2,4,5-Trisubstituted Pyrimidines as Potent HIV-1 NNRTIs: Rational Design, Synthesis, Activity Evaluation, and Crystallographic Studies

Abstract

There is an urgent unmet medical need for novel human immunodeficiency virus type 1 (HIV-1) inhibitors that are effective against a variety of NNRTI-resistance mutations. We report our research efforts aimed at discovering a novel chemotype of anti-HIV-1 agents with improved potency against a variety of NNRTI-resistance mutations in this paper. Structural modifications of the lead K-5a2 led to the identification of a potent inhibitor 16c. 16c yielded highly potent anti-HIV-1 activities and improved resistance profiles compared with the approved drug etravirine. The co-crystal structure revealed the key role of the water networks surrounding the NNIBP for binding and for resilience against resistance mutations, while suggesting further extension of 16c toward the NNRTI-adjacent site as a lead development strategy. Furthermore, 16c demonstrated favorable pharmacokinetic and safety properties, suggesting the potential of 16c as a promising anti-HIV-1 drug candidate.

Figure 1.

The chemical structures of ETR, RPV, and the piperidine-substituted thiophene[3,2-d]pyrimidine compounds K-5a2 and 25a.

Figure 2.

Rational design of novel NNRTIs bearing the 2,4,5-trisubstituted pyrimidine scaffold utilizing scaffold hopping strategy (truncation of the fused ring).

Figure 3.

Crystal structure of HIV-1 RT in complex with 16c (PDB ID: 7KWU). (A) 16c binding in the NNIBP, with hydrogen bonding-interactions with RT and water molecules. (B) Detail of the binding of the 4-pyridyl substituent. (C-E) Water molecule and networks involved in binding of 16c. (F) Overlay of the RT-16c structure with RT-RPV-1QP fragment (bound to the NNRTI Adjacent site, PDB ID 4KFB), with the distance between nearer atoms of each. (G) Surface representation of (F), displaying the labeled pockets, with surrounding crystallographic water molecules from the RT-16c structure. Color legend for carbon atoms: (i) RT p66 subdomains: fingers in blue, palm in dark red, thumb in green, and connection in yellow; (ii) RT p51 subunit in white, and water molecules in red unless otherwise indicated.

Figure 4.

(A) The plasma concentration–time profiles of 16c in rats following oral administration (20 mg.kg⁻¹) and intravenous administration (2 mg.kg⁻¹). (B) The relative body weight changes of Kunming mice in different groups.

Figure 5.

Activity of 16c against hERG potassium channel in HEK293 cells.

Scheme 1.

Synthesis of 11-13^{a a} Reagents and conditions: (i) K₂CO₃, DMF, 4-hydroxy-3,5-dimethylbenzonitrile, r.t.; (ii) K₂CO₃, DMF, tert-butyl 4-aminopiperidine-1-carboxylate, 120°C; (iii) NIS, HOAc, CH₃CN, r.t.; (iv) TFA, DCM, r.t.; (v) K₂CO₃, DMF, r.t.; (vi) Pd(PPh₃)₄, K₂CO₃, DMF, H₂O, 100°C.

Scheme 2.

Synthesis of 22-30 ^{a a} Reagents and conditions: (i) (E)-3-(4-hydroxy-3,5-dimethylphenyl)acrylonitrile, K₂CO₃, DMF, r.t.; (ii) K₂CO₃, DMF, tert-butyl 4-aminopiperidine-1-carboxylate, 120°C; (iii) NIS, HOAc, CH₃CN, r.t.; (iv) TFA, DCM, r.t.; (v) K₂CO₃, DMF, r.t.; (vi) Pd(PPh₃)₄, K₂CO₃, DMF, H₂O, 100°C.