Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere

Kröhn, Antonin; Redshaw, Sally; Ritchie, Jenny C.; Graves, Bradford; Hatada, Marcos

doi:10.1021/jm00115a028

Cited by 208 publications

(129 citation statements)

References 2 publications

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“…To reveal any altered interactions between SQV and the Thr80 variant proteases, the binding affinity and thermodynamic parameters of each variant and WT with respect to SQV were determined by isothermal titration calorimetry (Table 2). SQV was chosen because it is a well-characterized protease inhibitor (12,15,19,29,33,52,64). SQV is an entropically driven inhibitor.…”

Section: Resultsmentioning

confidence: 99%

“…The crystallographic statistics for these structures are listed in Table 1. The PDB structure of the WT HIV-1 protease bound to SQV (PDB code 1HXB) (29) has SQV in two orientations. In order to obtain the most accurate comparison between structures and because T80S behaved just as the WT did, the SQV T80N and SQV T80S structures were compared with each other.…”

Section: Resultsmentioning

confidence: 99%

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Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity

Foulkes

Prabu-Jeyabalan

Cooper

et al. 2006

J Virol

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Sequence variability associated with human immunodeficiency virus type 1 (HIV-1) is useful for inferring structural and/or functional constraints at specific residues within the viral protease. Positions that are invariant even in the presence of drug selection define critically important residues for protease function. While the importance of conserved active-site residues is easily understood, the role of other invariant residues is not. This work focuses on invariant Thr80 at the apex of the P1 loop of HIV-1, HIV-2, and simian immunodeficiency virus protease. In a previous study, we postulated, on the basis of a molecular dynamics simulation of the unliganded protease, that Thr80 may play a role in the mobility of the flaps of protease. In the present study, both experimental and computational methods were used to study the role of Thr80 in HIV protease. Three protease variants (T80V, T80N, and T80S) were examined for changes in structure, dynamics, enzymatic activity, affinity for protease inhibitors, and viral infectivity. While all three variants were structurally similar to the wild type, only T80S was functionally similar. Both T80V and T80N had decreased the affinity for saquinavir. T80V significantly decreased the ability of the enzyme to cleave a peptide substrate but maintained infectivity, while T80N abolished both activity and viral infectivity. Additionally, T80N decreased the conformational flexibility of the flap region, as observed by simulations of molecular dynamics. Taken together, these data indicate that HIV-1 protease functions best when residue 80 is a small polar residue and that mutations to other amino acids significantly impair enzyme function, possibly by affecting the flexibility of the flap domain.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity

Foulkes

Prabu-Jeyabalan

Cooper

et al. 2006

J Virol

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“…We compared the X-ray crystal structures of HIV-1 protease complexed with TL-3 (23), HIV-1 protease complexed with the Hoffmann-La Roche compound Saquinavir (also called Invirase) from the Protein Data Bank (PDB) entry 1HXB (18), and HIV-1 protease complexed with the Abbott compound Ritonavir (also called Norvir) from the PDB entry 1HXW (17). The "chimeric" inhibitors consisted of one half of TL-3 (P4 to P1) and one half of the Saquinavir or Ritonavir compounds.…”

Section: Methodsmentioning

confidence: 99%

Alteration of Substrate and Inhibitor Specificity of Feline Immunodeficiency Virus Protease

Lin¹,

Beck²,

Lee

et al. 2000

J Virol

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Feline immunodeficiency virus (FIV) protease is structurally very similar to human immunodeficiency virus (HIV) protease but exhibits distinct substrate and inhibitor specificities. We performed mutagenesis of subsite residues of FIV protease in order to define interactions that dictate this specificity. The I37V, N55M, M56I, V59I, and Q99V mutants yielded full activity. The I37V, N55M, V59I, and Q99V mutants showed a significant increase in activity against the HIV-1 reverse transcriptase/integrase and P2/nucleocapsid junction peptides compared with wild-type (wt) FIV protease. The I37V, V59I, and Q99V mutants also showed an increase in activity against two rapidly cleaved peptides selected by cleavage of a phage display library with HIV-1 protease. Mutations at Q54K, I98P, and L101I dramatically reduced activity. Mutants containing a I35D or I57G substitution showed no activity against either FIV or HIV substrates. FIV proteases all failed to cut HIV-1 matrix/capsid, P1/P6, P6/protease, and protease/reverse transcriptase junctions, indicating that none of the substitutions were sufficient to change the specificity completely. The I37V, N55M, M56I, V59I, and Q99V mutants, compared with wt FIV protease, all showed inhibitor specificity more similar to that of HIV-1 protease. The data also suggest that FIV protease prefers a hydrophobic P2/P2 residue like Val over Asn or Glu, which are utilized by HIV-1 protease, and that S2/S2 might play a critical role in distinguishing FIV and HIV-1 protease by specificity. The findings extend our observations regarding the interactions involved in substrate binding and aid in the development of broad-based inhibitors.

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“…However, the R configuration reported here is equivalent to S in the inhibitors mentioned above, with the difference being the result of the nomenclature only. It should also be kept in mind that the R configuration results in better binding for some short inhibitors with a hydroxyethylene insert, with a different binding mode (Krohn et al, 1991;Roberts et al, 1990). map.…”

Section: I F O Imentioning

confidence: 99%

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

Thanki¹,

Rao²,

Foundling³

et al. 1992

Protein Science

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The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been de- The bound inhibitor diastereomer has the R configurations at both of the hydroxyl chiral carbon atoms. One of the diol hydroxyl groups is positioned such that it forms hydrogen bonds with both the active site aspartates, whereas the other interacts with only one of them. Comparison of this X-ray structure with a model-built structure of the inhibitor, published earlier, reveals similar positioning of the backbone atoms and of the side-chain atoms in the P2-P2' region, where the interaction with the protein is strongest. However, the X-ray structure and the model differ considerably in the location of the P3 and P3' end groups, and also in the positioning of the second of the two central hydroxyl groups. Reconstruction of the central portion of the model revealed the source of the hydroxyl discrepancy, which, when corrected, provided a PI-PI' geometry very close to that seen in the X-ray structure.

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Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere

Cited by 208 publications

References 2 publications

Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity

Role of Invariant Thr80 in Human Immunodeficiency Virus Type 1 Protease Structure, Function, and Viral Infectivity

Alteration of Substrate and Inhibitor Specificity of Feline Immunodeficiency Virus Protease

Crystal structure of a complex of HIV‐1 protease with a dihydroxyethylene‐containing inhibitor: Comparisons with molecular modeling

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