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

S2 subsites of FP2 and FP3: surface representation of the S2 subsites of FP2 and FP3. Colors are in accordance with Figure 3. E64 is depicted in stick form.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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

fig4: S2 subsites of FP2 and FP3: surface representation of the S2 subsites of FP2 and FP3. Colors are in accordance with Figure 3. E64 is depicted in stick form.

Mentions: Glu243 in the FP3−leupeptin complex also points away from the inhibitor but, in contrast to the FP2−E64 complex, does point out toward the solvent. The conformation of the side chain is similar in both copies of the complex in the asymmetric unit and is stabilized in both monomers through the formation of a direct hydrogen bond to Tyr245. This part of the S2 subsite is more solvent exposed in monomer A, allowing additional stabilizing interactions through bridging water molecules with Ile94, Thr95, and the N-acetylcarbonyl of leupeptin. In comparison to Asp234 in FP2, the additional side chain carbon (and thus rotatable bond) in Glu243 of FP3 increases the size of the residue and the degree of side chain flexibility at this position. In the FP3−leupeptin structure, the outcome of a larger, more flexible residue at the bottom of the S2 subsite and the bulkier Leu84 to Tyr93 substitution above is to narrow the wall of the S2 subsite formed by Tyr93, Ile94, and Glu243 when compared with the same region in FP2 (Leu84, Ile85, and Asp234) (Figure 4).


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)

S2 subsites of FP2 and FP3: surface representation of the S2 subsites of FP2 and FP3. Colors are in accordance with Figure 3. E64 is depicted in stick form.
© Copyright Policy - open-access - ccc-price
Related In: Results  -  Collection

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

fig4: S2 subsites of FP2 and FP3: surface representation of the S2 subsites of FP2 and FP3. Colors are in accordance with Figure 3. E64 is depicted in stick form.
Mentions: Glu243 in the FP3−leupeptin complex also points away from the inhibitor but, in contrast to the FP2−E64 complex, does point out toward the solvent. The conformation of the side chain is similar in both copies of the complex in the asymmetric unit and is stabilized in both monomers through the formation of a direct hydrogen bond to Tyr245. This part of the S2 subsite is more solvent exposed in monomer A, allowing additional stabilizing interactions through bridging water molecules with Ile94, Thr95, and the N-acetylcarbonyl of leupeptin. In comparison to Asp234 in FP2, the additional side chain carbon (and thus rotatable bond) in Glu243 of FP3 increases the size of the residue and the degree of side chain flexibility at this position. In the FP3−leupeptin structure, the outcome of a larger, more flexible residue at the bottom of the S2 subsite and the bulkier Leu84 to Tyr93 substitution above is to narrow the wall of the S2 subsite formed by Tyr93, Ile94, and Glu243 when compared with the same region in FP2 (Leu84, Ile85, and Asp234) (Figure 4).

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