Limits...
Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein.

Al Olaby RR, Cocquerel L, Zemla A, Saas L, Dubuisson J, Vielmetter J, Marcotrigiano J, Khan AG, Vences Catalan F, Perryman AL, Freundlich JS, Forli S, Levy S, Balhorn R, Azzazy HM - PLoS ONE (2014)

Bottom Line: Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin.Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction.Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, The American University in Cairo, New Cairo, Egypt.

ABSTRACT
Hepatitis C Virus (HCV) infects 200 million individuals worldwide. Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin. Recently, two crystal structures of the core of the HCV E2 protein (E2c) have been determined, providing structural information that can now be used to target the E2 protein and develop drugs that disrupt the early stages of HCV infection by blocking E2's interaction with different host factors. Using the E2c structure as a template, we have created a structural model of the E2 protein core (residues 421-645) that contains the three amino acid segments that are not present in either structure. Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction. Surface plasmon resonance detection was used to screen the ligand set for binding to recombinant E2 protein, and the best binders were subsequently tested to identify compounds that inhibit the infection of Huh-7 cells by HCV. One compound, 281816, blocked E2 binding to CD81 and inhibited HCV infection in a genotype-independent manner with IC50's ranging from 2.2 µM to 4.6 µM. 281816 blocked the early and late steps of cell-free HCV entry and also abrogated the cell-to-cell transmission of HCV. Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.

Show MeSH

Related in: MedlinePlus

Location of ligand-binding sites on the E2 homology model used to select ligands for testing.Each of these sites either covers or is located immediately adjacent to amino acids or peptide segments of the E2 protein known to be important for HCV infectivity. H421–N423 (yellow): each amino acid in this region is important for infectivity. Antibodies binding to amino acids Y474–R492 (light cyan) have been shown to prevent infectivity, but this region of the protein has no effect on E2 binding CD81. W487 (dark cyan) is a key amino acid that is involved in E2 binding to E1. S522–G551 (light green) and Y527 and W529 (dark green) are critical for E2 binding to CD81. Site 4: P612, Y613, and H617–P619 (red) are critical for E2 binding to CD81; mutations to R614–W616 (pink) disrupt the structure of the region. The four views show the structure as it is rotated counterclockwise from left to right. Movie S1 shows the rotating structure.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4214736&req=5

pone-0111333-g003: Location of ligand-binding sites on the E2 homology model used to select ligands for testing.Each of these sites either covers or is located immediately adjacent to amino acids or peptide segments of the E2 protein known to be important for HCV infectivity. H421–N423 (yellow): each amino acid in this region is important for infectivity. Antibodies binding to amino acids Y474–R492 (light cyan) have been shown to prevent infectivity, but this region of the protein has no effect on E2 binding CD81. W487 (dark cyan) is a key amino acid that is involved in E2 binding to E1. S522–G551 (light green) and Y527 and W529 (dark green) are critical for E2 binding to CD81. Site 4: P612, Y613, and H617–P619 (red) are critical for E2 binding to CD81; mutations to R614–W616 (pink) disrupt the structure of the region. The four views show the structure as it is rotated counterclockwise from left to right. Movie S1 shows the rotating structure.

Mentions: Five ligand-binding sites on the HCV E2 homology model (Figure 3) were identified by docking the National Cancer Institute’s Diversity Set III library of ligands to the E2 model. Each of these sites is associated with or positioned next to one or more of the amino acid or peptide sequences that have been identified by others to either participate in E2 binding to CD81, E2 binding to E1, or to be important for HCV infectivity. While the accuracy of the structure of the modeled segments missing from E2c may be low, the docking and visual inspection processes focused on the regions of the target that were based on the crystal structure. The majority of the amino acids that make up or surround each of the cavities used for ligand docking and the neighboring amino acids that play a role in E2 binding to CD81 are all located in the core region of E2. The structure of this region of the model is known with high confidence, as it is essentially identical to the two recent crystal structures of the E2 protein core determined by two different groups [18], [19]. The locations of the grid boxes were also defined in such a manner that the amino acids in the modeled segments missing from the crystal structure of E2c would only be marginally considered during the docking. Only those residues in close contact with the core E2c structure were included in the boxes. In this way, the regions of the homology model with the least well-defined structures had a minimal impact on the docking results.


Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein.

