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Structural insights into the binding of MMP9 inhibitors.

Tandon A, Sinha S - Bioinformation (2011)

Bottom Line: Previous studies do not provide any conclusive information related to structural specificity of MMP9 inhibitors towards its active site, but with the availability of experimental structures it is now possible to study the structural specificity of MMP9 inhibitors.Our docking results demonstrate that thioester based zinc binding group gives favourable docking scores as compared to other two groups.Our study provides valuable insights on inhibitor specificity of MMP9 which provides valuable hints for future design of potent inhibitors and drugs.

View Article: PubMed Central - PubMed

ABSTRACT
Matrix Metalloproteinase are family of enzymes responsible for degradation of extracellular matrix. MMP9 (gelatinase B) is one of the common matrix metalloproteinase that is associated with tissue destruction in a number of disease states such as rheumatoid arthiritis, fibrotic lung disease, dilated cardiomyopathy, as well as cancer invasion and metastasis. Recent study demonstrates that increased expression of MMP9 results in augmentation of myopathy with increased inflammation and fibernecrosis. Previous studies do not provide any conclusive information related to structural specificity of MMP9 inhibitors towards its active site, but with the availability of experimental structures it is now possible to study the structural specificity of MMP9 inhibitors. In light of availability of this information, we have applied docking and molecular dynamics approach to study the binding of inhibitors to the active site of MMP9. Three categories of inhibitor consisting of sulfonamide hydroxamate, thioester, and carboxylic moieties as zinc binding groups (ZBG) were chosen in the present study. Our docking results demonstrate that thioester based zinc binding group gives favourable docking scores as compared to other two groups. Molecular Dynamics simulations further reveal that tight binding conformation for thioester group has high specificity for MMP9 active site. Our study provides valuable insights on inhibitor specificity of MMP9 which provides valuable hints for future design of potent inhibitors and drugs.

No MeSH data available.


Related in: MedlinePlus

Root mean square deviation between drug molecules and Backbone atoms of MMP9 structure for chosen inhibitors from the three groups.
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Related In: Results  -  Collection


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Figure 2: Root mean square deviation between drug molecules and Backbone atoms of MMP9 structure for chosen inhibitors from the three groups.

Mentions: For docking studies, a set of 54 inhibitors were chosen from three broad classes of MMP inhibitors: (1) carboxylic acid based inhibitors (2) Sulfonamide hydroxamate based inhibitors (3) Thio ester based inhibitors [17,18]. This classification is based upon the nature of zinc binding group (ZBG) present. All the inhibitors were then docked into the active site of MMP9. Active site of MMP9 comprises of catalytic zinc ion and is separated into small “lower” and large “upper” subdomain. These subdomains form Sn (n=1, 2, 3…) and Sn' (n'=1, 2, 3…) substrate binding pockets, small inhibitors bind to the S1' substrate binding pocket, formed by these two subdomains [19]. S1' pocket is framed in the center of active site cleft closest in proximity to active site zinc. This pocket comprises of Asp 185 ‐ Leu 188 and Pro 421-Tyr 423 which provide donors and acceptors for inter main chain hydrogen bonds to substrates or inhibitors. The wall of S1' cavity is formed by side chains of Leu 188, Leu 397, Val 398, His 401, and Leu 418, and the Met 422-Tyr 423 main chain. Leu 397 and Val 398 are specific to MMP9 [12]. The 25 docking conformations for each ligand were