EM2487). Also, in recent years new NRTIs, NNRTIs and PIs have been developed that possess, respectively, improved metabolic characteristics (i.e. phosphoramidate and cyclosaligenyl pronucleotides of d4T), or increased activity against NNRTI-resistant HIV strains, or, in the case of PIs, a different, non-peptidic scaffold. Given the multitude of molecular targets with which anti-HIV agents can interact, one should be cautious in extrapolating from cell-free enzymatic assays to the mode of action of these agents in intact cells. A number of compounds (i.e. zintevir and L-chicoric acid, on the one hand; and CGP64222 on the other hand) have recently been found to interact with virus-cell binding and viral entry in contrast to their proposed modes of action targeted at the integrase and transactivation process, respectively.
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Affiliation(s)
- E De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
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107
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Abstract
Interactions between biological macromolecules have characteristic values of affinity and specificity that are set according to the biological function that is served by the interaction in the organism. Here we examine the molecular mechanisms that are used to achieve the required values of affinity and specificity in various biological systems.
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Affiliation(s)
- D Szwajkajzer
- Princeton University, Department of Chemistry, NJ 08544, USA
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108
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Kotamarthi B, Bonin I, Benedetti F, Miertus S. Computational design of new cyclic urea inhibitors for improved binding of HIV-1 aspartic protease. Biochem Biophys Res Commun 2000; 268:384-9. [PMID: 10679213 DOI: 10.1006/bbrc.2000.2139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report in this paper the design, by means of computational techniques, of new cyclic urea inhibitors of the HIV aspartic protease. The relationship between the complexation energies of the enzyme with known inhibitors and the experimentally determined log K(i) have been studied and used to predict inhibition constants for new inhibitors.
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Affiliation(s)
- B Kotamarthi
- International Centre for Science and High Technology, UNIDO, Trieste, Italy
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109
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Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. Modeling Molecular Recognition: Theory and Application. J Biomol Struct Dyn 2000; 17 Suppl 1:89-94. [DOI: 10.1080/07391102.2000.10506608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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110
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Han W, Pelletier JC, Mersinger LJ, Kettner CA, Hodge CN. 7-Azabicycloheptane carboxylic acid: a proline replacement in a boroarginine thrombin inhibitor. Org Lett 1999; 1:1875-7. [PMID: 10836047 DOI: 10.1021/ol990294x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[formula: see text] The synthesis of thrombin inhibitor 3, which incorporates conformationally constrained 7-azabicycloheptane carboxylic acid (1) as a proline replacement, is described. The inhibition constant (Ki(thrombin) = 2.9 nM) indicates that 1 is a reasonable replacement of proline in the formation of a beta-turn tripeptide mimetic.
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Affiliation(s)
- W Han
- Department of Chemical and Physical Sciences, DuPont Pharmaceuticals Company, Experimental Station, Wilmington, Delaware 19880, USA.
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111
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Garg R, Gupta SP, Gao H, Babu MS, Debnath AK, Hansch C. Comparative Quantitative Structureminus signActivity Relationship Studies on Anti-HIV Drugs. Chem Rev 1999; 99:3525-3602. [PMID: 11849030 DOI: 10.1021/cr9703358] [Citation(s) in RCA: 204] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajni Garg
- Department of Chemistry, Pomona College, Claremont, California 91711, Departments of Chemistry and Pharmacy, Birla Institute of Technology and Science, Pilani 333031, India, Pharmacia & Upjohn, 301 Henrietta Street, Kalamazoo, Michigan 49007, and Biochemical Virology Laboratory, Lindsley F. Kimball Research Institute of The New York Blood Center, 310 E. 67th Street, New York, New York 10021
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112
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Gupta SP, Babu MS. Quantitative structure-activity relationship studies on cyclic cyanoguanidines acting as HIV-1 protease inhibitors. Bioorg Med Chem 1999; 7:2549-53. [PMID: 10632065 DOI: 10.1016/s0968-0896(99)00175-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A quantitative structure-activity relationship study has been performed on some cyclic cyanoguanidines that inhibit the enzyme HIV-1 protease (HIV-1-PR) and exhibit antiviral potency, and the results have been compared with those of cyclic urea derivatives. Both the enzyme inhibition activity and antiviral potency in cyclic cyanoguanidines as well as in cyclic urea derivatives are found to be primarily governed by hydrophobic property of substituents attached to nitrogen (P2/P2') and further enhanced by OH or NH2 group, if any, present in the substituents. However, aromatic substituents are found to be unfavourable to both the activities of cyclic cyanoguanidines but not to any activity of cyclic urea derivatives. Cyclic urea derivatives are indicated to be more potent than cyclic cyanoguanidines. A model for the interaction of cyclic cyanoguanidines with the receptor is proposed.