Al Olaby RR, Cocquerel L, Zemla A, Saas L, Dubuisson J, Vielmetter J, Marcotrigiano J, Khan AG, Vences Catalan F, Perryman AL, Freundlich JS, Forli S, Levy S, Balhorn R, Azzazy HM - PLoS ONE (2014)

Location of ligand-binding sites on the E2 homology model used to select ligands for testing.Each of these sites either covers or is located immediately adjacent to amino acids or peptide segments of the E2 protein known to be important for HCV infectivity. H421–N423 (yellow): each amino acid in this region is important for infectivity. Antibodies binding to amino acids Y474–R492 (light cyan) have been shown to prevent infectivity, but this region of the protein has no effect on E2 binding CD81. W487 (dark cyan) is a key amino acid that is involved in E2 binding to E1. S522–G551 (light green) and Y527 and W529 (dark green) are critical for E2 binding to CD81. Site 4: P612, Y613, and H617–P619 (red) are critical for E2 binding to CD81; mutations to R614–W616 (pink) disrupt the structure of the region. The four views show the structure as it is rotated counterclockwise from left to right. Movie S1 shows the rotating structure.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4214736&req=5

pone-0111333-g003: Location of ligand-binding sites on the E2 homology model used to select ligands for testing.Each of these sites either covers or is located immediately adjacent to amino acids or peptide segments of the E2 protein known to be important for HCV infectivity. H421–N423 (yellow): each amino acid in this region is important for infectivity. Antibodies binding to amino acids Y474–R492 (light cyan) have been shown to prevent infectivity, but this region of the protein has no effect on E2 binding CD81. W487 (dark cyan) is a key amino acid that is involved in E2 binding to E1. S522–G551 (light green) and Y527 and W529 (dark green) are critical for E2 binding to CD81. Site 4: P612, Y613, and H617–P619 (red) are critical for E2 binding to CD81; mutations to R614–W616 (pink) disrupt the structure of the region. The four views show the structure as it is rotated counterclockwise from left to right. Movie S1 shows the rotating structure.
Mentions: Five ligand-binding sites on the HCV E2 homology model (Figure 3) were identified by docking the National Cancer Institute’s Diversity Set III library of ligands to the E2 model. Each of these sites is associated with or positioned next to one or more of the amino acid or peptide sequences that have been identified by others to either participate in E2 binding to CD81, E2 binding to E1, or to be important for HCV infectivity. While the accuracy of the structure of the modeled segments missing from E2c may be low, the docking and visual inspection processes focused on the regions of the target that were based on the crystal structure. The majority of the amino acids that make up or surround each of the cavities used for ligand docking and the neighboring amino acids that play a role in E2 binding to CD81 are all located in the core region of E2. The structure of this region of the model is known with high confidence, as it is essentially identical to the two recent crystal structures of the E2 protein core determined by two different groups [18], [19]. The locations of the grid boxes were also defined in such a manner that the amino acids in the modeled segments missing from the crystal structure of E2c would only be marginally considered during the docking. Only those residues in close contact with the core E2c structure were included in the boxes. In this way, the regions of the homology model with the least well-defined structures had a minimal impact on the docking results.

Bottom Line: Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin.Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction.Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, The American University in Cairo, New Cairo, Egypt.

ABSTRACT
Hepatitis C Virus (HCV) infects 200 million individuals worldwide. Although several FDA approved drugs targeting the HCV serine protease and polymerase have shown promising results, there is a need for better drugs that are effective in treating a broader range of HCV genotypes and subtypes without being used in combination with interferon and/or ribavirin. Recently, two crystal structures of the core of the HCV E2 protein (E2c) have been determined, providing structural information that can now be used to target the E2 protein and develop drugs that disrupt the early stages of HCV infection by blocking E2's interaction with different host factors. Using the E2c structure as a template, we have created a structural model of the E2 protein core (residues 421-645) that contains the three amino acid segments that are not present in either structure. Computational docking of a diverse library of 1,715 small molecules to this model led to the identification of a set of 34 ligands predicted to bind near conserved amino acid residues involved in the HCV E2: CD81 interaction. Surface plasmon resonance detection was used to screen the ligand set for binding to recombinant E2 protein, and the best binders were subsequently tested to identify compounds that inhibit the infection of Huh-7 cells by HCV. One compound, 281816, blocked E2 binding to CD81 and inhibited HCV infection in a genotype-independent manner with IC50's ranging from 2.2 µM to 4.6 µM. 281816 blocked the early and late steps of cell-free HCV entry and also abrogated the cell-to-cell transmission of HCV. Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment.

Show MeSH
Related in: MedlinePlus