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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.

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Related in: MedlinePlus

Chemical structures of E64 and leupeptin. The positions that occupy the S1, S2, and S3 subsites (P1, P2, and P3, respectively) are labeled. Enzyme and inhibitor groups involved during covalent bond formation are highlighted in red.
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fig2: Chemical structures of E64 and leupeptin. The positions that occupy the S1, S2, and S3 subsites (P1, P2, and P3, respectively) are labeled. Enzyme and inhibitor groups involved during covalent bond formation are highlighted in red.

Mentions: The active sites of both enzymes are located in a cleft between the structurally distinct domains of the papain-like fold. Leupeptin and E64 interact with residues in the S1, S2, and S3 subsites of FP2 and FP3, corresponding to the P1, P2, and P3 positions of the ligands. The conserved catalytic residues of FP2 and FP3 (Gln36/45, Cys42/51, His174/183, Asn204/213, respectively) are similarly oriented with respect to the cocrystallized inhibitors. The active site cysteine forms a covalent, irreversible hemithioketal with the E64 epoxy carbon in the FP2−E64 complex and a covalent, reversible hemithioacetal with the asymmetric carbonyl carbon of leupeptin in the FP3−leupeptin complex (Figure 2).


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)

Chemical structures of E64 and leupeptin. The positions that occupy the S1, S2, and S3 subsites (P1, P2, and P3, respectively) are labeled. Enzyme and inhibitor groups involved during covalent bond formation are highlighted in red.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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

fig2: Chemical structures of E64 and leupeptin. The positions that occupy the S1, S2, and S3 subsites (P1, P2, and P3, respectively) are labeled. Enzyme and inhibitor groups involved during covalent bond formation are highlighted in red.
Mentions: The active sites of both enzymes are located in a cleft between the structurally distinct domains of the papain-like fold. Leupeptin and E64 interact with residues in the S1, S2, and S3 subsites of FP2 and FP3, corresponding to the P1, P2, and P3 positions of the ligands. The conserved catalytic residues of FP2 and FP3 (Gln36/45, Cys42/51, His174/183, Asn204/213, respectively) are similarly oriented with respect to the cocrystallized inhibitors. The active site cysteine forms a covalent, irreversible hemithioketal with the E64 epoxy carbon in the FP2−E64 complex and a covalent, reversible hemithioacetal with the asymmetric carbonyl carbon of leupeptin in the FP3−leupeptin complex (Figure 2).

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