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Affiliation(s)
- S P Gupta
- Birla Institute of Technology and Science, Pilani, India
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113
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Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 1999; 7:1047-55. [PMID: 10508781 DOI: 10.1016/s0969-2126(99)80172-5] [Citation(s) in RCA: 225] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND (1)H and (15)N transverse relaxation measurements on perdeuterated proteins are ideally suited for detecting backbone conformational fluctuations on the millisecond-microsecond timescale. The identification of conformational exchange on this timescale by measuring the relaxation of both (1)H and (15)N holds great promise for the elucidation of functionally relevant conformational changes in proteins. RESULTS We measured the transverse (1)H and (15)N relaxation rates of backbone amides of HIV-1 protease in its free and inhibitor-bound forms. An analysis of these rates, obtained as a function of the effective rotating frame field, provided information about the timescale of structural fluctuations in several regions of the protein. The flaps that cover the active site of the inhibitor-bound protein undergo significant changes of backbone (φ,psi) angles, on the 100 micros timescale, in the free protein. In addition, the intermonomer beta-sheet interface of the bound form, which from protease structure studies appears to be rigid, was found to fluctuate on the millisecond timescale. CONCLUSIONS We present a working model of the flap-opening mechanism in free HIV-1 protease which involves a transition from a semi-open to an open conformation that is facilitated by interaction of the Phe53 ring with the substrate. We also identify a surprising fluctuation of the beta-sheet intermonomer interface that suggests a structural requirement for maturation of the protease. Thus, slow conformational fluctuations identified by (1)H and (15)N transverse relaxation measurements can be related to the biological functions of proteins.
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Affiliation(s)
- R Ishima
- Molecular Structural Biology Unit National Institute of Dental and Craniofacial Research National Institutes of Health Bethesda, MD 20892, USA
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114
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Kosztin D, Gumport RI, Schulten K. Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analog. Nucleic Acids Res 1999; 27:3550-6. [PMID: 10446246 PMCID: PMC148600 DOI: 10.1093/nar/27.17.3550] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular dynamics simulations were performed on models of the dodecamer DNA double-stranded segment, [d(CGCGAATTCGCG)](2), in which each of the adenine residues, individually or jointly, was replaced by the water-mimicking analog 2'-deoxy-7-(hydroxy-methyl)-7-deazaadenosine (hm(7)c(7)dA) [Rockhill, J.K., Wilson,S.R. and Gumport,R.I. (1996) J. Am. Chem. Soc.,118, 10065-10068]. The simulations, when compared with those of the dodecamer itself, show that incorporation of the analog affects neither the overall DNA structure nor its hydrogen-bonding and stacking interactions when it replaces a single individual base. Furthermore, the water molecules near the bases in the singly-substituted oligonucleotides are similarly unaffected. Double substitutions lead to differences in all the aforementioned parameters with respect to the reference sequence. The results suggest that the analog provides a good mimic of specific 'ordered' water molecules observed in contact with DNA itself and at the interface between protein and DNA in specific complexes.
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Affiliation(s)
- D Kosztin
- Department of Chemistry, University of Illinois, Urbana, Champaign, 61801, USA
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115
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Abstract
We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of approximately -1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin-avidin.
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Affiliation(s)
- I D Kuntz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, USA.
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116
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Kurihara S, Tsumuraya T, Fujii I. Structure-based design of diaminopyranosides as a novel inhibitor core unit of HIV proteases. Bioorg Med Chem Lett 1999; 9:1179-84. [PMID: 10328309 DOI: 10.1016/s0960-894x(99)00154-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Novel HIV PR inhibitors, which contain a diaminopyranoside moiety as an inhibitor core unit, were designed based on the 3D structures of complexes of HIV-1 PR with transition-state mimics. These compounds were examined for their ability to inhibit the hydrolytic activity of a recombinant HIV-1 PR.
