Sponges biosynthesize α-methoxylated fatty acids with unusual biophysical and biological properties and in some cases they display enhanced anticancer activities. However, the antiprotozoal properties of the α-methoxylated fatty acids have been less studied. In this work, we describe the total synthesis of (5
Z,9
Z)-(±)-2-methoxy-5, 9-eicosadienoic acid (
1) and its acetylenic analog (±)-2-methoxy-5,9-eicosadiynoic acid (
2), and report that they inhibit (EC
50 values between 31 and 22 µM) the
Leishmania donovani DNA topoisomerase IB enzyme (
LdTopIB). The inhibition of
LdTopIB (EC
50 = 53 µM) by the acid (±)-2-methoxy-6-icosynoic acid (
12) was studied as well. The potency of
LdTopIB inhibition followed the trend
2 >
1 >
12, indicating that the effectiveness of inhibition depends on the degree of unsaturation. All of the studied α-methoxylated fatty acids failed to inhibit the human topoisomerase IB enzyme (
hTopIB) at 100 µM. However, the α-methoxylated fatty acids were capable of inhibiting an active but truncated
LdTopIB with which camptothecin (CPT) cannot interact suggesting that the methoxylated fatty acids inhibit
LdTopIB with a mechanism different from that of CPT. The diunsaturated fatty acids displayed low cytotoxicity towards
Leishmania infantum promastigotes (EC
50 values between 260 and 240 µM), but
12 displayed a better cytotoxicity towards
Leishmania donovani promastigotes (EC
50 = 100 µM) and a better therapeutic index.
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