divided into separate conformational clusters according to 2 Å RMSD criteria. Autodock ranks each conformational cluster by binding free energy evaluation to find the best binding mode [15]. Best ranking conformational clusters from each class of ligand were further docked using Flexidock module in SYBYL-X. Results from both autodock and flexidock show agreement with less than 1 Å RMSD deviation in the conformation of docked ligands. In our results best ranking conformations demonstrated a clear propensity to bind into the S1' subsite within the active site cleft. The orientation of ZBG in all of 54 best ranking clusters was similar to the orientation of ZBG of ligand in the experimental structure. Our docking results clearly show that co-ordinate bond formation between ZBG and active site zinc is facilitated by anchoring of functional groups of ligand with residues in S1' cavity. Highest ranking conformations in 43 of the 54 docks hydrogen bond either with upper domain Leu 188-Ala 189 or lower domain Gln 402-His 411. Anchoring in the upper part of S1' subsite is supported mainly by main chain amine moeity of Leu 188, which acts as a hydrogen bond donor to functional group of ligands. This interaction determines positioning of ligand within the ‘S1’ subsite. It was observed that bulkier functional group moieties bind deep into the upper domain Leu 188 pocket of the subsite while smaller functional group moieties show preference for Gln 402-His 411pocket. Apart from above mentioned residues, S1' wall residues Pro 421-Tyr 423 also act as hydrogen bond acceptor in few ligand conformations. Docking results reaffirm the fact that S1' subsite is likely the most important substrate recognition point in the active site cleft. The binding free energy evaluation by Autodock includes intermolecular energy (van der Waals energy, hydrogen bonding energy, desolvation energy, and electrostatic energy), internal energy and torsional energy. The first two items build up docking energy; the first and third items compose the binding energy. The difference in binding free energy of three different classes of inhibitors provides further insights into their binding mode with MMP9. Our docking results indicate that Thiol based ZBG Zinc Binding Group is energetically favored over carboxylic and hydroxamate Zinc Binding Groups. Analysis of docking poses of Thio ester based ZBG group suggests that while bivalent sulfur helps in co-ordinating monodentately with the catalytic zinc, with the two bulkier moieties attached to thio ester strongly interacting with S1' subsite (13 of the 18 top ranking conformations interact with both lower and upper domain S1' residues). In case of hydroxamate and carboxylic groups, only one functional group can co-ordinate with the catalytic zinc thus restricting the ability to interact with S1' subsite. Analysis of binding energies within each group demonstrates that ligands with bulkier side chains in functional groups have better binding energies than smaller side chains. It can be argued that the bulkier moieties attached to thio ester can also possibly extend into S1 and S2' subsites resulting in increased interactions between ligand and enzyme. Based on docking results, one enzyme-inhibitor conformation from each of the three groups was chosen for molecular dynamics studies (Table 1 see Table 1). This choice was based on the optimal binding conformation obtained by inhibitor in the group. The optimal conformation was ascertained on following criteria: docking energy, binding conformation, and hydrogen bonding with active site residues. We examined the mobility of inhibitors in active site through 1 ns MD simulation. This was done by calculating RMSD of inhibitors atom position to MMP9 backbone for all three systems (Figure 2). A comparison of RMSD deviation and subsequent conformational changes indicate binding mobility in all three groups of inhibitor.