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Affiliation(s)
- S Kurihara
- Biomolecular Engineering Research Institute, Suita, Osaka, Japan
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117
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Battistini L, Rassu G, Pinna L, Zanardi F, Casiraghi G. Diastereoselective synthesis of a novel lactam peptidomimetic exploiting vinylogous Mannich addition of 2-silyloxyfuran reagents. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0957-4166(99)00051-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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118
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Trylska J, Antosiewicz J, Geller M, Hodge CN, Klabe RM, Head MS, Gilson MK. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci 1999; 8:180-95. [PMID: 10210196 PMCID: PMC2144115 DOI: 10.1110/ps.8.1.180] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aspartyl dyad of free HIV-1 protease has apparent pK(a)s of approximately 3 and approximately 6, but recent NMR studies indicate that the aspartyl dyad is fixed in the doubly protonated form over a wide pH range when cyclic urea inhibitors are bound, and in the monoprotonated form when the inhibitor KNI-272 is bound. We present computations and measurements related to these changes in protonation and to the thermodynamic linkage between protonation and inhibition. The Poisson-Boltzmann model of electrostatics is used to compute the apparent pK(a)s of the aspartyl dyad in the free enzyme and in complexes with four different inhibitors. The calculations are done with two parameter sets. One assigns epsilon = 4 to the solute interior and uses a detailed model of ionization; the other uses epsilon = 20 for the solute interior and a simplified representation of ionization. For the free enzyme, both parameter sets agree well with previously measured apparent pK(a)s of approximately 3 and approximately 6. However, the calculations with an internal dielectric constant of 4 reproduce the large pKa shifts upon binding of inhibitors, but the calculations with an internal dielectric constant of 20 do not. This observation has implications for the accurate calculation of pK(a)s in complex protein environments. Because binding of a cyclic urea inhibitor shifts the pK(a)s of the aspartyl dyad, changing the pH is expected to change its apparent binding affinity. However, we find experimentally that the affinity is independent of pH from 5.5 to 7.0. Possible explanations for this discrepancy are discussed.
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Affiliation(s)
- J Trylska
- Department of Biophysics, University of Warsaw, Poland.
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119
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Abstract
A new class of tricyclic ureas containing a conformationally constrained proline was designed with the aid of molecular modeling. Efficient stereoselective intermolecular pinacol coupling represented the highlight of the synthesis. These rigid cyclic ureas are active towards HIV-1 protease, with 9 being the most potent compound (Ki = 9 nM) despite interacting with only three side chain binding pockets of HIV protease.
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Affiliation(s)
- W Han
- Department of Chemical and Physical Sciences, DuPont Pharmaceuticals Company, Wilmington, Delaware 19880-0500, USA
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120
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De Lucca GV, Jadhav PK, Waltermire RE, Aungst BJ, Erickson-Viitanen S, Lam PY. De novo design and discovery of cyclic HIV protease inhibitors capable of displacing the active-site structural water molecule. PHARMACEUTICAL BIOTECHNOLOGY 1998; 11:257-84. [PMID: 9760684 DOI: 10.1007/0-306-47384-4_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- G V De Lucca
- DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880-0500, USA
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121
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Rodgers JD, Lam PY, Johnson BL, Wang H, Li R, Ru Y, Ko SS, Seitz SP, Trainor GL, Anderson PS, Klabe RM, Bacheler LT, Cordova B, Garber S, Reid C, Wright MR, Chang CH, Erickson-Viitanen S. Design and selection of DMP 850 and DMP 851: the next generation of cyclic urea HIV protease inhibitors. CHEMISTRY & BIOLOGY 1998; 5:597-608. [PMID: 9818151 DOI: 10.1016/s1074-5521(98)90117-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND Recent clinical trials have demonstrated that HIV protease inhibitors are useful in the treatment of AIDS. It is necessary, however, to use HIV protease inhibitors in combination with other antiviral agents to inhibit the development of resistance. The daunting ability of the virus to rapidly generate resistant mutants suggests that there is an ongoing need for new HIV protease inhibitors with superior pharmacokinetic and efficacy profiles. In our attempts to design and select improved cyclic urea HIV protease inhibitors, we have simultaneously optimized potency, resistance profile, protein binding and oral bioavailability. RESULTS We have discovered that nonsymmetrical cyclic ureas containing a 3-aminoindazole P2 group are potent inhibitors of HIV protease with excellent oral bioavailability. Furthermore, the 3-aminoindazole group forms four hydrogen bonds with the enzyme and imparts a good resistance profile. The nonsymmetrical 3-aminoindazoles DMP 850 and DMP 851 were selected as our next generation of cyclic urea HIV protease inhibitors because they achieve 8 h trough blood levels in dog, with a 10 mg/kg dose, at or above the protein-binding-adjusted IC90 value for the worst single mutant--that containing the Ile84-->Val mutation. CONCLUSIONS In selecting our next generation of cyclic urea HIV protease inhibitors, we established a rigorous set of criteria designed to maximize chances for a sustained antiviral effect in HIV-infected individuals. As DMP 850 and DMP 851 provide plasma levels of free drug that are sufficient to inhibit wild-type HIV and several mutant forms of HIV, they could show improved ability to decrease viral load for clinically significant time periods. The ultimate success of DMP 850 and DMP 851 in clinical trials might depend on achieving or exceeding the oral bioavailability seen in dog.
