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Tyndall JDA, Pattenden LK, Reid RC, Hu SH, Alewood D, Alewood PF, Walsh T, Fairlie DP, Martin JL. Crystal Structures of Highly Constrained Substrate and Hydrolysis Products Bound to HIV-1 Protease. Implications for the Catalytic Mechanism. Biochemistry 2008; 47:3736-44. [DOI: 10.1021/bi7023157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joel D. A. Tyndall
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Leonard K. Pattenden
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Robert C. Reid
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Shu-Hong Hu
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Dianne Alewood
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Paul F. Alewood
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Terry Walsh
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - David P. Fairlie
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Jennifer L. Martin
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
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Johnson ECB, Malito E, Shen Y, Rich D, Tang WJ, Kent SBH. Modular total chemical synthesis of a human immunodeficiency virus type 1 protease. J Am Chem Soc 2007; 129:11480-90. [PMID: 17705484 DOI: 10.1021/ja072870n] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of our ongoing studies of the human immunodeficiency virus type 1 (HIV-1) protease enzyme, we set out to develop a modular chemical synthesis of the protein from multiple peptide segments. Our initial attempts were frustrated by the insolubility of intermediate peptide products. To overcome this problem, we designed a synthetic strategy combining the solubility-enhancing properties of C-terminal (Arg)n tags and the biological phenomenon of autoprocessing of the Gag-Pol polyprotein that occurs during maturation of the HIV-1 virus in vivo. Synthesis of a 119-residue peptide chain containing 10 residues of the reverse transcriptase (RT) open reading frame plus an (Arg)(10) tag at the C-terminus was straightforward by native chemical ligation followed by conversion of the Cys residues to Ala by Raney nickel desulfurization. The product polypeptide itself completed the final synthetic step by removing the C-terminal modification under folding conditions, to give the mature 99-residue polypeptide. High-purity homodimeric HIV-1 protease protein was obtained in excellent yield and had full enzymatic activity; the structure of the synthetic enzyme was confirmed by X-ray crystallography to a resolution of 1.07 A. This efficient modular synthesis by a biomimetic autoprocessing strategy will enable the facile synthesis of unique chemical analogues of the HIV-1 protease to further elucidate the molecular basis of enzyme catalysis.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Ben-May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA
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Reid RC, Pattenden LK, Tyndall JDA, Martin JL, Walsh T, Fairlie DP. Countering Cooperative Effects in Protease Inhibitors Using Constrained β-Strand-Mimicking Templates in Focused Combinatorial Libraries. J Med Chem 2004; 47:1641-51. [PMID: 15027855 DOI: 10.1021/jm030337m] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major problem in de novo design of enzyme inhibitors is the unpredictability of the induced fit, with the shape of both ligand and enzyme changing cooperatively and unpredictably in response to subtle structural changes within a ligand. We have investigated the possibility of dampening the induced fit by using a constrained template as a replacement for adjoining segments of a ligand. The template preorganizes the ligand structure, thereby organizing the local enzyme environment. To test this approach, we used templates consisting of constrained cyclic tripeptides, formed through side chain to main chain linkages, as structural mimics of the protease-bound extended beta-strand conformation of three adjoining amino acid residues at the N- or C-terminal sides of the scissile bond of substrates. The macrocyclic templates were derivatized to a range of 30 structurally diverse molecules via focused combinatorial variation of nonpeptidic appendages incorporating a hydroxyethylamine transition-state isostere. Most compounds in the library were potent inhibitors of the test protease (HIV-1 protease). Comparison of crystal structures for five protease-inhibitor complexes containing an N-terminal macrocycle and three protease-inhibitor complexes containing a C-terminal macrocycle establishes that the macrocycles fix their surrounding enzyme environment, thereby permitting independent variation of acyclic inhibitor components with only local disturbances to the protease. In this way, the location in the protease of various acyclic fragments on either side of the macrocyclic template can be accurately predicted. This type of templating strategy minimizes the problem of induced fit, reducing unpredictable cooperative effects in one inhibitor region caused by changes to adjacent enzyme-inhibitor interactions. This idea might be exploited in template-based approaches to inhibitors of other proteases, where a beta-strand mimetic is also required for recognition, and also other protein-binding ligands where different templates may be more appropriate.
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Affiliation(s)
- Robert C Reid
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Baca M, Kent SB. Protein Backbone Engineering through Total Chemical Synthesis: New Insight into the Mechanism of HIV-1 Protease Catalysis. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00835-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Tyndall JD, Reid RC, Tyssen DP, Jardine DK, Todd B, Passmore M, March DR, Pattenden LK, Bergman DA, Alewood D, Hu SH, Alewood PF, Birch CJ, Martin JL, Fairlie DP. Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease. J Med Chem 2000; 43:3495-504. [PMID: 11000004 DOI: 10.1021/jm000013n] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three new peptidomimetics (1-3) have been developed with highly stable and conformationally constrained macrocyclic components that replace tripeptide segments of protease substrates. Each compound inhibits both HIV-1 protease and viral replication (HIV-1, HIV-2) at nanomolar concentrations without cytotoxicity to uninfected cells below 10 microM. Their activities against HIV-1 protease (K(i) 1.7 nM (1), 0.6 nM (2), 0.3 nM (3)) are 1-2 orders of magnitude greater than their antiviral potencies against HIV-1-infected primary peripheral blood mononuclear cells (IC(50) 45 nM (1), 56 nM (2), 95 nM (3)) or HIV-1-infected MT2 cells (IC(50) 90 nM (1), 60 nM (2)), suggesting suboptimal cellular uptake. However their antiviral potencies are similar to those of indinavir and amprenavir under identical conditions. There were significant differences in their capacities to inhibit the replication of HIV-1 and HIV-2 in infected MT2 cells, 1 being ineffective against HIV-2 while 2 was equally effective against both virus types. Evidence is presented that 1 and 2 inhibit cleavage of the HIV-1 structural protein precursor Pr55(gag) to p24 in virions derived from chronically infected cells, consistent with inhibition of the viral protease in cells. Crystal structures refined to 1.75 A (1) and 1.85 A (2) for two of the macrocyclic inhibitors bound to HIV-1 protease establish structural mimicry of the tripeptides that the cycles were designed to imitate. Structural comparisons between protease-bound macrocyclic inhibitors, VX478 (amprenavir), and L-735,524 (indinavir) show that their common acyclic components share the same space in the active site of the enzyme and make identical interactions with enzyme residues. This substrate-mimicking minimalist approach to drug design could have benefits in the context of viral resistance, since mutations which induce inhibitor resistance may also be those which prevent substrate processing.
