A mechanistic and structural investigation of modified derivatives of the diaryltriazine class of NNRTIs targeting HIV-1 reverse transcriptase

Abstract

Background Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are vital in treating HIV-1 infection by inhibiting reverse transcriptase (RT). Drug toxicity and resistance drive the need for effective new inhibitors with improved physiochemical properties and potent antiviral activity. Computer-aided and structure-based drug design have guided the addition of solubilizing substituents to the diaryltriazine scaffold. These derivatives have markedly improved solubility and maintain low nanomolar antiviral activity against RT. The molecular and structural basis of inhibition for this series was determined to facilitate future inhibitor development with improved pharmacological profiles. Methods The molecular mechanism of inhibition was investigated using transient-state kinetic analysis. Crystal structures of RT in complex with each inhibitor were obtained to investigate the structural basis of inhibition. Results The diaryltriazine and its morpholine derivative have RT inhibition constants of 9±2 nM and 14±4 nM, respectively. They adopt differential binding modes within the non-nucleoside inhibitor binding pocket to distort the catalytic site geometry and primer grip regions. The novel morpholinopropoxy substituent extends into the RT/solvent interface of the NNIBP. Conclusions Kinetic and structural analyses show that these inhibitors behave as conventional NNRTIs and inhibit the polymerization step. This study confirms appending solubilizing substituents on the azine ring of diaryltriazine class of NNRTIs that extend into the RT/solvent interface effectively maintains low nanomolar potency and improves physiochemical properties. General Significance The modification of NNRTI scaffolds with solubilizing substituents, which extend into the RT/solvent interface, yields potent antivirals and is an effective strategy for developing novel inhibitors with improved pharmacological properties.

Computer-aided discovery of anti-HIV agents

“…The analogue with the cyanovinyl group replaced by a methyl group has similar solubility (15.3 μg/mL); the crystal structure for its complex with WT RT was subsequently determined and showed it was shifted 3-Å deeper into the NNRTI binding site than its analogue lacking the morpholinylpropoxy group. 70 The 2,6-difluoro-4-methyl analogue 34 is also interesting and more soluble at 22.9 μg/mL; it is extraordinarily potent towards the WT virus with an EC 50 of 0.190 nM (190 picomolar), while it shows 70 nM potency towards the double variant, but it oddly, like 33 , is significantly less potent at 350 nM towards the Y181C variant. Typically, the activity of an NNRTI is less towards the K103N/Y181C strain than it is towards either constituent single variant.…”

Molecular design opportunities presented by solvent‐exposed regions of target proteins

“…“Het‐NH‐Ph” NNRTIs 72 , 73 showed substantially improved solubility compared with lead molecule 71 and the structurally related drugs ETR and RPV, while retaining low‐nanomolar anti‐HIV activity . DATA derivatives 74 and 75 also showed low‐nanomolar activity similar to that of ETR against WT HIV‐1 and key resistant strains . Subsequently, the determined cocrystal structures of 74 and 76 bound to RT revealed several salient features considered to be related to the substantial improvement of solubility (Figure ) .…”

“…Subsequently, the determined cocrystal structures of 74 and 76 bound to RT revealed several salient features considered to be related to the substantial improvement of solubility (Figure ) . Specifically, the solubility enhancements appeared to result from strategic placement of the novel morpholinylalkoxy moiety at another RT/solvent interface (the entrance channel near Glu138) of the NNRTIs binding pocket …”

“…Illustration of the X‐ray crystal structures of 72 (pink, PDB ID: 4KKO) and 76 (yellow, PDB ID: 4O44) with HIV‐1 RT; the morpholinoethoxy side chain in 72 projects towards Glu28 [Color figure can be viewed at wileyonlinelibrary.com]…”

“…64,65 DATA derivatives 74 and 75 also showed low-nanomolar activity similar to that of ETR against WT HIV-1 and key resistant strains. 66 Subsequently, the determined cocrystal structures of 74 and 76 bound to RT revealed several salient features considered to be related to the substantial improvement of solubility ( Figure 13). 66 Specifically, the solubility enhancements appeared to result from strategic…”