Q59094000
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HIV protease (HIV PR) is a primary target for anti-HIV drug design. We have previously identified and characterized substituted metallacarboranes as a new class of HIV protease inhibitors. In a structure-guided drug design effort, we connected the two cobalt bis(dicarbollide) clusters with a linker to substituted ammonium group and obtained a set of compounds based on a lead formula [H(2)N-(8-(C(2)H(4)O)(2)-1,2-C(2)B(9)H(10))(1',2'-C(2)B(9)H(11))-3,3'-Co)(2)]Na. We explored inhibition properties of these compounds with various substitutions, determined the HIV PR:inhibitor crystal structure, and computationally explored the conformational space of the linker. Our results prove the capacity of linker-substituted dual-cage cobalt bis(dicarbollides) as lead compounds for design of more potent inhibitors of HIV PR.
- MeSH
- elektrony MeSH
- HIV-1 enzymologie účinky léků MeSH
- HIV-proteasa chemie metabolismus MeSH
- inhibitory HIV-proteasy farmakologie chemická syntéza chemie metabolismus MeSH
- kobalt chemie MeSH
- krystalografie rentgenová MeSH
- molekulární konformace MeSH
- molekulární modely MeSH
- racionální návrh léčiv MeSH
- sloučeniny boru chemická syntéza chemie farmakologie metabolismus MeSH
- uhlík chemie MeSH
- Publikační typ
- práce podpořená grantem MeSH
Lopinavir (LPV) is a second-generation HIV protease inhibitor (PI) designed to overcome resistance development in patients undergoing long-term antiviral therapy. The mutation of isoleucine at position 47 of the HIV protease (PR) to alanine is associated with a high level of resistance to LPV. In this study, we show that recombinant PR containing a single I47A substitution has the inhibition constant (K(i) ) value for lopinavir by two orders of magnitude higher than for the wild-type PR. The addition of the I47A substitution to the background of a multiply mutated PR species from an AIDS patient showed a three-order-of-magnitude increase in K(i) in vitro relative to the patient PR without the I47A mutation. The crystal structure of I47A PR in complex with LPV showed the loss of van der Waals interactions in the S2/S2' subsites. This is caused by the loss of three side-chain methyl groups due to the I47A substitution and by structural changes in the A47 main chain that lead to structural changes in the flap antiparallel beta-strand. Furthermore, we analyzed possible interaction of the I47A mutation with secondary mutations V32I and I54V. We show that both mutations in combination with I47A synergistically increase the relative resistance to LPV in vitro. The crystal structure of the I47A/I54V PR double mutant in complex with LPV shows that the I54V mutation leads to a compaction of the flap, and molecular modeling suggests that the introduction of the I54V mutation indirectly affects the strain of the bound inhibitor in the PR binding cleft.
- MeSH
- alanin metabolismus MeSH
- Escherichia coli genetika MeSH
- financování organizované MeSH
- HIV-proteasa MeSH
- inhibitory HIV-proteasy farmakologie chemie metabolismus MeSH
- katalýza MeSH
- kinetika MeSH
- koncentrace vodíkových iontů MeSH
- lidé MeSH
- molekulární modely MeSH
- náchylnost k nemoci MeSH
- pyrimidinony farmakologie chemie metabolismus MeSH
- rekombinantní proteiny antagonisté a inhibitory chemie izolace a purifikace MeSH
- sekundární struktura proteinů MeSH
- substituce aminokyselin MeSH
- virová léková rezistence genetika MeSH
- vodíková vazba MeSH
- výpočetní biologie MeSH
- Check Tag
- lidé MeSH
Deltahedral metallacarborane compounds have recently been discovered as potent, specific, stable, and nontoxic inhibitors of HIV-1 protease (PR), the major target for AIDS therapy. The 2.15 A-resolution X-ray structure has exhibited a nonsymmetrical binding of the parental compound [Co(3+)-(C2B9H11)2](-) (GB-18) into PR dimer and a symmetrical arrangement in the crystal of two PR dimer complexes into a tetramer. In order to explore structural and energetic details of the inhibitor binding, quantum mechanics coupled with molecular mechanics approach was utilized. Realizing the close positioning of anionic inhibitors in the active site cavity, the possibility of an exchange of structural water molecules Wat50 and Wat128 by Na+ counterions was studied. The energy profiles for the rotation of the GB-18 molecules along their longitudinal axes in complex with PR were calculated. The results show that two Na+ counterions are present in the active site cavity and provide energetically favorable and unfavorable positions for carbon atoms within the carborane cages. Eighty-one rotamer combinations of four molecules of GB-18 bound to PR out of 4 x 10(5) are predicted to be highly populated. These results lay ground for further calculations of interaction energies between GB-18 and amino acids of PR active site and will make it possible to interpret computationally the binding of similar metallacarborane molecules to PR as well as to resistant PR variants. Moreover, this computational tool will allow the design of new, more potent metallacarborane-based HIV-1 protease inhibitors.
HIV protease (PR) is a prime target for rational anti-HIV drug design. We have previously identified icosahedral metallacarboranes as a novel class of nonpeptidic protease inhibitors. Now we show that substituted metallacarboranes are potent and specific competitive inhibitors of drug-resistant HIV PRs prepared either by site-directed mutagenesis or cloned from HIV-positive patients. Molecular modeling explains the inhibition profile of metallacarboranes by their unconventional binding mode.
- MeSH
- financování organizované MeSH
- HIV-1 enzymologie účinky léků MeSH
- HIV-proteasa genetika chemie metabolismus MeSH
- inhibitory HIV-proteasy farmakologie chemie MeSH
- kovy chemie MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- mutace genetika MeSH
- sloučeniny boru farmakologie chemie MeSH
- virová léková rezistence účinky léků MeSH
Icosahedral heteroboranes and especially metallacarboranes, which have recently been shown to act as potent HIV-1 protease inhibitors, are a unique class of chemical compounds with unusual properties, one of which is the formation of dihydrogen bonds with biomolecules. In this study, we investigate the effect of various metal vertices and exo-substitutions on several series of heteroboranes, including 11-vertex carborane cages [nido-7,8-C2B9Hn]n-13(n= 11,12,13), closo-1-SB11H11, closo-1-NB11H12, metal bis(dicarbollides)[3,3'-M (1,2-C2B9H11)2]n(M/n=Fe/2-, Co/1-, Ni/0) and fluoro (F), amino (NH2) and hydroxo (OH) derivatives of the metal bis(dicarbollides). Besides the properties of isolated systems (geometries, electronic properties and hydration), we study their interactions with a tetrapeptide, which models their biomolecular partner. Calculations have confirmed that the extra hydrogen in [nido-7,8-C2B9H12]- forms a bridge, which fluctuates between two stationary states. Using RESP-derived charges, it was ascertained that the negative charge of heteroboranes is located mainly on boron-bound hydrogens. An increase of the negative total charge (from 0 to -1 or -2) of heteroboranes yields an increase in the stabilisation energies of heteroborane[dot dot dot]peptide complexes and also a substantial increase in the hydration free energies of heteroboranes. Compared to the substitutions of metal vertices, the exo-substitutions of metallacarboranes cause a larger increase in stabilisation energies and a smaller increase in desolvation penalties. These two terms, stabilisation energies and desolvation penalties, contribute in opposite directions to the total heteroborane-biomolecule binding energy and must both be taken into account when designing new HIV-1 protease inhibitors.