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Affiliation(s)
- J D Rodgers
- DuPont Merck Pharmaceutical Company, Wilmington, DE 19880-0500, USA.
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122
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Gupta SP, Babu MS, Garg R, Sowmya S. Quantitative structure-activity relationship studies on cyclic urea-based HIV protease inhibitors. JOURNAL OF ENZYME INHIBITION 1998; 13:399-407. [PMID: 9825304 DOI: 10.3109/14756369809020545] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A quantitative structure-activity relationship (QSAR) study is described on some cyclic ureas that inhibit the enzyme HIV-1 protease (HIV-1-PR) and exhibit antiviral potency. Both the enzyme inhibition activity and the antiviral potency were found to be primarily governed by the hydrophobic property of the substituents at the nitrogens (N2/N2') of the urea. Adjacent to the nitrogens, the C1/C1'-substituents are, however, found to affect the activity (inhibition) by their molecular size. The essential binding of the ureas with the receptor is, however, through multiple hydrogen bonding, where the substituents, too, can participate in such binding if they are capable of doing so. A schematic diagram of the overall interaction of the inhibitors with the receptor is presented.
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Affiliation(s)
- S P Gupta
- Birla Institute of Technology and Science, Pilani, India
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123
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Stone BR, Harris GD, Cann RO, Smyser TE, Confalone PN. Synthesis of unsymmetric cyclic urea diols, a novel class of HIV protease inhibitors. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01263-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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124
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Wlodawer A, Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:249-84. [PMID: 9646869 DOI: 10.1146/annurev.biophys.27.1.249] [Citation(s) in RCA: 486] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1) was identified over a decade ago as a potential target for structure-based drug design. This effort was very successful. Four drugs are already approved, and others are undergoing clinical trials. The techniques utilized in this remarkable example of structure-assisted drug design included crystallography, NMR, computational studies, and advanced chemical synthesis. The development of these drugs is discussed in detail. Other approaches to designing HIV-1 PR inhibitors, based on the concepts of symmetry and on the replacement of a water molecule that had been found tetrahedrally coordinated between the enzyme and the inhibitors, are also discussed. The emergence of drug-induced mutations of HIV-1 PR leads to rapid loss of potency of the existing drugs and to the need to continue the development process. The structural basis of drug resistance and the ways of overcoming this phenomenon are mentioned.
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Affiliation(s)
- A Wlodawer
- Macromolecular Structure Laboratory, ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702, USA.
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125
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Han Q, Chang CH, Li R, Ru Y, Jadhav PK, Lam PY. Cyclic HIV protease inhibitors: design and synthesis of orally bioavailable, pyrazole P2/P2' cyclic ureas with improved potency. J Med Chem 1998; 41:2019-28. [PMID: 9622543 DOI: 10.1021/jm9704199] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Highly potent HIV-1 protease (HIVPR) inhibitors have been designed and synthesized by introducing bidentate hydrogen-bonding oxime and pyrazole groups at the meta-position of the phenyl ring on the P2/P2' substituents of cyclic ureas. Nonsymmetrical cyclic ureas incorporating 3(1H)-pyrazolylbenzyl as P2 and hydrophilic functionalities as P2' show potent protease inhibition and antiviral activities against HIV and have good oral bioavailabilities. The X-ray structure of HIVPR.10A complex confirms that the two pyrazole rings of 10A form bidentate hydrogen bonds with the side-chain oxygen (C=O) and backbone nitrogen (N-H) of Asp30/30' of HIVPR.
