Synthesis and biological evaluation of novel 2-(substituted phenylaminocarbonylmethylthio)-6-(2,6-dichlorobenzyl)-pyrimidin-4(3H)-ones as potent HIV-1 NNRTIs

doi:10.1016/j.bmc.2009.09.035

Bioorganic & Medicinal Chemistry

Volume 17, Issue 22, 15 November 2009, Pages 7749-7754

https://doi.org/10.1016/j.bmc.2009.09.035 Get rights and content

Abstract

A series of novel 2-(phenylaminocarbonylmethylthio)-6-(2,6-dichlorobenzyl)-pyrimidin-4(3H)-ones have been designed and synthesized. All of the new compounds were evaluated for their anti-HIV activities in MT-4 cells. Most of these new compounds showed moderate to potent activities against wild-type HIV-1 with an EC₅₀ ranging from 4.48 μM to 0.18 μM. Among them, 2-[(4-bromophenylamino)carbonylmethylthio]-6-(2,6-dichlorobenzyl)-5-methylpyrimidin-4(3H)-one 4b3 was identified as the most promising compound (EC₅₀ = 0.18 ± 0.06 μM, CC₅₀ >243.56 μM, SI >1326). The structure–activity relationship (SAR) of these new congeners is discussed.

Graphical abstract

The compound 4b3 was docked into the NNRTIs binding pocket (NNIBP) of HIV-1 RT (PDB code: 1RT2) using Autodock Vina [http://vina.scripps.edu]. The docking result of 4b3 is showed by PyMOL [http://pymol.sourceforge.net].

Introduction

The current therapy against the human immunodeficiency virus type 1 (HIV-1), which is the etiological agent of acquired immunodeficiency syndrome (AIDS), is based on six of categories drugs: nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs); non-nucleoside reverse transcriptase inhibitors (NNRTIs); protease inhibitors (PIs); cell entry inhibitors [fusion inhibitors (FIs) and co-receptor inhibitors (CRIs)]; and integrase inhibitors (INIs).¹ Among them, the HIV-1 NNRTIs serve as a representative of most frontline AIDS combination therapies which are highly effective with less side effects.

NNRTIs are highly specific for HIV-1 and include more than 50 structurally different classes of molecules. Among NNRTIs, dihydroalkyloxybenzyloxopyrimidines (DABOs) are an interesting class of compounds active at nanomolar concentrations.2, 3 They were first disclosed in 19924, 5 and further developed into three generations during the following years: dihydroalkyloxybenzyl-oxopyrimidines (O-DABOs); dihydroalkylthiobenzyloxopyrimidines (S-DABOs); dihydroalkylaminodifluorobenzyloxopyrimidines (N-DABOs)6, 7, 8, 9 (Fig. 1).

Compared to O-DABOs, the S-DABOs were more potent and selective, with the C-2 alkylthio chain being the most peculiar determinant for exhibition of anti-HIV-1 activity. 6-(2,6-Dichlorobenzyl) substituent of S-DABOs have been suggested to exert their favorable effect on anti-HIV-1 activity by enhancement of the putative charge-transfer interactions between the π-stacking aromatic rings of the inhibitor and Y188 and Y181 in HIV-1 RT.10, 11, 12, 13, 14, 15 On the basis of these results, we kept the 6-(2,6-dichlorobenzyl) substituent fixed and systematically modified the C-2 position by increasing the length of the linker connecting the S atom to the phenyl ring. A new series of S-DABOs (Fig. 1) was prepared, by the insertion of a phenylaminocarbonylmethylthio chain at C-2, and hydrogen or methyl substituents at the C-5 position of the pyrimidine ring. We proposed that the introduction of the C-2 side chain of S-DABOs might enhance the interaction between the inhibitors and the RT, and further exploration of the structure–activity relationships of S-DABOs may yield the discovery of new more potent HIV-1 inhibitors. Herein, the detailed synthesis, anti-HIV activity and preliminary SAR studies of these new congeners are described.

Section snippets

Chemistry

The target compounds 4a1–4a9, 4b1–4b8 were prepared as depicted in Scheme 1. The β-ketoesters (2a, 2b) were prepared by a simple and high-yielding method of Clay et al.¹⁶ by the reaction of 2-(2,6-dichlorophenyl)acetic acid with N,N′-carbonyldiimidazole (CDI) followed by treatment with potassium ethyl malonate or 2-methylmalonate in the presence of anhydrous magnesium chloride and triethylamine, which were sufficiently pure to be used for subsequent reactions without further purification.

Conclusions

In summary, we designed and synthesized a series of novel 2-(substituted phenylaminocarbonylmethylthio)-6-(2,6-dichlorobenzyl)-pyrimidin-4(3H)-ones (S-DABOs), which were structurally confirmed by IR, ¹H NMR and MS spectral analysis and evaluated for their anti-HIV (HIV-1 III_B and HIV-2 ROD) activities by inhibition of HIV-induced cytopathogenicity in MT-4 cell cultures.

Some of the new compounds displayed anti-HIV-1 activity in the submicromolar range along with low cytotoxicity. Among them, the

Chemistry

All melting points were determined on a micromelting point apparatus and are uncorrected. Infrared spectra (IR) were recorded with a Nexus 470FT-IR Spectrometer. NMR spectra were obtained on a Brucker Avance-600 NMR-spectrometer in the indicated solvents. Chemical shifts are expressed in δ units and TMS as internal reference. Mass spectra were taken on a LC Autosampler Device: Standard G1313A instrument. TLC was performed on silica gel GF254 for TLC (Merck) and spots were visualized by iodine

Acknowledgements

Research work in the authors’ laboratory has been supported by the National Natural Science Foundation of China (NSFC Nos. 30371686, 30772629, 30873133), Key Project of The International Cooperation, Ministry of Science and Technology of China (2003DF000033) and Research Fund for the Doctoral Program of Higher Education of China (070422083). We are grateful to Kristien Erven and Kris Uyttersprot for technical assistance with the antiviral experiments.

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Synthesis and biological evaluation of novel 2-(substituted phenylaminocarbonylmethylthio)-6-(2,6-dichlorobenzyl)-pyrimidin-4(3H)-ones as potent HIV-1 NNRTIs

Abstract

Graphical abstract

Introduction

Section snippets

Chemistry

Conclusions

Chemistry

Acknowledgements

Int. J. Antimicrob. Agents

Bioorg. Med. Chem.

Eur. J. Med. Chem.

Bioorg. Med. Chem. Lett.

J. Virol. Methods

J. Med. Chem.

Recent Res. Dev. Med. Chem.

Drugs Future

Microbiology

J. Med. Chem.

J. Med. Chem.

J. Med. Chem.