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Affiliation(s)
- J D Tyndall
- Centre for Drug Design and Development, The University of Queensland, Brisbane, Queensland 4072, Australia
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Fairlie DP, Tyndall JD, Reid RC, Wong AK, Abbenante G, Scanlon MJ, March DR, Bergman DA, Chai CL, Burkett BA. Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. J Med Chem 2000; 43:1271-81. [PMID: 10753465 DOI: 10.1021/jm990315t] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.
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Affiliation(s)
- D P Fairlie
- Centre for Drug Design and Development, University of Queensland, Brisbane, Queensland 4072, Australia.
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7
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Martin JL, Begun J, Schindeler A, Wickramasinghe WA, Alewood D, Alewood PF, Bergman DA, Brinkworth RI, Abbenante G, March DR, Reid RC, Fairlie DP. Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. Biochemistry 1999; 38:7978-88. [PMID: 10387041 DOI: 10.1021/bi990174x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a beta-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 A N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba67,95]HIVPR and [Lys7,Ile33,Aba67,95]HIVPR used in this work were shown to have very similar crystal structures.
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Affiliation(s)
- J L Martin
- Centre for Drug Design and Development, University of Queensland, Brisbane QLD 4072, Australia.
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Fitzgerald MC, Laco GS, Elder JH, Kent SB. A continuous fluorometric assay for the feline immunodeficiency virus protease. Anal Biochem 1997; 254:226-30. [PMID: 9417781 DOI: 10.1006/abio.1997.2407] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A novel fluorogenic substrate for continuous feline immunodeficiency virus (FIV) protease (PR) assay was developed in which 2-aminobenzoic acid (Abz) and p-nitrophenylalanine (F(NO2)) were used as the fluorescent donor and acceptor, respectively. The 14-amino-acid fluorogenic substrate of sequence RALTK(Abz) VQ approximately F(NO2)VQSKGR (approximately indicates cleavage site) was modeled after a naturally occurring FIV PR capsid/nucleocapsid cleavage site in the gag polyprotein. The 2-aminobenzoyl group was attached to the epsilon amino group of a lysine (K(Abz)) in position P3 and the F(NO2) is in position P1' in order to promote efficient intramolecular quenching prior to cleavage by FIV PR. We measured a K(m) of 33 +/- 6 microM and a kcat of 0.29 +/- 0.02 s-1 for the enzymatic hydrolysis of this fluorogenic substrate by FIV PR under the conditions of our assay (0.05 M sodium citrate/0.1 M sodium phosphate buffer, pH 5.25, 0.2 M NaCl, 0.1 mM EDTA, and 1 mM dithiothreitol). This assay affords a rapid and convenient means for quantitating FIV PR activities and promises to be useful for judging the relative strength of inhibitors.
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Affiliation(s)
- M C Fitzgerald
- Scripps Research Institute, La Jolla, California 92037, USA.
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10
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Reid RC, Fairlie DP. Mimicking extended conformations of protease substrates. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s1874-5113(97)80005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Smith R, Brereton IM, Chai RY, Kent SB. Ionization states of the catalytic residues in HIV-1 protease. NATURE STRUCTURAL BIOLOGY 1996; 3:946-50. [PMID: 8901873 DOI: 10.1038/nsb1196-946] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Chemical synthesis was used to prepare the HIV-1 protease specifically 13C-labelled in the catalytically essential Asp 25 in each monomer. The NMR chemical shift of the 13C-enriched homodimeric enzyme was measured in the presence of the inhibitor pepstatin, a mimic of the tetrahedral intermediate formed in enzyme catalysis. In this complex, the catalytic carboxyls do not titrate in the pH range where the enzyme is active; throughout the range pH 2.5-6.5, one Asp 25 side chain is protonated and the other deprotonated. By contrast, in the absence of inhibitor the two Asp side chains are chemically equivalent and both deprotonated at pH6, the optimum for enzymatic activity. These direct observations of the chemical properties of the catalytic apparatus of the enzyme provide concrete information on which to base the design of improved HIV-1 protease inhibitors.
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Affiliation(s)
- R Smith
- Department of Biochemistry, University of Queensland, Australia.
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March DR, Abbenante G, Bergman DA, Brinkworth RI, Wickramasinghe W, Begun J, Martin JL, Fairlie DP. Substrate-Based Cyclic Peptidomimetics of Phe-Ile-Val That Inhibit HIV-1 Protease Using a Novel Enzyme-Binding Mode. J Am Chem Soc 1996. [DOI: 10.1021/ja953790z] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Darren R. March
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Giovanni Abbenante
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Douglas A. Bergman
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Ross I. Brinkworth
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Wasantha Wickramasinghe
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Jake Begun
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - Jennifer L. Martin
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
| | - David P. Fairlie
- Contribution from the Centre for Drug Design and Development, The University of Queensland, Brisbane Qld 4072, Australia
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