Design and Synthesis of Brain Penetrant Trypanocidal N-Myristoyltransferase Inhibitors

Abstract

N-Myristoyltransferase (NMT) represents a promising drug target within the parasitic protozoa Trypanosoma brucei (T. brucei), the causative agent for human African trypanosomiasis (HAT) or sleeping sickness. We have previously validated T. brucei NMT as a promising druggable target for the treatment of HAT in both stages 1 and 2 of the disease. We report on the use of the previously reported DDD85646 (1) as a starting point for the design of a class of potent, brain penetrant inhibitors of T. brucei NMT.

Figure 1

Compound 1. *Potencies were determined against recombinant TbNMT and HsNMT1, and against bloodstream form T. brucei brucei (T. br. brucei) and MRC-5 proliferation studies in vitro using 10 point curves replicated ≥2. ^aCalculated using Optibrium STARDROP software. ^bLigand efficiency (LE), calculated as 0.6·ln(IC₅₀)/(heavy atom count) using T. brucei NMT IC₅₀ potency. IC₅₀ values are shown as mean values of two or more determinations. Standard deviation was typically within 2-fold from the IC₅₀. ^cEnzyme selectivity calculated as HsNMT1 IC₅₀ (μM)/TbNMT IC₅₀ (μM).

Figure 2

Development of the chemistry scaffold. (A) Two-dimensional interaction map of 1 bound to AfNMT leading to the design of the minimal scaffold. (B) Crystal structure of 1 bound; key recognition residues are highlighted and labeled. (C) Proposed minimal scaffold (C atoms gold) docked into the crystal structure of AfNMT overlaid with peptomimetic compound PDB 2NMT (C atoms cyan); the key S/T K peptide recognition region is highlighted red.

Figure 3

Scaffold array chemistry and design. ^aFilter parameters calculated using the Optibrium STARDROP software.

Figure 4

Binding mode of 24. (A) Compound 24 (C atoms gold) bound to AfNMT (C atoms gray). PDB 5T5U. H-bonds are shown as dashed lines and key residues labeled. (B) Comparison of the binding mode of 24 with 1 bound to AfNMT (PDB 4CAX), highlighting the movement of Tyr273. Compound 1 and the side chain of Tyr273 (PDB 4CAX) are shown with cyan C atoms.

Scheme 1

Reagents and conditions: (a) polymer supported-PPh₃, DIAD, alcohol, THF; (b) dioxane/1 M aq K₃PO₄, Pd(PPh₃)₄; (c) TFA, DCM; (d) 2 M HCl in diethyl ether.

Figure 5

Compound 29 profile. ^aValues calculated using the Optibrium STARDROP software. ^bLigand efficiency (LE), calculated as 0.6·ln(IC₅₀)/(heavy atom count) using T. brucei NMT IC₅₀ potency. IC₅₀ values are shown as mean values of two or more determinations. Standard deviation was typically within 2-fold from the IC₅₀. nd = not determined. ^cEnzyme selectivity calculated as HsNMT1 IC₅₀ (μM)/TbNMT IC₅₀ (μM).

Figure 6

Binding mode of 29 (C atoms gold) bound to AfNMT (PDB 5T6C). Binding mode of 1 (C atoms cyan) is shown for comparison.

Scheme 2

Reagents and conditions: (a) Boc₂O, NEt₃, THF; (b) 4-bromo-2,6-dichlorophenol, MeCN/1 M aq K₃PO₄, Pd(dppf)₂Cl_2; (c) PS–PPh₃, DIAD, alcohol, THF; (d) TFA, DCM.

Figure 7

Binding mode of pyridyl headgroup modifications. (A) Binding mode of 49 (C atoms aquamarine; PDB 5T6H) compared with 29 (C atoms gold). The side chain of Phe278 rotates to accommodate the 4-methyl group. (B) Binding mode of 48 (C atoms aquamarine; PDB 5T6E); the interaction with Ser378 is now a water bridged interaction. (C) Compound 48 compared with 29.

Figure 8

Hybridization approach.

Scheme 3

Reagents and conditions: (a) 9-BBN, THF; (b) Pd(PPh₃), K₃PO₄, H₂O, DMF; (c) TFA, DCM; (d) CH₂O, Na(OAc₃)₃BH, CHCl₃.

Scheme 4

Reagents and conditions: (a) H₂SO₄, EtOH; (b) phenylboronic acid, 1 M K₃PO₄/dioxane, Pd(PPh₃)₄; (c) 2 M LiAlH₄ in THF, 0 °C; (d) Pd(^tBuP)₂, 0.5 M isobutylzinc bromide, anhydrous THF.

Figure 9

Comparison of 1 and 81.