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Affiliation(s)
- Q Han
- Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 19880-0500, USA
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Ala PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PY, Eyermann CJ, Hodge CN, Schadt MC, Lewandowski FA, Weber PC, McCabe DD, Duke JL, Chang CH. Molecular recognition of cyclic urea HIV-1 protease inhibitors. J Biol Chem 1998; 273:12325-31. [PMID: 9575185 DOI: 10.1074/jbc.273.20.12325] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As long as the threat of human immunodeficiency virus (HIV) protease drug resistance still exists, there will be a need for more potent antiretroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new interactions that might improve their therapeutic benefit. The structures reveal that the preorganized, C2 symmetric scaffolds of the inhibitors are anchored in the active site of the protease by six hydrogen bonds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibitors possess benzyl groups at P1 and P1', their relative binding affinities are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (Ki (inhibition constant) = 4.70 nM), possesses the smallest P2 and the lowest number of P2-S2 interactions; whereas SD146, the most potent inhibitor (Ki = 0.02 nM), contains a benzimidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and approximately 200 van der Waals interactions. This analysis identifies the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral protease increase the binding affinity of HIV protease inhibitors.
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Affiliation(s)
- P J Ala
- DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880, USA
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127
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Patel M, Kaltenbach RF, Nugiel DA, McHugh RJ, Jadhav PK, Bacheler LT, Cordova BC, Klabe RM, Erickson-Viitanen S, Garber S, Reid C, Seitz SP. The synthesis of symmetrical and unsymmetrical P1/P1' cyclic ureas as HIV protease inhibitors. Bioorg Med Chem Lett 1998; 8:1077-82. [PMID: 9871711 DOI: 10.1016/s0960-894x(98)00175-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cyclic urea SD146, a potent HIV protease inhibitor bearing a flat resistance profile, possessed poor solubility and bioavailability, which precluded further development of the compound. In an effort to improve upon the pharmacokinetic profile of the compound, several analogs modified at the P1/P1' residues were prepared and evaluated. Several of those compounds displayed significant improvement of physical properties.
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Affiliation(s)
- M Patel
- Department of Chemical & Physical Sciences, DuPont Merck Pharmaceutical Company, Wilmington, DE 19880-0500, USA
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128
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Jadhav PK, Woerner FJ, Man HW. Synthesis of 7-membered cyclic hydroxyguanidines: Novel HIV-1 protease inhibitors. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00121-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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129
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Smallheer JM, McHugh RJ, Chang CH, Kaltenbach RF, Worley TV, Klabe RM, Bacheler LT, Rayner MM, Erickson-Viitanen S, Seitz SP. Functionalized aliphatic P2/P2′ analogs of HIV-1 protease inhibitor DMP323. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00165-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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130
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131
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De Lucca GV. Synthesis and evaluation of delta lactams as nonpeptide HIV-protease inhibitors. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00007-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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132
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Cyclic HIV protease inhibitors capable of displacing the active site structural water molecule. Drug Discov Today 1997. [DOI: 10.1016/s1359-6446(96)10048-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Eyermann CJ, Jadhav P, Nicholas Hodge C, Chang CH, Rodgers JD, Y.S.L P. The role of computer-aided and structure-based design techniques in the discovery and optimization of cyclic urea inhibitors of hiv protease. ADVANCES IN AMINO ACID MIMETICS AND PEPTIDOMIMETICS 1997. [DOI: 10.1016/s1874-5113(97)80003-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Rodgers JD, Johnson BL, Wang H, Greenberg RA, Erickson-Viitanen S, Klabe RM, Cordova BC, Rayner MM, Lam GN, Chang CH. Potent cyclic urea HIV protease inhibitors with benzofused heterocycles as P2/P2′ groups. Bioorg Med Chem Lett 1996. [DOI: 10.1016/s0960-894x(96)00531-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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