Limits...
Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity.

Kerr ID, Lee JH, Pandey KC, Harrison A, Sajid M, Rosenthal PJ, Brinen LS - J. Med. Chem. (2009)

Bottom Line: Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite.Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions.The cumulative effect of subtle differences, including those at "gatekeeper" positions, may explain the observed kinetic differences between these two closely related enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Molecular Pharmacology and Department of Pathology, University of California, San Francisco, California 94158, USA.

ABSTRACT
Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite. We have determined the 2.9 A crystal structure of falcipain-2 in complex with the epoxysuccinate E64 and the 2.5 A crystal structure of falcipain-3 in complex with the aldehyde leupeptin. These complexes represent the first crystal structures of plasmodial cysteine proteases with small molecule inhibitors and the first reported crystal structure of falcipain-3. Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions. The cumulative effect of subtle differences, including those at "gatekeeper" positions, may explain the observed kinetic differences between these two closely related enzymes.

Show MeSH

Related in: MedlinePlus

Active sites of FP2 and FP3. (A) FP2−E64 complex. Important residues in the active site are colored blue and labeled. E64 is least flexible in monomer A (shown here) and colored gray. Interactions with the enzyme are in pink. (B) FP3−leupeptin complex. Important residues in the active site are colored yellow and labeled. Leupeptin is colored gray, and interactions with the enzyme are in pink. (C) Surface representations of FP2 (left) and FP3 (right) highlighting the contour of the S2 subsite and important residues therein. Ligands are depicted as in (A) and (B).
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651692&req=5

fig3: Active sites of FP2 and FP3. (A) FP2−E64 complex. Important residues in the active site are colored blue and labeled. E64 is least flexible in monomer A (shown here) and colored gray. Interactions with the enzyme are in pink. (B) FP3−leupeptin complex. Important residues in the active site are colored yellow and labeled. Leupeptin is colored gray, and interactions with the enzyme are in pink. (C) Surface representations of FP2 (left) and FP3 (right) highlighting the contour of the S2 subsite and important residues therein. Ligands are depicted as in (A) and (B).

Mentions: The peptidyl small molecule inhibitors are tethered to the main chains of FP2 and FP3 through a glycine residue that is highly conserved in the S3 subsite of clan CA cysteine proteases (Gly83 in FP2 and Gly92 in FP3). In each complex, this residue forms hydrogen bonds with the O and N atoms of the inhibitor backbone, similar to the pattern seen in β-sheet formation in protein secondary structure (parts A and B of Figure 3). In the FP2 active site, Gln36, Ser41 (monomer C only), Cys42, Asn81 (monomer A only), and His174 are involved in the formation of additional hydrogen bonds with E64 (18) (Table S1 in Supporting Information). In the FP3−leupeptin complex, Gln45, Cys51, and Asn182 also act as hydrogen-bonding partners to the inhibitor (Table S1 in Supporting Information). A series of possible hydrophobic interactions are found between enzyme and inhibitor, involving the nonpolar regions of Gly40, Tyr78, Gly82, Leu84, Ser149, Leu172, Asn173, and Ala175 in FP2 and Tyr90, Gly91, Tyr93, Ile94, and Ser158 in FP3. Several hydrogen bonds are formed between FP3 and leupeptin via bridging water molecules; however, the interactions are not conserved in both copies of the complex and are likely not ligand dependent.


Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity.

Kerr ID, Lee JH, Pandey KC, Harrison A, Sajid M, Rosenthal PJ, Brinen LS - J. Med. Chem. (2009)

Active sites of FP2 and FP3. (A) FP2−E64 complex. Important residues in the active site are colored blue and labeled. E64 is least flexible in monomer A (shown here) and colored gray. Interactions with the enzyme are in pink. (B) FP3−leupeptin complex. Important residues in the active site are colored yellow and labeled. Leupeptin is colored gray, and interactions with the enzyme are in pink. (C) Surface representations of FP2 (left) and FP3 (right) highlighting the contour of the S2 subsite and important residues therein. Ligands are depicted as in (A) and (B).
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651692&req=5

fig3: Active sites of FP2 and FP3. (A) FP2−E64 complex. Important residues in the active site are colored blue and labeled. E64 is least flexible in monomer A (shown here) and colored gray. Interactions with the enzyme are in pink. (B) FP3−leupeptin complex. Important residues in the active site are colored yellow and labeled. Leupeptin is colored gray, and interactions with the enzyme are in pink. (C) Surface representations of FP2 (left) and FP3 (right) highlighting the contour of the S2 subsite and important residues therein. Ligands are depicted as in (A) and (B).
Mentions: The peptidyl small molecule inhibitors are tethered to the main chains of FP2 and FP3 through a glycine residue that is highly conserved in the S3 subsite of clan CA cysteine proteases (Gly83 in FP2 and Gly92 in FP3). In each complex, this residue forms hydrogen bonds with the O and N atoms of the inhibitor backbone, similar to the pattern seen in β-sheet formation in protein secondary structure (parts A and B of Figure 3). In the FP2 active site, Gln36, Ser41 (monomer C only), Cys42, Asn81 (monomer A only), and His174 are involved in the formation of additional hydrogen bonds with E64 (18) (Table S1 in Supporting Information). In the FP3−leupeptin complex, Gln45, Cys51, and Asn182 also act as hydrogen-bonding partners to the inhibitor (Table S1 in Supporting Information). A series of possible hydrophobic interactions are found between enzyme and inhibitor, involving the nonpolar regions of Gly40, Tyr78, Gly82, Leu84, Ser149, Leu172, Asn173, and Ala175 in FP2 and Tyr90, Gly91, Tyr93, Ile94, and Ser158 in FP3. Several hydrogen bonds are formed between FP3 and leupeptin via bridging water molecules; however, the interactions are not conserved in both copies of the complex and are likely not ligand dependent.

Bottom Line: Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite.Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions.The cumulative effect of subtle differences, including those at "gatekeeper" positions, may explain the observed kinetic differences between these two closely related enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Molecular Pharmacology and Department of Pathology, University of California, San Francisco, California 94158, USA.

ABSTRACT
Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite. We have determined the 2.9 A crystal structure of falcipain-2 in complex with the epoxysuccinate E64 and the 2.5 A crystal structure of falcipain-3 in complex with the aldehyde leupeptin. These complexes represent the first crystal structures of plasmodial cysteine proteases with small molecule inhibitors and the first reported crystal structure of falcipain-3. Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions. The cumulative effect of subtle differences, including those at "gatekeeper" positions, may explain the observed kinetic differences between these two closely related enzymes.

Show MeSH
Related in: MedlinePlus