Transition-state inhibitors of purine salvage and other prospective enzyme targets in malaria

Abstract

Malaria is a leading cause of human death within the tropics. The gradual generation of drug resistance imposes an urgent need for the development of new and selective antimalarial agents. Kinetic isotope effects coupled to computational chemistry have provided the relevant details on geometry and charge of enzymatic transition states to facilitate the design of transition-state analogs. These features have been reproduced into chemically stable mimics through synthetic chemistry, generating inhibitors with dissociation constants in the pico- to femto-molar range. Transition-state analogs are expected to contribute to the control of malaria.

Figure 1. Life cycle of the Plasmodium species that cause human malaria

Reproduced from [201].

Figure 2. Purine salvage and polyamine pathways in an erythrocyte infected by Plasmodium falciparum

Bold arrows on reversible steps indicate the metabolically favored direction. MTA: 5′-methylthioadenosine; MTI: 5′-methylthioinosine; SAMP: Adenylosuccinate. Adapted from [33].

Figure 3. One of the reactions catalyzed by Plasmodium falciparum PNP in the purine salvage pathway

PfPNP catalyzes the reversible phosphorolysis of the N-glycosidic bond of β-purine (deoxy)ribonucleosides to generate α-(deoxy) ribose 1-phosphate and the corresponding purine bases. PfPNP: Plasmodium falciparum PNP.

Figure 4. Immucillins, transition-state analogs for PNP

DADMe–ImmH: 4′-deaza-1′-aza-2′-deoxy-1′-(9-methylene) –ImmH; DATMe–ImmH: 2′-deoxy-2′-amino-tetritol-N-(9-methylene) –ImmH; ImmH: Immucillin H; SA-ImmG: Simplified analog of Immucillin G; SerMe–ImmH: Serinol-N-(9-methylene) –ImmH.

Figure 5. One of the reactions catalyzed by Plasmodium falciparum ADA in the purine salvage pathway

PfADA catalyzes the Zn²⁺-dependent irreversible hydrolytic deamination of (deoxy)adenosine to generate (deoxy) inosine and ammonia. PfADA: Plasmodium falciparum ADA.

Figure 6. One of the reactions catalyzed by Plasmodium falciparum HGXPRT

PfHGXPRT catalyzes the Mg²⁺-dependent reversible conversion of 6-oxopurine bases to their respective nucleotides and PP_i, with the phosphoribosyl group being derived from phosphoribosyl pyrophosphate. PfHGXPRT: Plasmodium falciparum HGXPRT; PP_i: Inorganic pyrophosphate.

Figure 7. Reaction catalyzed by Plasmodium falciparum AdSS

PfAdSS catalyzes the first committed step in the synthesis of AMP, more specifically the Mg²⁺-dependent reversible formation of adenylosuccinate from IMP and aspartate, in a two-step reaction driven by the hydrolysis of GTP to GDP and inorganic phosphate. IMP: Inosine monophosphate; PfAdSS: Plasmodium falciparum AdSS.

Figure 8. Reaction catalyzed by Plasmodium falciparum AdSL

PfAdSL catalyzes the final step in AMP synthesis, more specifically the reversible cleavage of adenylosuccinate to AMP and fumarate. PfAdSL: Plasmodium falciparum AdSL.

Figure 9. Reaction catalyzed by Plasmodium falciparum GMPS

PfGMPS catalyzes the Mg²⁺-dependent irreversible biosynthesis of GMP from XMP and glutamine in the presence of ATP, producing GMP, inorganic pyrophosphate, AMP and glutamate. PfGMPS: Plasmodium falciparum GMPS.

Figure 10

Reaction catalyzed by Plasmodium falciparum OPRT with phosphonoacetic acid as the substrate, revealing the ribooxocarbenium ion formation, a fully dissociated orotate, and a partially bonded nucleophile transition-state structure.

Figure 11

Folate biosynthetic pathway in Plasmodium falciparum.

Figure 12. Reaction catalyzed by Plasmodium falciparum DHFR

P. falciparum DHFR catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate during the de novo folate biosynthetic pathway. PfDHFR: Plasmodium falciparum DHFR.

Figure 13

DHFR inhibitors.

Figure 14. Reaction catalyzed by Plasmodium falciparum DHPS

P. falciparum DHPS catalyzes the Mg²⁺-dependent reversible condensation of p-amino benzoic acid and 6-hydroxymethyl-7,8-dihydropterin pyrophosphate to yield 7,8-dihydropteroate during the de novo folate biosynthetic pathway. The reaction is likely to undergo an S_N1 mechanism, where a cationic intermediate is formed as a result of loss of PP_i from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate. PfDHPS: Plasmodium falciparum DHPS; PP_i: Inorganic pyrophosphate.

Figure 15. Protein database structures of aspartic proteases

(A) Homodimeric HIV-1 protease (3HVP). (B) Single chain polypeptide plasmepsin II (1LF4).