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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.

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Comparison of the crystal structure of E2c with the homology model.Structural superposition between E2c crystal structure from the PDB chain 4mwf_D (red) and the homology model (black) is illustrated using a ribbon representation. The crystal structure and homology model overlap in most of the regions, except the fragments where coordinates in the experimental structure are missing (red dashed lines).
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pone-0111333-g002: Comparison of the crystal structure of E2c with the homology model.Structural superposition between E2c crystal structure from the PDB chain 4mwf_D (red) and the homology model (black) is illustrated using a ribbon representation. The crystal structure and homology model overlap in most of the regions, except the fragments where coordinates in the experimental structure are missing (red dashed lines).

Mentions: Exhaustive structure similarity searches of 90 residue structural fragments of E2 conducted using the entire PDB database (255,302 PDB chains) revealed that no additional structural homologs could be found at the level of calculated structure similarities by LGA score [46] higher than LGA_S = 45%, suggesting that the HCV E2 protein represents a novel fold in the current PDB. Thus, the modeling of the structure of the insertions needed to fill in missing regions in the experimentally solved structures and to complete the model was a difficult task, and it was completed with a very low degree of confidence. By applying a combination of structural modeling and analysis methods to the E2 crystal structure (see Materials and Methods section), we were able to construct a model (Figure 2) that contains the 57 amino acids that are missing in the E2c structure, including an amino acid known to be critical for E1 binding (W487), key amino acids known to participate in CD81 binding (Figure 1C), as well as the exact sequence for the HCV genotype 1a E2 protein. Three regions of the protein that have been identified by others to be critical for E2 binding to CD81 [47]–[49] are contained in the model in their entirety. Currently, however, only three of the twenty-one Region 1 amino acids (H421–N423) are present in the model. A comparison of our model to the two E2c structures (see bar plots in Figure 1A and superposition of the E2c structure and the model in Figure 2) shows the main core regions are, as one would expect, very similar. The differences that are observed in the core region are small and appear to reflect only minor local deviations between experimentally solved structural templates. The large region that does differ corresponds to the missing peptide segments.


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)

Comparison of the crystal structure of E2c with the homology model.Structural superposition between E2c crystal structure from the PDB chain 4mwf_D (red) and the homology model (black) is illustrated using a ribbon representation. The crystal structure and homology model overlap in most of the regions, except the fragments where coordinates in the experimental structure are missing (red dashed lines).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111333-g002: Comparison of the crystal structure of E2c with the homology model.Structural superposition between E2c crystal structure from the PDB chain 4mwf_D (red) and the homology model (black) is illustrated using a ribbon representation. The crystal structure and homology model overlap in most of the regions, except the fragments where coordinates in the experimental structure are missing (red dashed lines).
Mentions: Exhaustive structure similarity searches of 90 residue structural fragments of E2 conducted using the entire PDB database (255,302 PDB chains) revealed that no additional structural homologs could be found at the level of calculated structure similarities by LGA score [46] higher than LGA_S = 45%, suggesting that the HCV E2 protein represents a novel fold in the current PDB. Thus, the modeling of the structure of the insertions needed to fill in missing regions in the experimentally solved structures and to complete the model was a difficult task, and it was completed with a very low degree of confidence. By applying a combination of structural modeling and analysis methods to the E2 crystal structure (see Materials and Methods section), we were able to construct a model (Figure 2) that contains the 57 amino acids that are missing in the E2c structure, including an amino acid known to be critical for E1 binding (W487), key amino acids known to participate in CD81 binding (Figure 1C), as well as the exact sequence for the HCV genotype 1a E2 protein. Three regions of the protein that have been identified by others to be critical for E2 binding to CD81 [47]–[49] are contained in the model in their entirety. Currently, however, only three of the twenty-one Region 1 amino acids (H421–N423) are present in the model. A comparison of our model to the two E2c structures (see bar plots in Figure 1A and superposition of the E2c structure and the model in Figure 2) shows the main core regions are, as one would expect, very similar. The differences that are observed in the core region are small and appear to reflect only minor local deviations between experimentally solved structural templates. The large region that does differ corresponds to the missing peptide segments.

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