Substituent-Modulated Affinities of Halobenzene Derivatives to the HIV-1 Integrase Recognition Site. Analyses of the Interaction Energies by Parallel Quantum Chemical and Polarizable Molecular Mechanics

2014 ◽  
Vol 118 (41) ◽  
pp. 9772-9782 ◽  
Author(s):  
Krystel El Hage ◽  
Jean-Philip Piquemal ◽  
Zeina Hobaika ◽  
Richard G. Maroun ◽  
Nohad Gresh
Keyword(s):  
Molecular Mechanics ◽  
Quantum Chemical ◽  
Recognition Site ◽  
Interaction Energies ◽  
Hiv 1

scholarly journals Specificity of the HIV-1 Protease on Substrates Representing the Cleavage Site in the Proximal Zinc-Finger of HIV-1 Nucleocapsid Protein

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1092
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
Stephen Oroszlan ◽  
József Tőzsér
Keyword(s):  
Amino Acid ◽  
Zinc Finger ◽  
Cleavage Site ◽  
Potential Role ◽  
Binding Mode ◽  
Interaction Energies ◽  
Vitro Assay ◽  
Hiv 1

To explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease’s specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1′ substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF↓NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1′ site. Second site substitutions have also been designed to produce “revertant” substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1′ substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable “revertants” showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the “revertant” mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.

Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

2015 ◽  
Vol 119 (30) ◽  
pp. 9477-9495 ◽  
Author(s):  
Nohad Gresh ◽  
Judit E. Sponer ◽  
Mike Devereux ◽  
Konstantinos Gkionis ◽  
Benoit de Courcy ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Intermolecular Interaction ◽  
Interaction Energies

scholarly journals How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters?

2020 ◽  
Vol 22 (7) ◽  
pp. 3855-3866 ◽  
Author(s):  
Junbo Chen ◽  
Bun Chan ◽  
Yihan Shao ◽  
Junming Ho
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
Solvent Interactions ◽  
Quantum Chemical Methods ◽  
Composite Methods ◽  
Wide Range

In this paper, the performance of ab initio composite methods, and a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water.

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