Discovery of Biphenyl-Substituted Diarylpyrimidines as New Non-Nucleoside HIV-1 Reverse Transcripttase Inhibitors ^†

Although Rilpivirine (1, RPV, TMC278) was approved by the FDA in 2011 as a non-nucleoside HIV-1 reverse transcriptase inhibitor to treat Human Immunodeficiency Virus (HIV) [1] for its potent activity against many clinically relevant wild-type (WT) and mutant HIV-1 strains, the corresponding dosing complexity, drug-drug interactions and long-term toxicity of this drug have severely compromised its efficacy [2].

To solve the above problem, herein a novel series of biphenyl-substituted diarylpyrimidine analogues (DAPYs) was designed, synthesized to evaluate the in vitro activity against HIV-1 in MT-4 cells. Some of these compounds exhibited excellent activity with the low nanomolar EC₅₀ to wild-type (WT), single-mutant, and double-mutant HIV-1 strains. The most potent compound 2a displayed an EC₅₀ value of 1 nM against HIV-1 ⅢB, 1.3 nM against L100I, 0.84 nM against K103N, 1.5 nM against Y181C, 11 nM against Y188L, 2 nM against E138K, 10 nM against K103N + Y181C, nearly 110 nM against F227L + V106 with a selectivity index (SI) value above 2059.

To investigate the possible interaction model between the new chemical entity and the biological target, compound 2a was docked into the allosteric non-nucleoside bind pocket (NNIBP) of HIV-1 RT (PDB code: 2ZD1) [3] by using Sybyl-X 1.2. Compound 2a exhibited a series of well-known kinds of interactions: the biphenyl moiety fitted well into the aromatic-rich sub-pocket consisting of amino acid residues including Tyr181, Tyr188, Phe227 and Trp229, showing the positive face-to-face π–π stacking interactions with the amino acid residues of Tyr181, Tyr188 and Trp229, excluding Phe227. The p-cyano group is protruding toward a tunnel formed by Phe227 and Trp229, indicating a possible polar interaction. The right aromatic ring extended to a solvent exposure region, which was surrounded by amino acid residues His235, Pro236 and Try 318. Additionally, two hydrogen bonds between compound 2a and NNIBP of HIV-1 RT were formed altogether; one is between the NH-linker and the oxygen atom of the carbonyl group on the back-bone of Lys101, another is between the 1-nitrogen atom on pyrimidine between the terminal amino group of Lys101.

Deep SAR analysis of the anti-HIV-1 profile of all the compounds showed that beside keeping the 2,6-dimethyl groups on the left ring of DAPY analogues, introducing a para-substituted cyano group on the second phenyl ring (B) on the biphenyl group might be crucial for enhancing the biological activity against both wild-type and mutant-type HIV-1. This important discovery on the biphenyl-substituted DAPY analogs might guide the further structural modification of our ongoing project of HIV-1 RT inhibitors.

Figure 1. Design of new DAPY-NNRTIs based on the biphenyl-substituted pyrimidine scaffold.

Figure 1. Design of new DAPY-NNRTIs based on the biphenyl-substituted pyrimidine scaffold.