Discovery and Mechanistic Investigation of Piperazinone Phenylalanine Derivatives with Terminal Indole or Benzene Ring as Novel HIV-1 Capsid Modulators

Abstract

HIV-1 capsid (CA) performs multiple roles in the viral life cycle and is a promising target for antiviral development. In this work, we describe the design, synthesis, assessment of antiviral activity, and mechanistic investigation of 20 piperazinone phenylalanine derivatives with a terminal indole or benzene ring. Among them, F2-7f exhibited moderate anti-HIV-1 activity with an EC50 value of 5.89 μM, which was slightly weaker than the lead compound PF74 (EC50 = 0.75 μM). Interestingly, several compounds showed a preference for HIV-2 inhibitory activity, represented by 7f with an HIV-2 EC50 value of 4.52 μM and nearly 5-fold increased potency over anti-HIV-1 (EC50 = 21.81 μM), equivalent to PF74 (EC50 = 4.16 μM). Furthermore, F2-7f preferred to bind to the CA hexamer rather than to the monomer, similar to PF74, according to surface plasmon resonance results. Molecular dynamics simulation indicated that F2-7f and PF74 bound at the same site. Additionally, we computationally analyzed the ADMET properties for 7f and F2-7f. Based on this analysis, 7f and F2-7f were predicted to have improved drug-like properties and metabolic stability over PF74, and no toxicities were predicted based on the chemotype of 7f and F2-7f. Finally, the experimental metabolic stability results of F2-7f in human liver microsomes and human plasma moderately correlated with our computational prediction. Our findings show that F2-7f is a promising small molecule targeting the HIV-1 CA protein with considerable development potential.

Discovery, Crystallographic Studies, and Mechanistic Investigations of Novel Phenylalanine Derivatives Bearing a Quinazolin-4-one Scaffold as Potent HIV Capsid Modulators

“…The presence of NO 2 in the R 4 position favored the F-substituted and unsubstituted compounds for anti-HIV-1 activity, and Cl-substituted ( 12c1 – 12c2 ) R 1 was found to maintain the same potency level with unmodified counterpart ( 12a1 – 12a2 ) when with NH 2 in R 4 . The anti-HIV-1 activity of R 2 with F substitution was superior to that of unsubstituted R 2 , consistent with previously reported data . This observation could be attributed to the fact that the 3,5-difluoro­phenyl substituent was embedded within a hydrophobic subpocket surrounded by Leu56, Val59, Met66, Leu69, Lys70, and Ile73 .…”

“…While scaffolds II and VII , also contained the piperazinone structure, the sulfonyl group replaced by the acyl group might disrupt the active conformation of the compounds, leading to a significant reduction of their anti-HIV activity.…”

“…This facilitates hydrogen bond interactions between Lys70/Arg70 and the carbonyl group on the piperazinone or the carbonyl group on the amide bond, which could explain why these two scaffolds display high anti-HIV-1 and anti-HIV-2 activity. However, arginine is more basic and has more polar hydrogens than lysine, resulting in a stronger hydrogen bond formation profile, resulting in these compounds prefer suppressing HIV-2 over HIV-1. While scaffolds II and VII , also contained the piperazinone structure, the sulfonyl group replaced by the acyl group might disrupt the active conformation of the compounds, leading to a significant reduction of their anti-HIV activity. The anti-HIV-2 activities of scaffold III were significantly superior to their anti-HIV-1 activities, making them selective HIV-2 CA modulators. This might be attributed to the fact that the benzene ring can simultaneously form cation-π interactions with Arg70 and Arg173, thereby exhibiting better anti-HIV-2 activity.…”

“…We also aimed to tackle a key drawback associated with metabolic instability. Employing computational methods ,,, and subsequent experimental validations, we assessed the metabolic stability of 12a2 and 21a2 in human liver microsomes and plasma. The moderate stability displayed by these compounds provides a valuable starting point for further PK optimization.…”

Synthesis of Piperazin-2-one Derivatives via Cascade Double Nucleophilic Substitution

“…11,12 Amongst the heterocyclic skeletons, piperazinones are considered to be a privileged structure in medicinal chemistry. 13,14 It is a structural part of many drugs and natural products (Figure 1) [15][16][17][18] but its particular value is associated with peptidomimetic properties resulting from the specific positioning of the heteroatoms. 19,20 Significance of piperazinone motif, perhaps primarily in medicinal chemistry, prompted development of various synthetic methodologies for its preparation.…”