Structural insights into the binding of MMP9 inhibitors.

Tandon A, Sinha S - Bioinformation (2011)

Root mean square deviation between drug molecules and Backbone atoms of MMP9 structure for chosen inhibitors from the three groups.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3046033&req=5

Figure 2: Root mean square deviation between drug molecules and Backbone atoms of MMP9 structure for chosen inhibitors from the three groups.
Mentions: For docking studies, a set of 54 inhibitors were chosen from three broad classes of MMP inhibitors: (1) carboxylic acid based inhibitors (2) Sulfonamide hydroxamate based inhibitors (3) Thio ester based inhibitors [17,18]. This classification is based upon the nature of zinc binding group (ZBG) present. All the inhibitors were then docked into the active site of MMP9. Active site of MMP9 comprises of catalytic zinc ion and is separated into small “lower” and large “upper” subdomain. These subdomains form Sn (n=1, 2, 3…) and Sn' (n'=1, 2, 3…) substrate binding pockets, small inhibitors bind to the S1' substrate binding pocket, formed by these two subdomains [19]. S1' pocket is framed in the center of active site cleft closest in proximity to active site zinc. This pocket comprises of Asp 185 ‐ Leu 188 and Pro 421-Tyr 423 which provide donors and acceptors for inter main chain hydrogen bonds to substrates or inhibitors. The wall of S1' cavity is formed by side chains of Leu 188, Leu 397, Val 398, His 401, and Leu 418, and the Met 422-Tyr 423 main chain. Leu 397 and Val 398 are specific to MMP9 [12]. The 25 docking conformations for each ligand were divided into separate conformational clusters according to 2 Å RMSD criteria. Autodock ranks each conformational cluster by binding free energy evaluation to find the best binding mode [15]. Best ranking conformational clusters from each class of ligand were further docked using Flexidock module in SYBYL-X. Results from both autodock and flexidock show agreement with less than 1 Å RMSD deviation in the conformation of docked ligands. In our results best ranking conformations demonstrated a clear propensity to bind into the S1' subsite within the active site cleft. The orientation of ZBG in all of 54 best ranking clusters was similar to the orientation of ZBG of ligand in the experimental structure. Our docking results clearly show that co-ordinate bond formation between ZBG and active site zinc is facilitated by anchoring of functional groups of ligand with residues in S1' cavity. Highest ranking conformations in 43 of the 54 docks hydrogen bond either with upper domain Leu 188-Ala 189 or lower domain Gln 402-His 411. Anchoring in the upper part of S1' subsite is supported mainly by main chain amine moeity of Leu 188, which acts as a hydrogen bond donor to functional group of ligands. This interaction determines positioning of ligand within the ‘S1’ subsite. It was observed that bulkier functional group moieties bind deep into the upper domain Leu 188 pocket of the subsite while smaller functional group moieties show preference for Gln 402-His 411pocket. Apart from above mentioned residues, S1' wall residues Pro 421-Tyr 423 also act as hydrogen bond acceptor in few ligand conformations. Docking results reaffirm the fact that S1' subsite is likely the most important substrate recognition point in the active site cleft. The binding free energy evaluation by Autodock includes intermolecular energy (van der Waals energy, hydrogen bonding energy, desolvation energy, and electrostatic energy), internal energy and torsional energy. The first two items build up docking energy; the first and third items compose the binding energy. The difference in binding free energy of three different classes of inhibitors provides further insights into their binding mode with MMP9. Our docking results indicate that Thiol based ZBG Zinc Binding Group is energetically favored over carboxylic and hydroxamate Zinc Binding Groups. Analysis of docking poses of Thio ester based ZBG group suggests that while bivalent sulfur helps in co-ordinating monodentately with the catalytic zinc, with the two bulkier moieties attached to thio ester strongly interacting with S1' subsite (13 of the 18 top ranking conformations interact with both lower and upper domain S1' residues). In case of hydroxamate and carboxylic groups, only one functional group can co-ordinate with the catalytic zinc thus restricting the ability to interact with S1' subsite. Analysis of binding energies within each group demonstrates that ligands with bulkier side chains in functional groups have better binding energies than smaller side chains. It can be argued that the bulkier moieties attached to thio ester can also possibly extend into S1 and S2' subsites resulting in increased interactions between ligand and enzyme. Based on docking results, one enzyme-inhibitor conformation from each of the three groups was chosen for molecular dynamics studies (Table 1 see Table 1). This choice was based on the optimal binding conformation obtained by inhibitor in the group. The optimal conformation was ascertained on following criteria: docking energy, binding conformation, and hydrogen bonding with active site residues. We examined the mobility of inhibitors in active site through 1 ns MD simulation. This was done by calculating RMSD of inhibitors atom position to MMP9 backbone for all three systems (Figure 2). A comparison of RMSD deviation and subsequent conformational changes indicate binding mobility in all three groups of inhibitor.

Bottom Line: Previous studies do not provide any conclusive information related to structural specificity of MMP9 inhibitors towards its active site, but with the availability of experimental structures it is now possible to study the structural specificity of MMP9 inhibitors.Our docking results demonstrate that thioester based zinc binding group gives favourable docking scores as compared to other two groups.Our study provides valuable insights on inhibitor specificity of MMP9 which provides valuable hints for future design of potent inhibitors and drugs.

View Article: PubMed Central - PubMed

ABSTRACT
Matrix Metalloproteinase are family of enzymes responsible for degradation of extracellular matrix. MMP9 (gelatinase B) is one of the common matrix metalloproteinase that is associated with tissue destruction in a number of disease states such as rheumatoid arthiritis, fibrotic lung disease, dilated cardiomyopathy, as well as cancer invasion and metastasis. Recent study demonstrates that increased expression of MMP9 results in augmentation of myopathy with increased inflammation and fibernecrosis. Previous studies do not provide any conclusive information related to structural specificity of MMP9 inhibitors towards its active site, but with the availability of experimental structures it is now possible to study the structural specificity of MMP9 inhibitors. In light of availability of this information, we have applied docking and molecular dynamics approach to study the binding of inhibitors to the active site of MMP9. Three categories of inhibitor consisting of sulfonamide hydroxamate, thioester, and carboxylic moieties as zinc binding groups (ZBG) were chosen in the present study. Our docking results demonstrate that thioester based zinc binding group gives favourable docking scores as compared to other two groups. Molecular Dynamics simulations further reveal that tight binding conformation for thioester group has high specificity for MMP9 active site. Our study provides valuable insights on inhibitor specificity of MMP9 which provides valuable hints for future design of potent inhibitors and drugs.

No MeSH data available.


Related in: MedlinePlus